Starting phenix.real_space_refine on Sun Mar 24 12:10:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt2_23974/03_2024/7mt2_23974_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt2_23974/03_2024/7mt2_23974.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt2_23974/03_2024/7mt2_23974_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt2_23974/03_2024/7mt2_23974_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt2_23974/03_2024/7mt2_23974_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt2_23974/03_2024/7mt2_23974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt2_23974/03_2024/7mt2_23974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt2_23974/03_2024/7mt2_23974_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mt2_23974/03_2024/7mt2_23974_updated.pdb" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 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 6 6.06 5 P 4835 5.49 5 Mg 443 5.21 5 S 90 5.16 5 C 73562 2.51 5 N 27699 2.21 5 O 41419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ARG 6": "NH1" <-> "NH2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "8 ARG 9": "NH1" <-> "NH2" Residue "8 ARG 17": "NH1" <-> "NH2" Residue "8 ARG 53": "NH1" <-> "NH2" Residue "8 ARG 60": "NH1" <-> "NH2" Residue "8 ARG 74": "NH1" <-> "NH2" Residue "8 ARG 103": "NH1" <-> "NH2" Residue "8 ARG 126": "NH1" <-> "NH2" Residue "8 ARG 134": "NH1" <-> "NH2" Residue "8 ARG 164": "NH1" <-> "NH2" Residue "8 ARG 207": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "K TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 94": "NH1" <-> "NH2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "P TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 102": "NH1" <-> "NH2" Residue "V TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 73": "NH1" <-> "NH2" Residue "d TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 69": "NH1" <-> "NH2" Residue "d ARG 141": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "g ARG 41": "NH1" <-> "NH2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 32": "NH1" <-> "NH2" Residue "i ARG 33": "NH1" <-> "NH2" Residue "i ARG 41": "NH1" <-> "NH2" Residue "i ARG 78": "NH1" <-> "NH2" Residue "i ARG 151": "NH1" <-> "NH2" Residue "k ARG 103": "NH1" <-> "NH2" Residue "k ARG 136": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "o ARG 77": "NH1" <-> "NH2" Residue "p ARG 92": "NH1" <-> "NH2" Residue "q ARG 49": "NH1" <-> "NH2" Residue "q ARG 60": "NH1" <-> "NH2" Residue "s ARG 3": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 148054 Number of models: 1 Model: "" Number of chains: 69 Chain: "0" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 429 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "1" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "2" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "4" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 446 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain breaks: 1 Chain: "7" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 186 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "8" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1704 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain: "A" Number of atoms: 66959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3118, 66959 Classifications: {'RNA': 3118} Modifications used: {'rna2p': 1, 'rna2p_pur': 298, 'rna2p_pyr': 158, 'rna3p': 2, 'rna3p_pur': 1483, 'rna3p_pyr': 1176} Link IDs: {'rna2p': 457, 'rna3p': 2660} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2458 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 54, 'rna3p_pyr': 48} Link IDs: {'rna2p': 12, 'rna3p': 102} Chain breaks: 1 Chain: "C" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2088 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "G" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1330 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 350 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "J" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "K" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "L" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1075 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "M" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "O" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 905 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "Q" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "R" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 860 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 741 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1319 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "W" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 564 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "X" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 468 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "Y" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 560 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "Z" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 476 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "a" Number of atoms: 32620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32620 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 117, 'rna2p_pyr': 93, 'rna3p': 6, 'rna3p_pur': 733, 'rna3p_pyr': 569} Link IDs: {'rna2p': 211, 'rna3p': 1307} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1654 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain: "d" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1650 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "e" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1222 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain: "f" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "g" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "h" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1006 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 992 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "j" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "k" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 873 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "l" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 959 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 945 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "n" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 718 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 884 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "q" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "r" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "s" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 672 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "t" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 652 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'TRANS': 84} Chain: "y" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "z" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 302 Unusual residues: {' MG': 302} Classifications: {'undetermined': 302} Link IDs: {None: 301} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 128 Unusual residues: {' MG': 128} Classifications: {'undetermined': 128} Link IDs: {None: 127} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 497 SG CYS 1 15 117.166 178.988 188.166 1.00 59.26 S ATOM 519 SG CYS 1 18 117.200 182.444 186.327 1.00 60.15 S ATOM 734 SG CYS 1 42 120.437 181.257 187.398 1.00 53.45 S ATOM 755 SG CYS 1 45 118.561 183.175 190.025 1.00 56.66 S ATOM 1778 SG CYS 4 11 184.354 98.337 135.993 1.00 80.19 S ATOM 1801 SG CYS 4 14 184.967 101.589 134.689 1.00 77.46 S ATOM 1911 SG CYS 4 27 186.325 98.798 132.588 1.00 73.40 S ATOM 2121 SG CYS 6 16 114.052 112.910 223.933 1.00 90.63 S ATOM 2280 SG CYS 6 38 117.800 112.334 224.040 1.00 85.30 S ATOM 2301 SG CYS 6 41 115.757 109.705 222.694 1.00 85.74 S ATOM 94974 SG CYS X 5 91.572 200.448 123.434 1.00 51.91 S ATOM 94996 SG CYS X 8 93.330 202.661 125.860 1.00 53.63 S ATOM 95339 SG CYS X 52 91.260 199.500 127.235 1.00 54.20 S ATOM 95358 SG CYS X 55 89.824 202.817 127.060 1.00 57.75 S ATOM A0VW0 SG CYS n 24 89.964 55.655 170.521 1.00 62.86 S ATOM A0VWL SG CYS n 27 91.955 56.513 167.349 1.00 62.60 S ATOM A0VZJ SG CYS n 40 88.957 59.246 168.905 1.00 61.44 S ATOM A0W08 SG CYS n 43 88.118 56.097 167.252 1.00 62.75 S ATOM A0XYF SG CYS r 20 34.619 120.878 109.447 1.00 80.93 S ATOM A0XZ3 SG CYS r 23 34.278 119.433 105.887 1.00 84.67 S ATOM A0Y6O SG CYS r 57 37.959 119.775 106.867 1.00 69.34 S Time building chain proxies: 56.91, per 1000 atoms: 0.38 Number of scatterers: 148054 At special positions: 0 Unit cell: (240.62, 270.3, 243.8, 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 6 29.99 S 90 16.00 P 4835 15.00 Mg 443 11.99 O 41419 8.00 N 27699 7.00 C 73562 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 56.35 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 1 101 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 42 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 18 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 15 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 45 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 32 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 27 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 38 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 16 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 41 " pdb=" ZN X 101 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 5 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 55 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 8 " pdb="ZN ZN X 101 " - pdb=" SG CYS X 52 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " pdb=" ZN r 101 " pdb="ZN ZN r 101 " - pdb=" ND1 HIS r 60 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 57 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 23 " pdb="ZN ZN r 101 " - pdb=" SG CYS r 20 " Number of angles added : 24 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10258 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 160 helices and 73 sheets defined 35.9% alpha, 18.8% beta 1228 base pairs and 2772 stacking pairs defined. Time for finding SS restraints: 69.78 Creating SS restraints... Processing helix chain '0' and resid 9 through 21 removed outlier: 3.953A pdb=" N ARG 0 14 " --> pdb=" O ARG 0 10 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER 0 15 " --> pdb=" O SER 0 11 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG 0 16 " --> pdb=" O ASN 0 12 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG 0 17 " --> pdb=" O THR 0 13 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN 0 19 " --> pdb=" O SER 0 15 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS 0 21 " --> pdb=" O ARG 0 17 " (cutoff:3.500A) Processing helix chain '0' and resid 40 through 50 removed outlier: 3.642A pdb=" N LEU 0 44 " --> pdb=" O PRO 0 40 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LYS 0 45 " --> pdb=" O ARG 0 41 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA 0 46 " --> pdb=" O ARG 0 42 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG 0 48 " --> pdb=" O LEU 0 44 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU 0 49 " --> pdb=" O LYS 0 45 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 19 removed outlier: 3.598A pdb=" N ALA 2 16 " --> pdb=" O ASN 2 12 " (cutoff:3.500A) Processing helix chain '2' and resid 20 through 28 removed outlier: 3.998A pdb=" N ARG 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR 2 27 " --> pdb=" O LEU 2 23 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ARG 2 28 " --> pdb=" O ARG 2 24 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 41 removed outlier: 3.911A pdb=" N ILE 2 33 " --> pdb=" O ALA 2 29 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS 2 40 " --> pdb=" O SER 2 36 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 14 removed outlier: 3.932A pdb=" N LYS 3 12 " --> pdb=" O SER 3 8 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG 3 13 " --> pdb=" O GLY 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 45 removed outlier: 3.543A pdb=" N ARG 3 42 " --> pdb=" O SER 3 38 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG 3 43 " --> pdb=" O THR 3 39 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP 3 45 " --> pdb=" O THR 3 41 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 63 removed outlier: 5.346A pdb=" N LYS 3 56 " --> pdb=" O ALA 3 52 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ARG 3 57 " --> pdb=" O ASN 3 53 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR 3 59 " --> pdb=" O THR 3 55 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 47 removed outlier: 4.052A pdb=" N THR 6 46 " --> pdb=" O HIS 6 42 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY 6 47 " --> pdb=" O PRO 6 43 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 42 through 47' Processing helix chain '6' and resid 56 through 65 removed outlier: 3.726A pdb=" N ARG 6 60 " --> pdb=" O GLY 6 56 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE 6 61 " --> pdb=" O ARG 6 57 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU 6 62 " --> pdb=" O VAL 6 58 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS 6 63 " --> pdb=" O ALA 6 59 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 12 removed outlier: 3.554A pdb=" N ARG 7 6 " --> pdb=" O ALA 7 2 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG 7 9 " --> pdb=" O GLY 7 5 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG 7 11 " --> pdb=" O LYS 7 7 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYS 7 12 " --> pdb=" O LYS 7 8 " (cutoff:3.500A) Processing helix chain '8' and resid 5 through 13 removed outlier: 5.384A pdb=" N ALA 8 12 " --> pdb=" O TYR 8 8 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA 8 13 " --> pdb=" O ARG 8 9 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 38 removed outlier: 4.512A pdb=" N THR 8 36 " --> pdb=" O GLU 8 32 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS 8 37 " --> pdb=" O THR 8 33 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN 8 38 " --> pdb=" O SER 8 34 " (cutoff:3.500A) Processing helix chain '8' and resid 81 through 91 removed outlier: 4.862A pdb=" N ASP 8 85 " --> pdb=" O GLY 8 81 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL 8 88 " --> pdb=" O ALA 8 84 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA 8 89 " --> pdb=" O ASP 8 85 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA 8 90 " --> pdb=" O ALA 8 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY 8 91 " --> pdb=" O ALA 8 87 " (cutoff:3.500A) Processing helix chain '8' and resid 99 through 107 removed outlier: 3.971A pdb=" N ARG 8 103 " --> pdb=" O ASP 8 99 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY 8 107 " --> pdb=" O ARG 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 117 through 125 removed outlier: 5.195A pdb=" N ALA 8 122 " --> pdb=" O PRO 8 118 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS 8 123 " --> pdb=" O ASP 8 119 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY 8 125 " --> pdb=" O MET 8 121 " (cutoff:3.500A) Processing helix chain '8' and resid 126 through 135 removed outlier: 6.303A pdb=" N VAL 8 130 " --> pdb=" O ARG 8 126 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU 8 131 " --> pdb=" O ILE 8 127 " (cutoff:3.500A) Proline residue: 8 133 - end of helix Processing helix chain '8' and resid 148 through 159 removed outlier: 3.697A pdb=" N VAL 8 153 " --> pdb=" O VAL 8 149 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA 8 154 " --> pdb=" O ALA 8 150 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE 8 156 " --> pdb=" O ALA 8 152 " (cutoff:3.500A) Processing helix chain '8' and resid 181 through 200 removed outlier: 3.648A pdb=" N ASN 8 188 " --> pdb=" O LEU 8 184 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA 8 192 " --> pdb=" O ASN 8 188 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE 8 193 " --> pdb=" O TYR 8 189 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU 8 197 " --> pdb=" O ILE 8 193 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG 8 198 " --> pdb=" O ASP 8 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.195A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY C 216 " --> pdb=" O MET C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.084A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASN C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 227' Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.574A pdb=" N ILE C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 269' Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.533A pdb=" N GLY D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.998A pdb=" N ILE D 105 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE D 106 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 102 through 107' Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.543A pdb=" N GLY D 46 " --> pdb=" O THR D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'E' and resid 36 through 52 removed outlier: 4.218A pdb=" N GLN E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 6.649A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 removed outlier: 3.710A pdb=" N ASN E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 155 removed outlier: 3.887A pdb=" N ALA E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 removed outlier: 3.529A pdb=" N ALA E 172 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 removed outlier: 3.651A pdb=" N ALA E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ASP E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.592A pdb=" N ASN E 208 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 27 removed outlier: 3.505A pdb=" N GLU F 13 " --> pdb=" O PRO F 9 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE F 19 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASP F 21 " --> pdb=" O SER F 17 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 removed outlier: 5.554A pdb=" N ASP F 53 " --> pdb=" O GLU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 5.504A pdb=" N GLY F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL F 61 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 113 removed outlier: 3.506A pdb=" N TRP F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 154 removed outlier: 4.004A pdb=" N ILE F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASP F 154 " --> pdb=" O VAL F 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 149 through 154' Processing helix chain 'F' and resid 169 through 181 removed outlier: 3.547A pdb=" N LEU F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY F 181 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 4.053A pdb=" N SER G 64 " --> pdb=" O ARG G 60 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL G 73 " --> pdb=" O SER G 69 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN G 75 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU G 76 " --> pdb=" O LEU G 72 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 153 removed outlier: 3.618A pdb=" N ILE G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 5.788A pdb=" N GLY H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 47 removed outlier: 3.816A pdb=" N LYS H 45 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.731A pdb=" N LEU J 35 " --> pdb=" O ALA J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 71 removed outlier: 3.654A pdb=" N LEU J 69 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS J 71 " --> pdb=" O ASP J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 65 through 71' Processing helix chain 'J' and resid 88 through 96 removed outlier: 4.203A pdb=" N GLN J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 removed outlier: 3.898A pdb=" N VAL J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 4.310A pdb=" N ARG J 116 " --> pdb=" O ASN J 112 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN J 117 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS J 121 " --> pdb=" O GLN J 117 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU J 122 " --> pdb=" O ILE J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 110 removed outlier: 4.923A pdb=" N ARG K 107 " --> pdb=" O GLY K 103 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 103 through 110' Processing helix chain 'K' and resid 111 through 118 removed outlier: 3.678A pdb=" N ILE K 115 " --> pdb=" O PHE K 111 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER K 116 " --> pdb=" O MET K 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 43 removed outlier: 3.965A pdb=" N ARG L 42 " --> pdb=" O GLY L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 61 removed outlier: 4.084A pdb=" N LEU L 60 " --> pdb=" O ILE L 56 " (cutoff:3.500A) Proline residue: L 61 - end of helix Processing helix chain 'L' and resid 78 through 86 removed outlier: 3.561A pdb=" N ASN L 83 " --> pdb=" O VAL L 79 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG L 84 " --> pdb=" O GLY L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 101 removed outlier: 3.530A pdb=" N ALA L 99 " --> pdb=" O ASP L 95 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY L 101 " --> pdb=" O LEU L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 140 removed outlier: 3.847A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA L 139 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY L 140 " --> pdb=" O ILE L 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 59 removed outlier: 3.527A pdb=" N ILE M 52 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE M 54 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE M 58 " --> pdb=" O ILE M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 126 removed outlier: 3.651A pdb=" N ALA M 114 " --> pdb=" O ASN M 110 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG M 120 " --> pdb=" O ALA M 116 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA M 121 " --> pdb=" O ALA M 117 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Proline residue: M 126 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.889A pdb=" N GLN N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 58 removed outlier: 3.553A pdb=" N ALA N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Proline residue: N 46 - end of helix removed outlier: 3.552A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS N 50 " --> pdb=" O PRO N 46 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU N 51 " --> pdb=" O TYR N 47 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS N 54 " --> pdb=" O LYS N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 70 removed outlier: 4.398A pdb=" N LYS N 69 " --> pdb=" O GLU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 89 removed outlier: 3.798A pdb=" N ILE N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 3.597A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASP N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 24 removed outlier: 3.527A pdb=" N ARG O 9 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG O 16 " --> pdb=" O SER O 12 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR O 18 " --> pdb=" O LEU O 14 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS O 22 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYS O 23 " --> pdb=" O ARG O 19 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 68 removed outlier: 3.825A pdb=" N GLY O 67 " --> pdb=" O ALA O 63 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 91 removed outlier: 3.877A pdb=" N ARG O 78 " --> pdb=" O ALA O 74 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL O 79 " --> pdb=" O ARG O 75 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE O 83 " --> pdb=" O VAL O 79 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA O 89 " --> pdb=" O GLU O 85 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA O 90 " --> pdb=" O ARG O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 119 removed outlier: 3.867A pdb=" N GLU O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN O 118 " --> pdb=" O ALA O 114 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 12 removed outlier: 3.744A pdb=" N ASP P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) Proline residue: P 10 - end of helix Processing helix chain 'P' and resid 97 through 103 removed outlier: 4.878A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 103' Processing helix chain 'Q' and resid 8 through 22 removed outlier: 4.229A pdb=" N LYS Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG Q 14 " --> pdb=" O ALA Q 10 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE Q 17 " --> pdb=" O LYS Q 13 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.542A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.727A pdb=" N ASN Q 44 " --> pdb=" O LEU Q 40 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA Q 46 " --> pdb=" O SER Q 42 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG Q 70 " --> pdb=" O ASN Q 66 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.550A pdb=" N ILE Q 80 " --> pdb=" O TYR Q 76 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN Q 81 " --> pdb=" O ASN Q 77 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY Q 87 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.746A pdb=" N ALA Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 117 removed outlier: 3.827A pdb=" N ALA Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 60 removed outlier: 3.923A pdb=" N ALA R 57 " --> pdb=" O ALA R 53 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LYS R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ALA R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 35 removed outlier: 4.314A pdb=" N VAL S 30 " --> pdb=" O LYS S 26 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP S 32 " --> pdb=" O ARG S 28 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL S 34 " --> pdb=" O VAL S 30 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG S 35 " --> pdb=" O ILE S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 49 removed outlier: 4.276A pdb=" N ASP S 44 " --> pdb=" O SER S 40 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE S 45 " --> pdb=" O ASP S 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG S 47 " --> pdb=" O LEU S 43 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP S 48 " --> pdb=" O ASP S 44 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 71 removed outlier: 4.870A pdb=" N GLY S 55 " --> pdb=" O GLN S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.837A pdb=" N VAL S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER S 63 " --> pdb=" O LYS S 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 12 removed outlier: 4.579A pdb=" N ILE T 10 " --> pdb=" O ASP T 6 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE T 11 " --> pdb=" O PRO T 7 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU T 12 " --> pdb=" O ARG T 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 6 through 12' Processing helix chain 'T' and resid 17 through 27 removed outlier: 4.278A pdb=" N GLY T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP T 25 " --> pdb=" O TYR T 21 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP T 26 " --> pdb=" O GLY T 22 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN T 27 " --> pdb=" O LEU T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 50 Processing helix chain 'U' and resid 67 through 72 removed outlier: 4.369A pdb=" N VAL U 71 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N MET U 72 " --> pdb=" O VAL U 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 67 through 72' Processing helix chain 'V' and resid 18 through 29 Processing helix chain 'V' and resid 48 through 59 removed outlier: 5.497A pdb=" N TYR V 52 " --> pdb=" O PRO V 48 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA V 54 " --> pdb=" O HIS V 50 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU V 56 " --> pdb=" O TYR V 52 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG V 57 " --> pdb=" O ALA V 53 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N SER V 59 " --> pdb=" O VAL V 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 59 removed outlier: 3.794A pdb=" N ALA X 58 " --> pdb=" O SER X 54 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLY X 59 " --> pdb=" O CYS X 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 13 removed outlier: 3.611A pdb=" N LEU Y 10 " --> pdb=" O SER Y 6 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG Y 11 " --> pdb=" O PRO Y 7 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU Y 12 " --> pdb=" O GLY Y 8 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU Y 13 " --> pdb=" O GLU Y 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 6 through 13' Processing helix chain 'Y' and resid 14 through 39 removed outlier: 6.341A pdb=" N LEU Y 18 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA Y 19 " --> pdb=" O ASP Y 15 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG Y 23 " --> pdb=" O ALA Y 19 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU Y 24 " --> pdb=" O GLU Y 20 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU Y 28 " --> pdb=" O GLU Y 24 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA Y 37 " --> pdb=" O ARG Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 67 removed outlier: 4.705A pdb=" N ARG Y 48 " --> pdb=" O ASN Y 44 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.919A pdb=" N SER Z 22 " --> pdb=" O LYS Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 removed outlier: 3.862A pdb=" N ARG Z 44 " --> pdb=" O ASN Z 40 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.745A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 3.612A pdb=" N LYS c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU c 34 " --> pdb=" O GLU c 30 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA c 37 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG c 39 " --> pdb=" O ASP c 35 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG c 40 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU c 41 " --> pdb=" O ALA c 37 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER c 44 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLY c 45 " --> pdb=" O LEU c 41 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU c 46 " --> pdb=" O LEU c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 77 removed outlier: 4.253A pdb=" N ILE c 76 " --> pdb=" O PRO c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 4.333A pdb=" N ASP c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG c 85 " --> pdb=" O THR c 81 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU c 90 " --> pdb=" O ILE c 86 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU c 93 " --> pdb=" O ASP c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 7.374A pdb=" N ALA c 112 " --> pdb=" O PRO c 108 " (cutoff:3.500A) Processing helix chain 'c' and resid 113 through 126 removed outlier: 3.645A pdb=" N GLN c 117 " --> pdb=" O GLN c 113 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN c 122 " --> pdb=" O GLY c 118 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER c 124 " --> pdb=" O ALA c 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN c 125 " --> pdb=" O GLU c 121 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 143 removed outlier: 3.940A pdb=" N ARG c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLN c 143 " --> pdb=" O SER c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.394A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER d 12 " --> pdb=" O VAL d 8 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG d 16 " --> pdb=" O SER d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 30 removed outlier: 4.728A pdb=" N GLU d 27 " --> pdb=" O ASP d 23 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS d 28 " --> pdb=" O GLN d 24 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG d 29 " --> pdb=" O ALA d 25 " (cutoff:3.500A) Proline residue: d 30 - end of helix No H-bonds generated for 'chain 'd' and resid 23 through 30' Processing helix chain 'd' and resid 44 through 61 removed outlier: 3.794A pdb=" N LEU d 48 " --> pdb=" O SER d 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU d 52 " --> pdb=" O LEU d 48 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS d 53 " --> pdb=" O GLN d 49 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA d 56 " --> pdb=" O GLU d 52 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR d 59 " --> pdb=" O LYS d 55 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR d 60 " --> pdb=" O ALA d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 78 removed outlier: 3.952A pdb=" N ARG d 69 " --> pdb=" O LYS d 65 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG d 76 " --> pdb=" O GLU d 72 " (cutoff:3.500A) Proline residue: d 78 - end of helix Processing helix chain 'd' and resid 80 through 92 removed outlier: 4.450A pdb=" N GLU d 84 " --> pdb=" O LYS d 80 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU d 86 " --> pdb=" O GLY d 82 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 removed outlier: 3.504A pdb=" N GLY d 101 " --> pdb=" O ILE d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 116 removed outlier: 3.715A pdb=" N GLN d 111 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL d 113 " --> pdb=" O ALA d 109 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY d 116 " --> pdb=" O LEU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 157 removed outlier: 4.056A pdb=" N ALA d 153 " --> pdb=" O PRO d 149 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG d 154 " --> pdb=" O PHE d 150 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR d 156 " --> pdb=" O ILE d 152 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 192 through 201 removed outlier: 3.921A pdb=" N VAL d 196 " --> pdb=" O GLU d 192 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR d 199 " --> pdb=" O ILE d 195 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER d 200 " --> pdb=" O VAL d 196 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 102 removed outlier: 3.733A pdb=" N LYS e 93 " --> pdb=" O ALA e 89 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU e 96 " --> pdb=" O ALA e 92 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS e 100 " --> pdb=" O GLU e 96 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER e 101 " --> pdb=" O GLU e 97 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE e 102 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 140 through 150 removed outlier: 4.029A pdb=" N ALA e 144 " --> pdb=" O GLY e 140 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL e 145 " --> pdb=" O ALA e 141 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU e 146 " --> pdb=" O ALA e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 163 through 179 removed outlier: 3.658A pdb=" N VAL e 168 " --> pdb=" O ALA e 164 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU e 177 " --> pdb=" O ALA e 173 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU e 178 " --> pdb=" O ALA e 174 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLN e 179 " --> pdb=" O LEU e 175 " (cutoff:3.500A) Processing helix chain 'e' and resid 180 through 189 removed outlier: 3.578A pdb=" N ALA e 185 " --> pdb=" O PRO e 181 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA e 186 " --> pdb=" O GLU e 182 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG e 187 " --> pdb=" O GLU e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 196 removed outlier: 3.892A pdb=" N VAL e 195 " --> pdb=" O PRO e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 197 through 209 removed outlier: 3.564A pdb=" N LEU e 201 " --> pdb=" O PRO e 197 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS e 202 " --> pdb=" O ALA e 198 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG e 204 " --> pdb=" O MET e 200 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG e 205 " --> pdb=" O LEU e 201 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS e 206 " --> pdb=" O LYS e 202 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER e 207 " --> pdb=" O ALA e 203 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU e 208 " --> pdb=" O ARG e 204 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 32 removed outlier: 3.753A pdb=" N VAL f 19 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ALA f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Proline residue: f 21 - end of helix removed outlier: 3.505A pdb=" N GLU f 24 " --> pdb=" O ALA f 20 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR f 25 " --> pdb=" O PRO f 21 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE f 26 " --> pdb=" O SER f 22 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL f 29 " --> pdb=" O THR f 25 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG f 31 " --> pdb=" O LEU f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 83 removed outlier: 3.598A pdb=" N VAL f 72 " --> pdb=" O ALA f 68 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG f 77 " --> pdb=" O SER f 73 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLU f 83 " --> pdb=" O LEU f 79 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.296A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN g 28 " --> pdb=" O THR g 24 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS g 29 " --> pdb=" O GLN g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.606A pdb=" N GLY g 45 " --> pdb=" O ARG g 41 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP g 52 " --> pdb=" O GLU g 48 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS g 53 " --> pdb=" O GLN g 49 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR g 54 " --> pdb=" O ALA g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.895A pdb=" N ASN g 68 " --> pdb=" O ARG g 64 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.634A pdb=" N THR g 98 " --> pdb=" O ASP g 94 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN g 110 " --> pdb=" O GLY g 106 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG g 111 " --> pdb=" O TYR g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.646A pdb=" N LEU g 125 " --> pdb=" O ALA g 121 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY g 130 " --> pdb=" O ASP g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 153 removed outlier: 3.623A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG g 137 " --> pdb=" O ALA g 133 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG g 138 " --> pdb=" O SER g 134 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU g 139 " --> pdb=" O VAL g 135 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS g 143 " --> pdb=" O GLU g 139 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE g 151 " --> pdb=" O ALA g 147 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA g 152 " --> pdb=" O ASN g 148 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS g 153 " --> pdb=" O ARG g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.540A pdb=" N ALA h 17 " --> pdb=" O ARG h 13 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.512A pdb=" N ASN h 35 " --> pdb=" O LYS h 31 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE h 39 " --> pdb=" O ASN h 35 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY h 44 " --> pdb=" O LEU h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 3.557A pdb=" N GLN h 121 " --> pdb=" O GLN h 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 60 Processing helix chain 'i' and resid 62 through 77 removed outlier: 3.611A pdb=" N GLN i 66 " --> pdb=" O ASN i 62 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU i 68 " --> pdb=" O VAL i 64 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS i 70 " --> pdb=" O GLN i 66 " (cutoff:3.500A) Proline residue: i 72 - end of helix removed outlier: 3.537A pdb=" N THR i 75 " --> pdb=" O ALA i 71 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL i 76 " --> pdb=" O PRO i 72 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 112 removed outlier: 3.569A pdb=" N LEU i 102 " --> pdb=" O GLY i 98 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE i 109 " --> pdb=" O ALA i 105 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU i 110 " --> pdb=" O ARG i 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL i 111 " --> pdb=" O ALA i 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 115 through 123 removed outlier: 3.903A pdb=" N LYS i 121 " --> pdb=" O PRO i 117 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA i 122 " --> pdb=" O ALA i 118 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY i 123 " --> pdb=" O LEU i 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.857A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA j 20 " --> pdb=" O GLU j 16 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER j 21 " --> pdb=" O ALA j 17 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA j 22 " --> pdb=" O ILE j 18 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU j 27 " --> pdb=" O ARG j 23 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR j 28 " --> pdb=" O LYS j 24 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY j 33 " --> pdb=" O VAL j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.635A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 61 removed outlier: 5.081A pdb=" N GLY k 61 " --> pdb=" O SER k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 69 through 88 removed outlier: 3.535A pdb=" N ALA k 73 " --> pdb=" O THR k 69 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU k 78 " --> pdb=" O GLN k 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS k 83 " --> pdb=" O ASN k 79 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N HIS k 87 " --> pdb=" O LYS k 83 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY k 88 " --> pdb=" O ALA k 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 102 through 114 removed outlier: 3.716A pdb=" N ALA k 106 " --> pdb=" O GLY k 102 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE k 107 " --> pdb=" O ARG k 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN k 111 " --> pdb=" O ILE k 107 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA k 112 " --> pdb=" O ARG k 108 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY k 114 " --> pdb=" O LEU k 110 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 removed outlier: 3.998A pdb=" N LEU l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 118 removed outlier: 5.535A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.635A pdb=" N LEU m 19 " --> pdb=" O MET m 15 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR m 20 " --> pdb=" O GLU m 16 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.595A pdb=" N GLU m 32 " --> pdb=" O THR m 28 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU m 34 " --> pdb=" O SER m 30 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA m 35 " --> pdb=" O ASN m 31 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA m 36 " --> pdb=" O GLU m 32 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR m 37 " --> pdb=" O ILE m 33 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 4.042A pdb=" N LEU m 48 " --> pdb=" O ARG m 44 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR m 49 " --> pdb=" O THR m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 63 removed outlier: 3.864A pdb=" N HIS m 55 " --> pdb=" O GLU m 51 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU m 56 " --> pdb=" O GLN m 52 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP m 58 " --> pdb=" O ILE m 54 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR m 59 " --> pdb=" O HIS m 55 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE m 60 " --> pdb=" O LEU m 56 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA m 62 " --> pdb=" O ASP m 58 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 85 removed outlier: 5.865A pdb=" N ARG m 71 " --> pdb=" O GLU m 67 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU m 73 " --> pdb=" O ASP m 69 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE m 82 " --> pdb=" O ILE m 78 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY m 85 " --> pdb=" O LYS m 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 95 removed outlier: 4.004A pdb=" N ARG m 94 " --> pdb=" O LEU m 90 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY m 95 " --> pdb=" O ARG m 91 " (cutoff:3.500A) Processing helix chain 'm' and resid 107 through 112 removed outlier: 4.203A pdb=" N GLY m 112 " --> pdb=" O ARG m 108 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 13 removed outlier: 3.501A pdb=" N ASN n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA n 10 " --> pdb=" O LEU n 6 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA n 11 " --> pdb=" O VAL n 7 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 removed outlier: 3.532A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET n 47 " --> pdb=" O CYS n 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.893A pdb=" N LYS o 9 " --> pdb=" O ALA o 5 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU o 10 " --> pdb=" O GLU o 6 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER o 14 " --> pdb=" O GLU o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.629A pdb=" N LYS o 34 " --> pdb=" O ALA o 30 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU o 41 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N HIS o 46 " --> pdb=" O HIS o 42 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 4.316A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP o 74 " --> pdb=" O ILE o 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.577A pdb=" N SER o 80 " --> pdb=" O GLU o 76 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG o 84 " --> pdb=" O SER o 80 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 63 removed outlier: 5.923A pdb=" N ALA p 56 " --> pdb=" O ASN p 52 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLN p 57 " --> pdb=" O SER p 53 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR p 58 " --> pdb=" O GLU p 54 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU p 60 " --> pdb=" O ALA p 56 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 removed outlier: 3.846A pdb=" N LYS p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU p 73 " --> pdb=" O PRO p 69 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE p 76 " --> pdb=" O LYS p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 79 through 85 removed outlier: 3.782A pdb=" N PHE p 83 " --> pdb=" O ASP p 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 114 removed outlier: 3.549A pdb=" N PHE p 106 " --> pdb=" O LYS p 102 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA p 113 " --> pdb=" O ALA p 109 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 26 removed outlier: 4.530A pdb=" N LYS r 26 " --> pdb=" O PHE r 22 " (cutoff:3.500A) Processing helix chain 'r' and resid 34 through 42 removed outlier: 3.571A pdb=" N LEU r 38 " --> pdb=" O ASP r 34 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR r 40 " --> pdb=" O ALA r 36 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N TYR r 41 " --> pdb=" O LEU r 37 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE r 42 " --> pdb=" O LEU r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 50 through 55 removed outlier: 3.698A pdb=" N THR r 54 " --> pdb=" O ALA r 50 " (cutoff:3.500A) Processing helix chain 'r' and resid 57 through 75 removed outlier: 3.667A pdb=" N GLU r 73 " --> pdb=" O LYS r 69 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 removed outlier: 3.814A pdb=" N LYS s 17 " --> pdb=" O GLU s 13 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU s 24 " --> pdb=" O ASP s 20 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.960A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 8 through 40 removed outlier: 3.575A pdb=" N GLU t 15 " --> pdb=" O ASN t 11 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG t 16 " --> pdb=" O ARG t 12 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA t 23 " --> pdb=" O LEU t 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL t 24 " --> pdb=" O ARG t 20 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA t 34 " --> pdb=" O THR t 30 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA t 38 " --> pdb=" O ALA t 34 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 removed outlier: 3.745A pdb=" N ALA t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU t 51 " --> pdb=" O ALA t 47 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA t 52 " --> pdb=" O ALA t 48 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER t 53 " --> pdb=" O GLU t 49 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG t 56 " --> pdb=" O ALA t 52 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS t 57 " --> pdb=" O SER t 53 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY t 65 " --> pdb=" O ALA t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 86 removed outlier: 3.714A pdb=" N ALA t 78 " --> pdb=" O ASN t 74 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS t 85 " --> pdb=" O GLN t 81 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU t 86 " --> pdb=" O ALA t 82 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 28 through 31 removed outlier: 3.543A pdb=" N VAL 0 30 " --> pdb=" O HIS 0 37 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '1' and resid 8 through 13 removed outlier: 3.929A pdb=" N LYS 1 27 " --> pdb=" O PRO 1 9 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '3' and resid 22 through 25 removed outlier: 6.315A pdb=" N ILE 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '6' and resid 20 through 25 removed outlier: 4.647A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLY 6 31 " --> pdb=" O GLU 6 11 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE 6 33 " --> pdb=" O THR 6 13 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL 6 15 " --> pdb=" O ILE 6 33 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '8' and resid 75 through 78 Processing sheet with id= 6, first strand: chain '8' and resid 169 through 176 removed outlier: 6.050A pdb=" N ALA 8 169 " --> pdb=" O LEU 8 48 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE 8 46 " --> pdb=" O LEU 8 171 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE 8 175 " --> pdb=" O VAL 8 42 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL 8 42 " --> pdb=" O ILE 8 175 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS 8 211 " --> pdb=" O ARG 8 47 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE 8 212 " --> pdb=" O VAL 8 224 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL 8 214 " --> pdb=" O ILE 8 222 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.524A pdb=" N TYR C 6 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 16 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'C' and resid 81 through 84 removed outlier: 3.617A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU C 94 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASP C 115 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLY C 128 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU C 118 " --> pdb=" O GLY C 128 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 138 through 143 removed outlier: 7.349A pdb=" N ALA C 138 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLY C 167 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR C 140 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.056A pdb=" N GLU C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 91 through 97 removed outlier: 5.074A pdb=" N ARG C 91 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 4 through 8 removed outlier: 5.775A pdb=" N LYS D 4 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP D 173 " --> pdb=" O SER D 118 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 12 through 18 removed outlier: 3.814A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 184 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 48 through 55 removed outlier: 5.461A pdb=" N SER D 48 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 110 through 113 removed outlier: 4.404A pdb=" N SER D 110 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 9 through 13 removed outlier: 5.941A pdb=" N LEU E 9 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY E 22 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'E' and resid 129 through 132 Processing sheet with id= 19, first strand: chain 'F' and resid 72 through 76 removed outlier: 4.614A pdb=" N VAL F 92 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL F 94 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS F 40 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLY F 46 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLY F 158 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET F 159 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'F' and resid 79 through 82 removed outlier: 7.459A pdb=" N LYS F 79 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLU F 88 " --> pdb=" O LYS F 79 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 23 through 27 removed outlier: 3.616A pdb=" N LEU G 35 " --> pdb=" O ILE G 24 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 41 through 46 removed outlier: 3.830A pdb=" N ASN G 46 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA G 50 " --> pdb=" O ASN G 46 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'G' and resid 95 through 100 removed outlier: 3.708A pdb=" N ARG G 96 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS G 100 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU G 104 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'G' and resid 122 through 127 removed outlier: 6.365A pdb=" N LYS G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N THR G 130 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY G 162 " --> pdb=" O PHE G 91 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'H' and resid 3 through 6 removed outlier: 7.436A pdb=" N LEU H 35 " --> pdb=" O THR H 6 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'H' and resid 7 through 10 removed outlier: 7.664A pdb=" N ALA H 7 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE H 15 " --> pdb=" O ALA H 7 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.987A pdb=" N ASP J 19 " --> pdb=" O TYR J 140 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 74 through 78 removed outlier: 3.519A pdb=" N SER J 78 " --> pdb=" O GLY J 83 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLY J 83 " --> pdb=" O SER J 78 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.837A pdb=" N SER K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN K 82 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU K 81 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'K' and resid 38 through 41 Processing sheet with id= 31, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.531A pdb=" N ARG K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE K 77 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'L' and resid 74 through 77 Processing sheet with id= 33, first strand: chain 'L' and resid 121 through 124 No H-bonds generated for sheet with id= 33 Processing sheet with id= 34, first strand: chain 'M' and resid 62 through 66 removed outlier: 4.104A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS M 128 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.216A pdb=" N MET N 110 " --> pdb=" O ILE N 100 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N TYR N 94 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'O' and resid 31 through 37 removed outlier: 6.636A pdb=" N ARG O 32 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE O 42 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA O 56 " --> pdb=" O LEU O 46 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.614A pdb=" N THR P 24 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS P 28 " --> pdb=" O HIS P 82 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS P 82 " --> pdb=" O HIS P 28 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'P' and resid 48 through 51 removed outlier: 3.813A pdb=" N ARG P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLU P 56 " --> pdb=" O VAL P 75 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'R' and resid 14 through 17 removed outlier: 3.711A pdb=" N LEU R 42 " --> pdb=" O ILE R 7 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL R 43 " --> pdb=" O THR R 50 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR R 50 " --> pdb=" O VAL R 43 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR R 48 " --> pdb=" O ASP R 45 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'R' and resid 20 through 24 removed outlier: 4.215A pdb=" N ASP R 21 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL R 97 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N THR R 62 " --> pdb=" O THR R 101 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'R' and resid 69 through 80 removed outlier: 5.464A pdb=" N LYS R 70 " --> pdb=" O LEU R 95 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU R 95 " --> pdb=" O LYS R 70 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLN R 93 " --> pdb=" O PRO R 72 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS R 80 " --> pdb=" O TYR R 85 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR R 85 " --> pdb=" O LYS R 80 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'S' and resid 11 through 18 removed outlier: 6.756A pdb=" N VAL S 116 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N THR S 78 " --> pdb=" O ARG S 120 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'S' and resid 83 through 89 removed outlier: 5.084A pdb=" N THR S 110 " --> pdb=" O GLY S 89 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'T' and resid 28 through 33 removed outlier: 4.373A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LYS T 65 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER T 78 " --> pdb=" O GLN T 63 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLN T 63 " --> pdb=" O SER T 78 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS T 80 " --> pdb=" O ASN T 61 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN T 61 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA T 82 " --> pdb=" O THR T 59 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR T 59 " --> pdb=" O ALA T 82 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL T 84 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL T 57 " --> pdb=" O VAL T 84 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.634A pdb=" N GLN U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'V' and resid 73 through 77 removed outlier: 4.812A pdb=" N ASN V 7 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU V 9 " --> pdb=" O THR V 66 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL V 11 " --> pdb=" O ASP V 68 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS V 44 " --> pdb=" O ARG V 14 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS V 92 " --> pdb=" O HIS V 82 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N HIS V 82 " --> pdb=" O GLN V 91 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR V 89 " --> pdb=" O HIS V 84 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'V' and resid 120 through 124 Processing sheet with id= 48, first strand: chain 'V' and resid 127 through 133 removed outlier: 5.680A pdb=" N ASN V 127 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA V 133 " --> pdb=" O VAL V 104 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL V 111 " --> pdb=" O LEU V 142 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'W' and resid 66 through 71 Processing sheet with id= 50, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.755A pdb=" N ARG X 27 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.364A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU Z 53 " --> pdb=" O VAL Z 9 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'c' and resid 53 through 58 removed outlier: 4.177A pdb=" N ASP c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR c 69 " --> pdb=" O LEU c 103 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'c' and resid 165 through 170 removed outlier: 3.604A pdb=" N GLY c 148 " --> pdb=" O TYR c 203 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR c 191 " --> pdb=" O GLY c 194 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'd' and resid 135 through 139 removed outlier: 4.157A pdb=" N ASP d 136 " --> pdb=" O ILE d 177 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 42 through 47 removed outlier: 6.731A pdb=" N LEU e 67 " --> pdb=" O VAL e 47 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'e' and resid 115 through 119 removed outlier: 5.897A pdb=" N VAL e 124 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA e 130 " --> pdb=" O ASP e 153 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASP e 153 " --> pdb=" O ALA e 130 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE e 154 " --> pdb=" O GLY e 135 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'e' and resid 63 through 72 removed outlier: 4.974A pdb=" N GLY e 82 " --> pdb=" O ALA e 66 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET e 76 " --> pdb=" O ASP e 72 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'f' and resid 35 through 38 removed outlier: 7.510A pdb=" N ASP f 64 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLU f 57 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE f 6 " --> pdb=" O ILE f 63 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'f' and resid 39 through 44 removed outlier: 4.066A pdb=" N LYS f 39 " --> pdb=" O ASP f 64 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP f 64 " --> pdb=" O LYS f 39 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'f' and resid 45 through 48 removed outlier: 3.500A pdb=" N GLY f 58 " --> pdb=" O ARG f 46 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU f 48 " --> pdb=" O ALA f 56 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ALA f 56 " --> pdb=" O LEU f 48 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.419A pdb=" N ALA g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG g 78 " --> pdb=" O TYR g 85 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'h' and resid 23 through 28 removed outlier: 6.471A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'h' and resid 76 through 79 removed outlier: 4.510A pdb=" N GLY h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TRP h 132 " --> pdb=" O GLY h 76 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL h 103 " --> pdb=" O VAL h 131 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'i' and resid 27 through 32 removed outlier: 4.617A pdb=" N ILE i 27 " --> pdb=" O LEU i 42 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU i 42 " --> pdb=" O ILE i 27 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY i 31 " --> pdb=" O VAL i 38 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY i 89 " --> pdb=" O VAL i 37 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG i 39 " --> pdb=" O HIS i 87 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS i 87 " --> pdb=" O ARG i 39 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE i 85 " --> pdb=" O ARG i 41 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'j' and resid 7 through 12 removed outlier: 3.780A pdb=" N ARG j 9 " --> pdb=" O ASN j 99 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'j' and resid 39 through 42 removed outlier: 5.085A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'k' and resid 39 through 46 removed outlier: 3.974A pdb=" N ASN k 39 " --> pdb=" O THR k 36 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU k 116 " --> pdb=" O ARG k 90 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY k 118 " --> pdb=" O VAL k 92 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL k 94 " --> pdb=" O GLY k 118 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'l' and resid 29 through 33 removed outlier: 3.759A pdb=" N VAL l 80 " --> pdb=" O GLY l 32 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU l 81 " --> pdb=" O ILE l 98 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'l' and resid 35 through 41 removed outlier: 4.954A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR l 38 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'p' and resid 5 through 11 removed outlier: 5.380A pdb=" N GLN p 17 " --> pdb=" O LEU p 10 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'q' and resid 59 through 63 removed outlier: 3.695A pdb=" N ARG q 60 " --> pdb=" O LEU q 113 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY q 62 " --> pdb=" O VAL q 111 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N SER q 112 " --> pdb=" O VAL q 128 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'q' and resid 71 through 82 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 's' and resid 46 through 52 removed outlier: 4.670A pdb=" N HIS s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) 1325 hydrogen bonds defined for protein. 3930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3017 hydrogen bonds 4830 hydrogen bond angles 0 basepair planarities 1228 basepair parallelities 2772 stacking parallelities Total time for adding SS restraints: 283.95 Time building geometry restraints manager: 61.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 12402 1.30 - 1.43: 72740 1.43 - 1.55: 65707 1.55 - 1.68: 9668 1.68 - 1.81: 150 Bond restraints: 160667 Sorted by residual: bond pdb=" C5 5MU A2177 " pdb=" C6 5MU A2177 " ideal model delta sigma weight residual 1.155 1.443 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C4 5MU A2177 " pdb=" C5 5MU A2177 " ideal model delta sigma weight residual 1.802 1.597 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C8 G7M a 518 " pdb=" N7 G7M a 518 " ideal model delta sigma weight residual 1.348 1.505 -0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" N9 G7M a 518 " pdb=" C8 G7M a 518 " ideal model delta sigma weight residual 1.348 1.503 -0.155 2.00e-02 2.50e+03 6.01e+01 bond pdb=" N7 G7M a 518 " pdb=" C5 G7M a 518 " ideal model delta sigma weight residual 1.329 1.438 -0.109 2.00e-02 2.50e+03 3.00e+01 ... (remaining 160662 not shown) Histogram of bond angle deviations from ideal: 98.43 - 106.30: 29055 106.30 - 114.17: 101163 114.17 - 122.05: 75418 122.05 - 129.92: 32984 129.92 - 137.80: 2478 Bond angle restraints: 241098 Sorted by residual: angle pdb=" C1' OMG A2791 " pdb=" N9 OMG A2791 " pdb=" C4 OMG A2791 " ideal model delta sigma weight residual 108.29 131.75 -23.46 3.00e+00 1.11e-01 6.11e+01 angle pdb=" N VAL j 26 " pdb=" CA VAL j 26 " pdb=" C VAL j 26 " ideal model delta sigma weight residual 111.91 105.04 6.87 8.90e-01 1.26e+00 5.96e+01 angle pdb=" C1' OMG A2791 " pdb=" N9 OMG A2791 " pdb=" C8 OMG A2791 " ideal model delta sigma weight residual 142.82 120.06 22.76 3.00e+00 1.11e-01 5.76e+01 angle pdb=" C1' OMG A2489 " pdb=" N9 OMG A2489 " pdb=" C4 OMG A2489 " ideal model delta sigma weight residual 108.29 130.62 -22.33 3.00e+00 1.11e-01 5.54e+01 angle pdb=" C1' OMG A2489 " pdb=" N9 OMG A2489 " pdb=" C8 OMG A2489 " ideal model delta sigma weight residual 142.82 120.75 22.07 3.00e+00 1.11e-01 5.41e+01 ... (remaining 241093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 92204 35.87 - 71.74: 9983 71.74 - 107.61: 1316 107.61 - 143.47: 5 143.47 - 179.34: 24 Dihedral angle restraints: 103532 sinusoidal: 87567 harmonic: 15965 Sorted by residual: dihedral pdb=" C4' A B 3 " pdb=" C3' A B 3 " pdb=" C2' A B 3 " pdb=" C1' A B 3 " ideal model delta sinusoidal sigma weight residual -35.00 32.11 -67.11 1 8.00e+00 1.56e-02 9.17e+01 dihedral pdb=" CA ALA l 113 " pdb=" C ALA l 113 " pdb=" N ARG l 114 " pdb=" CA ARG l 114 " ideal model delta harmonic sigma weight residual 180.00 132.92 47.08 0 5.00e+00 4.00e-02 8.87e+01 dihedral pdb=" C5' A B 3 " pdb=" C4' A B 3 " pdb=" C3' A B 3 " pdb=" O3' A B 3 " ideal model delta sinusoidal sigma weight residual 147.00 81.57 65.43 1 8.00e+00 1.56e-02 8.76e+01 ... (remaining 103529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 29130 0.084 - 0.169: 1628 0.169 - 0.253: 78 0.253 - 0.338: 12 0.338 - 0.422: 1 Chirality restraints: 30849 Sorted by residual: chirality pdb=" CB VAL g 75 " pdb=" CA VAL g 75 " pdb=" CG1 VAL g 75 " pdb=" CG2 VAL g 75 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" C3' A B 3 " pdb=" C4' A B 3 " pdb=" O3' A B 3 " pdb=" C2' A B 3 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB VAL k 131 " pdb=" CA VAL k 131 " pdb=" CG1 VAL k 131 " pdb=" CG2 VAL k 131 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 30846 not shown) Planarity restraints: 12624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2489 " 0.032 2.00e-02 2.50e+03 5.78e-01 7.52e+03 pdb=" C4' OMG A2489 " 0.437 2.00e-02 2.50e+03 pdb=" O4' OMG A2489 " 0.668 2.00e-02 2.50e+03 pdb=" C3' OMG A2489 " -0.595 2.00e-02 2.50e+03 pdb=" O3' OMG A2489 " -0.565 2.00e-02 2.50e+03 pdb=" C2' OMG A2489 " -0.219 2.00e-02 2.50e+03 pdb=" O2' OMG A2489 " 0.904 2.00e-02 2.50e+03 pdb=" C1' OMG A2489 " 0.221 2.00e-02 2.50e+03 pdb=" N9 OMG A2489 " -0.884 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a 959 " 0.003 2.00e-02 2.50e+03 5.48e-01 6.76e+03 pdb=" C4' 2MG a 959 " 0.428 2.00e-02 2.50e+03 pdb=" O4' 2MG a 959 " 0.648 2.00e-02 2.50e+03 pdb=" C3' 2MG a 959 " -0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG a 959 " -0.504 2.00e-02 2.50e+03 pdb=" C2' 2MG a 959 " -0.245 2.00e-02 2.50e+03 pdb=" O2' 2MG a 959 " 0.850 2.00e-02 2.50e+03 pdb=" C1' 2MG a 959 " 0.225 2.00e-02 2.50e+03 pdb=" N9 2MG a 959 " -0.817 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2791 " 0.017 2.00e-02 2.50e+03 5.42e-01 6.61e+03 pdb=" C4' OMG A2791 " 0.421 2.00e-02 2.50e+03 pdb=" O4' OMG A2791 " 0.603 2.00e-02 2.50e+03 pdb=" C3' OMG A2791 " -0.588 2.00e-02 2.50e+03 pdb=" O3' OMG A2791 " -0.507 2.00e-02 2.50e+03 pdb=" C2' OMG A2791 " -0.237 2.00e-02 2.50e+03 pdb=" O2' OMG A2791 " 0.862 2.00e-02 2.50e+03 pdb=" C1' OMG A2791 " 0.234 2.00e-02 2.50e+03 pdb=" N9 OMG A2791 " -0.804 2.00e-02 2.50e+03 ... (remaining 12621 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 1667 2.58 - 3.16: 102808 3.16 - 3.74: 272126 3.74 - 4.32: 398226 4.32 - 4.90: 538002 Nonbonded interactions: 1312829 Sorted by model distance: nonbonded pdb=" OP1 U A 955 " pdb="MG MG A3280 " model vdw 2.005 2.170 nonbonded pdb=" OP2 U A2920 " pdb="MG MG A3341 " model vdw 2.015 2.170 nonbonded pdb=" OP1 C A 807 " pdb="MG MG A3203 " model vdw 2.016 2.170 nonbonded pdb=" OP1 C A 916 " pdb="MG MG A3264 " model vdw 2.017 2.170 nonbonded pdb=" OP1 C A2274 " pdb="MG MG A3285 " model vdw 2.026 2.170 ... (remaining 1312824 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: 1.810 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: 0.140 Extract box with map and model: 12.440 Check model and map are aligned: 1.570 Set scattering table: 0.980 Process input model: 587.820 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 620.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.007 0.288 160667 Z= 0.419 Angle : 0.770 23.457 241098 Z= 0.387 Chirality : 0.042 0.422 30849 Planarity : 0.012 0.578 12624 Dihedral : 22.208 179.342 93274 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.33 % Favored : 93.56 % Rotamer: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.09), residues: 5526 helix: -4.69 (0.05), residues: 1538 sheet: -2.02 (0.14), residues: 1048 loop : -2.41 (0.09), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP Q 61 HIS 0.025 0.003 HIS M 13 PHE 0.038 0.003 PHE E 90 TYR 0.040 0.003 TYR E 104 ARG 0.026 0.001 ARG Q 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1039 time to evaluate : 5.939 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: 1 22 ASN cc_start: 0.9134 (m-40) cc_final: 0.8933 (m-40) REVERT: 8 39 ASP cc_start: 0.5034 (p0) cc_final: 0.3924 (t70) REVERT: C 35 ARG cc_start: 0.7679 (mmt-90) cc_final: 0.7312 (mmt-90) REVERT: C 158 SER cc_start: 0.8192 (m) cc_final: 0.7964 (t) REVERT: G 41 ILE cc_start: 0.8295 (mm) cc_final: 0.7988 (mm) REVERT: J 13 ARG cc_start: 0.8577 (mtt90) cc_final: 0.8313 (mtt-85) REVERT: M 104 PHE cc_start: 0.7828 (m-80) cc_final: 0.7454 (m-10) REVERT: N 78 THR cc_start: 0.8971 (p) cc_final: 0.8719 (t) REVERT: R 7 ILE cc_start: 0.8823 (mt) cc_final: 0.8608 (mp) REVERT: T 26 ASP cc_start: 0.7638 (m-30) cc_final: 0.7338 (t0) REVERT: V 144 VAL cc_start: 0.8336 (t) cc_final: 0.8035 (p) REVERT: Y 12 GLU cc_start: 0.7263 (mp0) cc_final: 0.7045 (mp0) REVERT: Y 65 GLU cc_start: 0.7860 (pt0) cc_final: 0.7629 (pt0) REVERT: Z 56 VAL cc_start: 0.9239 (p) cc_final: 0.8883 (t) REVERT: d 84 GLU cc_start: 0.7820 (mp0) cc_final: 0.7559 (mp0) REVERT: e 43 LEU cc_start: 0.8604 (mp) cc_final: 0.8371 (mt) REVERT: e 128 ARG cc_start: 0.8169 (ttt90) cc_final: 0.7960 (ttm-80) REVERT: g 114 LYS cc_start: 0.8349 (mmtp) cc_final: 0.8098 (mmpt) REVERT: h 72 ARG cc_start: 0.8450 (mpt-90) cc_final: 0.8114 (mtt90) REVERT: l 70 GLU cc_start: 0.7598 (pm20) cc_final: 0.7282 (pm20) REVERT: l 79 MET cc_start: 0.7672 (mmp) cc_final: 0.7444 (mmt) REVERT: m 47 ASP cc_start: 0.8171 (m-30) cc_final: 0.7950 (m-30) REVERT: p 51 ILE cc_start: 0.9157 (mm) cc_final: 0.8941 (mp) REVERT: r 49 ARG cc_start: 0.8581 (mtt-85) cc_final: 0.8310 (mtt90) outliers start: 3 outliers final: 0 residues processed: 1041 average time/residue: 2.5739 time to fit residues: 3658.4888 Evaluate side-chains 704 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 704 time to evaluate : 5.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 861 optimal weight: 1.9990 chunk 773 optimal weight: 20.0000 chunk 428 optimal weight: 4.9990 chunk 264 optimal weight: 7.9990 chunk 521 optimal weight: 6.9990 chunk 413 optimal weight: 0.9990 chunk 799 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 chunk 486 optimal weight: 1.9990 chunk 595 optimal weight: 3.9990 chunk 926 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 20 HIS 7 17 ASN 8 57 GLN 8 67 HIS 8 231 ASN C 81 HIS C 129 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN E 47 GLN E 127 ASN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 ASN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN J 119 GLN J 147 GLN L 106 ASN M 57 HIS M 96 ASN N 61 HIS O 36 HIS P 79 ASN P 82 HIS Q 44 ASN Q 122 ASN U 70 ASN ** V 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 GLN c 176 HIS d 95 ASN e 117 GLN e 163 ASN h 121 GLN i 52 ASN i 65 HIS i 66 GLN l 105 GLN o 7 GLN o 51 HIS p 15 ASN s 57 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 160667 Z= 0.222 Angle : 0.613 19.214 241098 Z= 0.318 Chirality : 0.036 0.300 30849 Planarity : 0.006 0.130 12624 Dihedral : 22.991 178.104 82335 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.34 % Favored : 94.59 % Rotamer: Outliers : 2.90 % Allowed : 11.95 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.10), residues: 5526 helix: -2.89 (0.10), residues: 1605 sheet: -1.48 (0.15), residues: 1055 loop : -1.96 (0.10), residues: 2866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 22 HIS 0.006 0.001 HIS N 54 PHE 0.035 0.002 PHE i 85 TYR 0.021 0.001 TYR g 85 ARG 0.013 0.001 ARG g 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 804 time to evaluate : 5.901 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: 1 22 ASN cc_start: 0.9131 (m-40) cc_final: 0.8915 (m-40) REVERT: 8 29 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8997 (mm) REVERT: 8 58 MET cc_start: 0.7898 (ptp) cc_final: 0.6928 (ppp) REVERT: 8 209 LEU cc_start: 0.7744 (pt) cc_final: 0.7534 (pp) REVERT: C 164 GLN cc_start: 0.8217 (tt0) cc_final: 0.7968 (tt0) REVERT: E 32 ASP cc_start: 0.8150 (t0) cc_final: 0.7806 (t0) REVERT: F 76 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8005 (mtt90) REVERT: F 85 LYS cc_start: 0.8749 (mttp) cc_final: 0.8345 (ttmm) REVERT: G 17 VAL cc_start: 0.7717 (OUTLIER) cc_final: 0.7379 (t) REVERT: L 21 VAL cc_start: 0.9091 (p) cc_final: 0.8890 (m) REVERT: M 45 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7119 (mtt90) REVERT: M 56 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7631 (mtt180) REVERT: M 81 THR cc_start: 0.8373 (p) cc_final: 0.8171 (p) REVERT: O 47 VAL cc_start: 0.8380 (m) cc_final: 0.8165 (p) REVERT: P 55 ARG cc_start: 0.8706 (mtm-85) cc_final: 0.8397 (mtm-85) REVERT: R 87 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8181 (ttmt) REVERT: T 26 ASP cc_start: 0.7720 (m-30) cc_final: 0.7402 (t0) REVERT: U 25 GLN cc_start: 0.8413 (tt0) cc_final: 0.8183 (tt0) REVERT: V 12 THR cc_start: 0.8608 (t) cc_final: 0.8143 (p) REVERT: V 73 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6790 (tp30) REVERT: V 107 GLU cc_start: 0.7294 (pm20) cc_final: 0.7090 (pm20) REVERT: V 144 VAL cc_start: 0.7878 (t) cc_final: 0.7546 (p) REVERT: Y 12 GLU cc_start: 0.7207 (mp0) cc_final: 0.6923 (mp0) REVERT: Y 48 ARG cc_start: 0.7706 (ttp80) cc_final: 0.7170 (ttp-170) REVERT: d 69 ARG cc_start: 0.8373 (mtp85) cc_final: 0.8110 (mtp-110) REVERT: d 141 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7884 (mmt90) REVERT: f 46 ARG cc_start: 0.8750 (mmm-85) cc_final: 0.8542 (mtt-85) REVERT: f 84 SER cc_start: 0.9062 (m) cc_final: 0.8804 (p) REVERT: g 68 ASN cc_start: 0.8850 (m-40) cc_final: 0.8618 (m110) REVERT: i 78 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7597 (mtp85) REVERT: k 48 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7941 (mt0) REVERT: l 70 GLU cc_start: 0.7626 (pm20) cc_final: 0.7258 (pm20) REVERT: l 79 MET cc_start: 0.7764 (mmp) cc_final: 0.7539 (mmt) REVERT: m 79 ARG cc_start: 0.8326 (tpp80) cc_final: 0.7953 (ttm-80) REVERT: m 96 MET cc_start: 0.7940 (tpp) cc_final: 0.7691 (mmt) REVERT: m 101 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8632 (mp10) REVERT: p 72 LYS cc_start: 0.8588 (tptt) cc_final: 0.8368 (mmmt) REVERT: q 42 LYS cc_start: 0.6118 (mttt) cc_final: 0.5844 (mmtp) REVERT: r 49 ARG cc_start: 0.8588 (mtt-85) cc_final: 0.8330 (mtt90) outliers start: 133 outliers final: 56 residues processed: 855 average time/residue: 2.2338 time to fit residues: 2717.2090 Evaluate side-chains 804 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 738 time to evaluate : 5.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 8 residue 29 LEU Chi-restraints excluded: chain 8 residue 165 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 56 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 79 LYS Chi-restraints excluded: chain V residue 73 GLU Chi-restraints excluded: chain V residue 162 LEU Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 36 MET Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 40 ASN Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain d residue 141 ARG Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 48 GLN Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain m residue 101 GLN Chi-restraints excluded: chain m residue 117 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain q residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 514 optimal weight: 6.9990 chunk 287 optimal weight: 60.0000 chunk 770 optimal weight: 30.0000 chunk 630 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 927 optimal weight: 8.9990 chunk 1002 optimal weight: 9.9990 chunk 826 optimal weight: 9.9990 chunk 920 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 744 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 67 HIS C 129 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN E 47 GLN E 141 ASN E 159 GLN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN J 119 GLN L 106 ASN M 96 ASN P 50 GLN U 70 ASN V 8 GLN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 GLN g 153 HIS i 52 ASN j 70 HIS k 59 HIS k 111 GLN l 105 GLN o 7 GLN s 22 GLN t 81 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.084 160667 Z= 0.589 Angle : 0.780 17.469 241098 Z= 0.388 Chirality : 0.046 0.308 30849 Planarity : 0.007 0.142 12624 Dihedral : 22.873 177.917 82335 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.61 % Favored : 93.27 % Rotamer: Outliers : 4.58 % Allowed : 13.35 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.10), residues: 5526 helix: -1.90 (0.11), residues: 1607 sheet: -1.19 (0.16), residues: 1054 loop : -1.81 (0.11), residues: 2865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 22 HIS 0.015 0.002 HIS 3 31 PHE 0.041 0.003 PHE i 85 TYR 0.034 0.002 TYR n 34 ARG 0.014 0.001 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 762 time to evaluate : 5.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 29 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8957 (mm) REVERT: 8 31 LYS cc_start: 0.6517 (mmmt) cc_final: 0.5812 (pttm) REVERT: 8 58 MET cc_start: 0.7991 (ptp) cc_final: 0.7035 (ppp) REVERT: C 64 MET cc_start: 0.7470 (mtt) cc_final: 0.7122 (mtt) REVERT: C 68 ARG cc_start: 0.8342 (mmt90) cc_final: 0.8043 (mpt180) REVERT: D 38 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8042 (tpt-90) REVERT: E 32 ASP cc_start: 0.8243 (t0) cc_final: 0.7896 (t0) REVERT: E 52 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8255 (mtp180) REVERT: E 145 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7589 (ttpm) REVERT: F 10 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7891 (ptt-90) REVERT: F 76 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8122 (mtt90) REVERT: G 17 VAL cc_start: 0.7773 (OUTLIER) cc_final: 0.7419 (t) REVERT: L 21 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8799 (m) REVERT: M 45 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7253 (mtt90) REVERT: M 56 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7598 (mtt180) REVERT: M 81 THR cc_start: 0.8434 (p) cc_final: 0.8229 (p) REVERT: N 71 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8070 (mtm-85) REVERT: T 26 ASP cc_start: 0.7857 (m-30) cc_final: 0.7380 (t0) REVERT: U 79 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8587 (mmmm) REVERT: V 12 THR cc_start: 0.8648 (t) cc_final: 0.8194 (p) REVERT: X 27 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8630 (ptm160) REVERT: Y 12 GLU cc_start: 0.7184 (mp0) cc_final: 0.6842 (mp0) REVERT: Z 44 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7246 (mtp85) REVERT: c 47 GLU cc_start: 0.7790 (pm20) cc_final: 0.7291 (pp20) REVERT: c 85 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7645 (tpp-160) REVERT: d 141 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8263 (mmt-90) REVERT: d 179 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8374 (pt0) REVERT: f 46 ARG cc_start: 0.8768 (mmm-85) cc_final: 0.8559 (mtt-85) REVERT: g 64 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.6884 (ttp80) REVERT: i 32 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6841 (ptt90) REVERT: i 78 ARG cc_start: 0.8325 (mtp85) cc_final: 0.7844 (mtp85) REVERT: l 70 GLU cc_start: 0.7601 (pm20) cc_final: 0.7211 (pm20) REVERT: m 57 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7494 (tmm-80) REVERT: m 79 ARG cc_start: 0.8414 (tpp80) cc_final: 0.8016 (ttm-80) REVERT: m 96 MET cc_start: 0.7986 (tpp) cc_final: 0.7737 (mmt) REVERT: p 6 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8639 (ptmt) REVERT: r 49 ARG cc_start: 0.8652 (mtt-85) cc_final: 0.8368 (mtt90) outliers start: 210 outliers final: 119 residues processed: 853 average time/residue: 2.2405 time to fit residues: 2740.3525 Evaluate side-chains 870 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 730 time to evaluate : 5.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 43 LEU Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 34 VAL Chi-restraints excluded: chain 8 residue 29 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 10 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 56 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 83 ILE Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 22 LYS Chi-restraints excluded: chain U residue 79 LYS Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Y residue 36 MET Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 65 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 40 ASN Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 85 ARG Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain d residue 123 VAL Chi-restraints excluded: chain d residue 141 ARG Chi-restraints excluded: chain d residue 148 VAL Chi-restraints excluded: chain d residue 179 GLN Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 44 ILE Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 98 ILE Chi-restraints excluded: chain m residue 41 ARG Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 54 ILE Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 117 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 61 SER Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 102 LYS Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 81 MET Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain s residue 11 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 916 optimal weight: 7.9990 chunk 697 optimal weight: 10.0000 chunk 481 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 442 optimal weight: 8.9990 chunk 623 optimal weight: 8.9990 chunk 931 optimal weight: 10.0000 chunk 985 optimal weight: 3.9990 chunk 486 optimal weight: 0.5980 chunk 882 optimal weight: 0.9980 chunk 265 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN L 106 ASN M 96 ASN U 70 ASN V 8 GLN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 ASN g 153 HIS l 105 GLN o 7 GLN r 56 ASN t 81 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 160667 Z= 0.233 Angle : 0.604 15.136 241098 Z= 0.317 Chirality : 0.037 0.290 30849 Planarity : 0.006 0.128 12624 Dihedral : 22.949 176.738 82335 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.30 % Rotamer: Outliers : 4.32 % Allowed : 14.83 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.11), residues: 5526 helix: -1.34 (0.12), residues: 1620 sheet: -1.00 (0.16), residues: 1079 loop : -1.64 (0.11), residues: 2827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 22 HIS 0.007 0.001 HIS L 126 PHE 0.039 0.002 PHE i 85 TYR 0.019 0.002 TYR d 4 ARG 0.010 0.001 ARG g 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 723 time to evaluate : 5.440 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: 4 33 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8265 (mtmt) REVERT: 8 29 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.8978 (mm) REVERT: 8 58 MET cc_start: 0.7989 (ptp) cc_final: 0.7036 (ppp) REVERT: 8 185 LEU cc_start: 0.7006 (tm) cc_final: 0.6524 (pt) REVERT: C 68 ARG cc_start: 0.8328 (mmt90) cc_final: 0.8035 (mpt180) REVERT: E 48 ARG cc_start: 0.7777 (mmm-85) cc_final: 0.7409 (mmp-170) REVERT: E 52 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8181 (mtp180) REVERT: F 10 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7792 (ptt-90) REVERT: F 70 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7962 (pt0) REVERT: F 76 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8081 (mtt90) REVERT: G 17 VAL cc_start: 0.7651 (OUTLIER) cc_final: 0.7319 (t) REVERT: M 10 ARG cc_start: 0.8192 (mtp-110) cc_final: 0.7904 (mtm110) REVERT: M 45 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7178 (mtt90) REVERT: M 56 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7516 (mtt180) REVERT: M 81 THR cc_start: 0.8354 (p) cc_final: 0.8147 (p) REVERT: M 83 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8462 (mmp) REVERT: N 71 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8237 (mtt180) REVERT: P 93 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.6909 (mtp85) REVERT: Q 5 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8956 (mmtp) REVERT: R 87 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8188 (ttmt) REVERT: T 26 ASP cc_start: 0.7834 (m-30) cc_final: 0.7377 (t0) REVERT: U 25 GLN cc_start: 0.8369 (tt0) cc_final: 0.8167 (tt0) REVERT: U 79 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8587 (mmmm) REVERT: X 27 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8658 (ptm160) REVERT: Y 12 GLU cc_start: 0.7129 (mp0) cc_final: 0.6766 (mp0) REVERT: Z 44 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7161 (mtp85) REVERT: c 47 GLU cc_start: 0.7730 (pm20) cc_final: 0.7220 (pp20) REVERT: c 85 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7584 (tpp-160) REVERT: d 179 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: e 180 ARG cc_start: 0.8366 (ttm110) cc_final: 0.8103 (mtm110) REVERT: f 46 ARG cc_start: 0.8730 (mmm-85) cc_final: 0.8411 (mtt-85) REVERT: g 64 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6820 (ttp80) REVERT: h 25 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8135 (p) REVERT: i 32 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.6720 (ptt90) REVERT: i 78 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7627 (mtp85) REVERT: l 70 GLU cc_start: 0.7567 (pm20) cc_final: 0.7204 (pm20) REVERT: m 57 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7501 (tmm-80) REVERT: m 79 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7954 (ttm-80) REVERT: m 96 MET cc_start: 0.7951 (tpp) cc_final: 0.7688 (mmt) REVERT: m 101 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: p 6 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8637 (ptmt) REVERT: r 49 ARG cc_start: 0.8601 (mtt-85) cc_final: 0.8337 (mtt90) outliers start: 198 outliers final: 119 residues processed: 826 average time/residue: 2.2047 time to fit residues: 2626.5387 Evaluate side-chains 849 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 705 time to evaluate : 5.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 17 ARG Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 34 VAL Chi-restraints excluded: chain 8 residue 29 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 10 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 56 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 5 LYS Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 79 LYS Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 162 LEU Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 27 ARG Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Y residue 36 MET Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 65 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 40 ASN Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 85 ARG Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain d residue 123 VAL Chi-restraints excluded: chain d residue 148 VAL Chi-restraints excluded: chain d residue 179 GLN Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 84 SER Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 44 ILE Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 98 ILE Chi-restraints excluded: chain m residue 41 ARG Chi-restraints excluded: chain m residue 54 ILE Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 101 GLN Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 117 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 81 MET Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 821 optimal weight: 5.9990 chunk 559 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 734 optimal weight: 8.9990 chunk 406 optimal weight: 7.9990 chunk 841 optimal weight: 9.9990 chunk 681 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 503 optimal weight: 0.9980 chunk 884 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN D 34 ASN D 130 HIS E 141 ASN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 ASN S 88 GLN U 70 ASN W 40 GLN g 68 ASN g 153 HIS l 105 GLN o 7 GLN r 56 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 160667 Z= 0.266 Angle : 0.596 13.750 241098 Z= 0.310 Chirality : 0.036 0.286 30849 Planarity : 0.005 0.130 12624 Dihedral : 22.842 177.402 82335 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.17 % Favored : 93.76 % Rotamer: Outliers : 4.60 % Allowed : 15.36 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.78 (0.11), residues: 5526 helix: -0.89 (0.13), residues: 1633 sheet: -0.77 (0.16), residues: 1062 loop : -1.47 (0.11), residues: 2831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 22 HIS 0.007 0.001 HIS S 112 PHE 0.025 0.002 PHE i 85 TYR 0.026 0.001 TYR E 104 ARG 0.009 0.001 ARG m 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 722 time to evaluate : 5.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 33 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8361 (mtpt) REVERT: 8 29 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8974 (mm) REVERT: 8 58 MET cc_start: 0.7981 (ptp) cc_final: 0.7037 (ppp) REVERT: 8 185 LEU cc_start: 0.7158 (tm) cc_final: 0.6693 (pt) REVERT: 8 199 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7587 (tp) REVERT: C 68 ARG cc_start: 0.8330 (mmt90) cc_final: 0.7998 (mpt180) REVERT: C 270 ARG cc_start: 0.8046 (ttm170) cc_final: 0.7827 (ttm170) REVERT: E 52 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8086 (mtp180) REVERT: F 12 LYS cc_start: 0.8595 (tttt) cc_final: 0.8169 (ttpp) REVERT: F 49 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7203 (pp20) REVERT: F 70 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7989 (pt0) REVERT: F 76 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8091 (mtp85) REVERT: F 85 LYS cc_start: 0.8709 (mttp) cc_final: 0.8267 (ttmm) REVERT: G 17 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7375 (t) REVERT: G 100 LYS cc_start: 0.7604 (mmtt) cc_final: 0.7281 (mmtt) REVERT: G 171 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8207 (ptm160) REVERT: J 112 ASN cc_start: 0.8567 (p0) cc_final: 0.8277 (p0) REVERT: M 10 ARG cc_start: 0.8218 (mtp-110) cc_final: 0.7850 (mtp-110) REVERT: M 45 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7165 (mtt90) REVERT: M 56 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7493 (mtt180) REVERT: N 71 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8013 (mtm-85) REVERT: P 93 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7021 (mtp85) REVERT: R 87 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8219 (ttmt) REVERT: T 26 ASP cc_start: 0.7851 (m-30) cc_final: 0.7368 (t0) REVERT: U 39 ASN cc_start: 0.8440 (p0) cc_final: 0.8078 (p0) REVERT: V 73 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6428 (mm-30) REVERT: W 71 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8765 (mm) REVERT: Y 12 GLU cc_start: 0.7120 (mp0) cc_final: 0.6705 (mp0) REVERT: Z 44 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7063 (mtp85) REVERT: c 47 GLU cc_start: 0.7755 (pm20) cc_final: 0.7263 (pp20) REVERT: c 85 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7565 (tpp-160) REVERT: c 134 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7630 (mmt-90) REVERT: d 179 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8254 (pt0) REVERT: g 64 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.6695 (ttp80) REVERT: g 131 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8627 (tm) REVERT: h 25 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8134 (p) REVERT: i 32 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.6727 (ptt90) REVERT: i 78 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7708 (mtp85) REVERT: l 70 GLU cc_start: 0.7545 (pm20) cc_final: 0.7226 (pm20) REVERT: m 96 MET cc_start: 0.7971 (tpp) cc_final: 0.7705 (mmt) REVERT: p 6 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8635 (ptmt) REVERT: p 62 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8448 (t) REVERT: q 42 LYS cc_start: 0.6119 (mttt) cc_final: 0.5814 (mmtp) REVERT: r 49 ARG cc_start: 0.8606 (mtt-85) cc_final: 0.8355 (mtt90) outliers start: 211 outliers final: 129 residues processed: 828 average time/residue: 2.0494 time to fit residues: 2451.7405 Evaluate side-chains 860 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 705 time to evaluate : 5.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 17 ARG Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 16 LEU Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 34 VAL Chi-restraints excluded: chain 8 residue 29 LEU Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 56 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain T residue 93 ILE Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 55 VAL Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 73 GLU Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 162 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Y residue 36 MET Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 65 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 40 ASN Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain c residue 85 ARG Chi-restraints excluded: chain c residue 134 ARG Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 123 VAL Chi-restraints excluded: chain d residue 148 VAL Chi-restraints excluded: chain d residue 179 GLN Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 84 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 82 LYS Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 44 ILE Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 98 ILE Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 54 ILE Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 117 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 94 LYS Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 331 optimal weight: 8.9990 chunk 887 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 578 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 986 optimal weight: 3.9990 chunk 819 optimal weight: 4.9990 chunk 456 optimal weight: 9.9990 chunk 82 optimal weight: 30.0000 chunk 326 optimal weight: 7.9990 chunk 518 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 ASN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 ASN U 70 ASN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 GLN g 153 HIS l 105 GLN o 7 GLN r 56 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 160667 Z= 0.361 Angle : 0.634 13.863 241098 Z= 0.325 Chirality : 0.039 0.301 30849 Planarity : 0.006 0.132 12624 Dihedral : 22.818 177.962 82335 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.95 % Favored : 93.97 % Rotamer: Outliers : 4.80 % Allowed : 16.40 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.62 (0.11), residues: 5526 helix: -0.66 (0.13), residues: 1619 sheet: -0.72 (0.16), residues: 1078 loop : -1.43 (0.11), residues: 2829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 22 HIS 0.009 0.001 HIS S 112 PHE 0.028 0.002 PHE i 85 TYR 0.018 0.002 TYR E 104 ARG 0.018 0.001 ARG g 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 720 time to evaluate : 6.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 29 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9014 (mm) REVERT: 8 58 MET cc_start: 0.7930 (ptp) cc_final: 0.7017 (ppp) REVERT: 8 175 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.6922 (tt) REVERT: 8 199 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7686 (tp) REVERT: C 35 ARG cc_start: 0.7726 (mtt-85) cc_final: 0.7485 (mmt-90) REVERT: C 270 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7852 (ttm170) REVERT: E 30 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8652 (tp) REVERT: E 52 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8200 (mtp180) REVERT: F 10 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7836 (ptt-90) REVERT: F 12 LYS cc_start: 0.8565 (tttt) cc_final: 0.8126 (ttpp) REVERT: F 49 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7308 (pp20) REVERT: F 70 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: F 76 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8105 (mtp85) REVERT: G 17 VAL cc_start: 0.7629 (OUTLIER) cc_final: 0.7280 (t) REVERT: G 171 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8173 (ptm160) REVERT: J 73 MET cc_start: 0.7886 (mmm) cc_final: 0.7649 (mmm) REVERT: J 112 ASN cc_start: 0.8619 (p0) cc_final: 0.8334 (p0) REVERT: M 10 ARG cc_start: 0.8246 (mtp-110) cc_final: 0.7978 (mtm110) REVERT: M 45 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7200 (mtt90) REVERT: M 56 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7473 (mtt180) REVERT: N 71 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8024 (mtm-85) REVERT: N 101 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: R 87 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8232 (ttmt) REVERT: T 26 ASP cc_start: 0.7885 (m-30) cc_final: 0.7347 (t0) REVERT: U 39 ASN cc_start: 0.8447 (p0) cc_final: 0.8131 (p0) REVERT: V 14 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.6952 (mtp85) REVERT: V 73 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6457 (mm-30) REVERT: V 166 VAL cc_start: 0.8347 (t) cc_final: 0.8009 (m) REVERT: W 71 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8797 (mm) REVERT: Y 12 GLU cc_start: 0.7150 (mp0) cc_final: 0.6703 (mp0) REVERT: Z 44 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6897 (mtp85) REVERT: c 47 GLU cc_start: 0.7729 (pm20) cc_final: 0.7313 (pp20) REVERT: c 85 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7621 (tpp-160) REVERT: d 127 VAL cc_start: 0.9403 (OUTLIER) cc_final: 0.9189 (t) REVERT: d 179 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: e 180 ARG cc_start: 0.8486 (ttm110) cc_final: 0.8038 (mtm110) REVERT: g 64 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6662 (ttp80) REVERT: g 112 ARG cc_start: 0.7534 (mmm160) cc_final: 0.7305 (mmm160) REVERT: g 131 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8699 (tm) REVERT: h 25 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8175 (p) REVERT: i 32 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.6625 (ptt90) REVERT: i 78 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7756 (mtp85) REVERT: k 40 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8709 (m) REVERT: l 70 GLU cc_start: 0.7528 (pm20) cc_final: 0.7220 (pm20) REVERT: m 79 ARG cc_start: 0.8355 (tpp80) cc_final: 0.7978 (ttm-80) REVERT: m 96 MET cc_start: 0.7993 (tpp) cc_final: 0.7732 (mmt) REVERT: p 6 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8689 (ptmt) REVERT: q 42 LYS cc_start: 0.6107 (mttt) cc_final: 0.5783 (mmtp) REVERT: r 49 ARG cc_start: 0.8627 (mtt-85) cc_final: 0.8345 (mtt90) outliers start: 220 outliers final: 141 residues processed: 822 average time/residue: 2.1803 time to fit residues: 2590.4011 Evaluate side-chains 871 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 701 time to evaluate : 5.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 43 LEU Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 17 ARG Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 16 LEU Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 34 VAL Chi-restraints excluded: chain 8 residue 29 LEU Chi-restraints excluded: chain 8 residue 175 ILE Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 10 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 56 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 101 GLU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 14 ARG Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 73 GLU Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 132 GLU Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 162 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Y residue 36 MET Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 65 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 40 ASN Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 85 ARG Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 123 VAL Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 148 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 179 GLN Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 84 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 82 LYS Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 44 ILE Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 98 ILE Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 54 ILE Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 117 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 94 LYS Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 951 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 562 optimal weight: 2.9990 chunk 720 optimal weight: 10.0000 chunk 558 optimal weight: 5.9990 chunk 830 optimal weight: 6.9990 chunk 551 optimal weight: 4.9990 chunk 983 optimal weight: 5.9990 chunk 615 optimal weight: 0.3980 chunk 599 optimal weight: 8.9990 chunk 453 optimal weight: 1.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 GLN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN J 94 GLN M 96 ASN U 70 ASN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 GLN d 77 GLN g 153 HIS l 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 160667 Z= 0.246 Angle : 0.588 13.817 241098 Z= 0.307 Chirality : 0.036 0.288 30849 Planarity : 0.005 0.129 12624 Dihedral : 22.848 177.554 82335 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.03 % Rotamer: Outliers : 4.23 % Allowed : 17.30 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.48 (0.11), residues: 5526 helix: -0.50 (0.13), residues: 1627 sheet: -0.63 (0.16), residues: 1057 loop : -1.37 (0.11), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 22 HIS 0.006 0.001 HIS S 112 PHE 0.027 0.002 PHE i 85 TYR 0.019 0.001 TYR E 104 ARG 0.011 0.001 ARG m 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 703 time to evaluate : 5.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 29 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9008 (mm) REVERT: 8 58 MET cc_start: 0.7923 (ptp) cc_final: 0.7015 (ppp) REVERT: 8 199 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7706 (tp) REVERT: C 270 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7805 (ttm170) REVERT: E 52 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8170 (mtp180) REVERT: F 10 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7812 (ptt-90) REVERT: F 12 LYS cc_start: 0.8570 (tttt) cc_final: 0.8137 (ttpp) REVERT: F 49 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7235 (pp20) REVERT: F 70 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: F 76 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8117 (mtp85) REVERT: G 171 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8175 (ptm160) REVERT: J 112 ASN cc_start: 0.8604 (p0) cc_final: 0.8339 (p0) REVERT: L 7 ASP cc_start: 0.8361 (m-30) cc_final: 0.8110 (m-30) REVERT: M 10 ARG cc_start: 0.8238 (mtp-110) cc_final: 0.7999 (mtm110) REVERT: M 45 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7160 (mtt90) REVERT: M 56 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7453 (mtt180) REVERT: N 71 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8196 (mtt180) REVERT: N 101 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: P 93 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7093 (mtp85) REVERT: R 87 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8231 (ttmt) REVERT: T 26 ASP cc_start: 0.7844 (m-30) cc_final: 0.7301 (t0) REVERT: U 39 ASN cc_start: 0.8384 (p0) cc_final: 0.8089 (p0) REVERT: V 73 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6481 (mm-30) REVERT: V 166 VAL cc_start: 0.8339 (t) cc_final: 0.8005 (m) REVERT: Y 12 GLU cc_start: 0.7132 (mp0) cc_final: 0.6656 (mp0) REVERT: Z 44 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6880 (mtp85) REVERT: c 47 GLU cc_start: 0.7750 (pm20) cc_final: 0.7270 (pp20) REVERT: c 85 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7613 (tpp-160) REVERT: c 134 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7640 (mmt-90) REVERT: d 179 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8199 (pt0) REVERT: e 180 ARG cc_start: 0.8453 (ttm110) cc_final: 0.8007 (mtm110) REVERT: g 64 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6694 (ttp80) REVERT: g 131 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8693 (tm) REVERT: h 25 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8144 (p) REVERT: i 32 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7698 (mtm-85) REVERT: i 78 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7739 (mtp85) REVERT: k 40 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8705 (m) REVERT: l 70 GLU cc_start: 0.7533 (pm20) cc_final: 0.7233 (pm20) REVERT: m 79 ARG cc_start: 0.8325 (tpp80) cc_final: 0.7953 (ttm-80) REVERT: m 96 MET cc_start: 0.7987 (tpp) cc_final: 0.7721 (mmt) REVERT: p 6 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8683 (ptmt) REVERT: q 42 LYS cc_start: 0.6100 (mtmt) cc_final: 0.5772 (mmtp) REVERT: r 49 ARG cc_start: 0.8612 (mtt-85) cc_final: 0.8348 (mtt90) REVERT: t 5 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8699 (tttm) outliers start: 194 outliers final: 138 residues processed: 797 average time/residue: 2.1547 time to fit residues: 2488.5281 Evaluate side-chains 860 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 696 time to evaluate : 5.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 43 LEU Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 17 ARG Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 16 LEU Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 34 VAL Chi-restraints excluded: chain 8 residue 29 LEU Chi-restraints excluded: chain 8 residue 185 LEU Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 10 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 56 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 101 GLU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 73 GLU Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 162 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Y residue 36 MET Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 65 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 40 ASN Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 85 ARG Chi-restraints excluded: chain c residue 134 ARG Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain d residue 148 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 179 GLN Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 84 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 82 LYS Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 44 ILE Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 54 ILE Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 117 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 94 LYS Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain t residue 5 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 608 optimal weight: 9.9990 chunk 392 optimal weight: 5.9990 chunk 587 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 625 optimal weight: 2.9990 chunk 669 optimal weight: 10.0000 chunk 486 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 772 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 63 ASN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 HIS M 96 ASN U 70 ASN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 GLN d 77 GLN g 153 HIS l 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 160667 Z= 0.488 Angle : 0.706 13.926 241098 Z= 0.355 Chirality : 0.043 0.310 30849 Planarity : 0.006 0.136 12624 Dihedral : 22.817 178.156 82335 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.64 % Favored : 93.27 % Rotamer: Outliers : 4.58 % Allowed : 17.32 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.55 (0.11), residues: 5526 helix: -0.57 (0.13), residues: 1628 sheet: -0.67 (0.16), residues: 1053 loop : -1.41 (0.11), residues: 2845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 22 HIS 0.011 0.002 HIS S 112 PHE 0.032 0.002 PHE i 85 TYR 0.021 0.002 TYR d 4 ARG 0.013 0.001 ARG h 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 721 time to evaluate : 5.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8116 (p) REVERT: 8 29 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8999 (mp) REVERT: 8 31 LYS cc_start: 0.6038 (mmmt) cc_final: 0.5363 (pttm) REVERT: 8 58 MET cc_start: 0.7941 (ptp) cc_final: 0.7037 (ppp) REVERT: 8 199 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7706 (tp) REVERT: C 35 ARG cc_start: 0.7738 (mmt-90) cc_final: 0.7508 (mtt-85) REVERT: C 64 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7043 (mtt) REVERT: F 10 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7941 (ptt-90) REVERT: F 12 LYS cc_start: 0.8567 (tttt) cc_final: 0.8125 (ttpp) REVERT: F 70 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8150 (pt0) REVERT: F 76 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8128 (mtp85) REVERT: G 17 VAL cc_start: 0.7659 (OUTLIER) cc_final: 0.7300 (t) REVERT: G 171 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8211 (ptm160) REVERT: M 5 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7730 (ptm-80) REVERT: M 10 ARG cc_start: 0.8267 (mtp-110) cc_final: 0.7972 (mtm110) REVERT: M 45 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7230 (mtt90) REVERT: M 56 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7479 (mtt180) REVERT: M 68 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8116 (mm) REVERT: N 71 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8052 (mtm-85) REVERT: N 101 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: P 93 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7330 (mtp85) REVERT: R 87 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8243 (ttmt) REVERT: T 26 ASP cc_start: 0.7977 (m-30) cc_final: 0.7514 (t0) REVERT: U 39 ASN cc_start: 0.8479 (p0) cc_final: 0.8203 (p0) REVERT: V 12 THR cc_start: 0.8624 (t) cc_final: 0.8200 (p) REVERT: V 14 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.6938 (mtp85) REVERT: V 73 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6478 (mm-30) REVERT: V 166 VAL cc_start: 0.8349 (t) cc_final: 0.8028 (m) REVERT: W 71 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8812 (mm) REVERT: Y 12 GLU cc_start: 0.7184 (mp0) cc_final: 0.6695 (mp0) REVERT: Z 44 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6906 (mtp85) REVERT: c 47 GLU cc_start: 0.7761 (pm20) cc_final: 0.7374 (pp20) REVERT: c 134 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7661 (mmt-90) REVERT: d 179 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: g 131 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8726 (tm) REVERT: h 25 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8245 (p) REVERT: i 32 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.6645 (ptt90) REVERT: i 78 ARG cc_start: 0.8238 (mtp85) cc_final: 0.7783 (mtp85) REVERT: k 40 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8731 (m) REVERT: l 70 GLU cc_start: 0.7565 (pm20) cc_final: 0.7262 (pm20) REVERT: m 79 ARG cc_start: 0.8365 (tpp80) cc_final: 0.8058 (ttm-80) REVERT: m 96 MET cc_start: 0.8021 (tpp) cc_final: 0.7777 (mmt) REVERT: p 6 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8680 (ptmt) REVERT: q 42 LYS cc_start: 0.6190 (mtmt) cc_final: 0.5829 (mmtp) outliers start: 210 outliers final: 149 residues processed: 823 average time/residue: 2.0940 time to fit residues: 2505.6834 Evaluate side-chains 878 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 701 time to evaluate : 5.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 43 LEU Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 17 ARG Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 16 LEU Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 34 VAL Chi-restraints excluded: chain 8 residue 29 LEU Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 10 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain M residue 5 ARG Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 56 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain N residue 101 GLU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 101 SER Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 14 ARG Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 73 GLU Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 132 GLU Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 162 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Y residue 36 MET Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 65 GLU Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 40 ASN Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 134 ARG Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 123 VAL Chi-restraints excluded: chain d residue 148 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 179 GLN Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 84 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 82 LYS Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 44 ILE Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 54 ILE Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 117 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 94 LYS Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 894 optimal weight: 1.9990 chunk 941 optimal weight: 10.0000 chunk 859 optimal weight: 0.9980 chunk 916 optimal weight: 0.0170 chunk 551 optimal weight: 2.9990 chunk 399 optimal weight: 5.9990 chunk 719 optimal weight: 10.0000 chunk 281 optimal weight: 4.9990 chunk 827 optimal weight: 9.9990 chunk 866 optimal weight: 4.9990 chunk 912 optimal weight: 10.0000 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 63 ASN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 HIS F 162 ASN J 58 ASN J 94 GLN M 96 ASN S 71 ASN U 70 ASN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 GLN d 77 GLN g 153 HIS i 66 GLN l 105 GLN t 70 ASN t 74 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 160667 Z= 0.183 Angle : 0.549 13.855 241098 Z= 0.289 Chirality : 0.034 0.273 30849 Planarity : 0.005 0.126 12624 Dihedral : 22.818 177.546 82335 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.28 % Favored : 94.64 % Rotamer: Outliers : 3.47 % Allowed : 18.72 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.11), residues: 5526 helix: -0.15 (0.13), residues: 1635 sheet: -0.50 (0.16), residues: 1047 loop : -1.27 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 201 HIS 0.005 0.001 HIS S 112 PHE 0.019 0.001 PHE i 85 TYR 0.016 0.001 TYR C 104 ARG 0.012 0.000 ARG h 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 693 time to evaluate : 5.980 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: 0 30 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8077 (p) REVERT: 8 58 MET cc_start: 0.7896 (ptp) cc_final: 0.7007 (ppp) REVERT: 8 185 LEU cc_start: 0.7907 (tt) cc_final: 0.7549 (pt) REVERT: 8 199 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7715 (tp) REVERT: C 35 ARG cc_start: 0.7692 (mmt-90) cc_final: 0.7423 (mtt-85) REVERT: C 51 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8807 (p) REVERT: C 64 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6913 (mtt) REVERT: D 162 LYS cc_start: 0.8403 (ttmt) cc_final: 0.8183 (ttmm) REVERT: F 10 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7977 (ptt-90) REVERT: F 49 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7163 (pp20) REVERT: J 112 ASN cc_start: 0.8612 (p0) cc_final: 0.8352 (p0) REVERT: L 7 ASP cc_start: 0.8358 (m-30) cc_final: 0.8128 (m-30) REVERT: M 5 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7710 (ptm-80) REVERT: M 10 ARG cc_start: 0.8264 (mtp-110) cc_final: 0.8020 (mtm110) REVERT: M 45 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7121 (mtt90) REVERT: M 56 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7431 (mtt180) REVERT: M 83 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8321 (mmp) REVERT: N 21 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8324 (mt) REVERT: N 71 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8205 (mtt180) REVERT: P 30 LYS cc_start: 0.8789 (mttm) cc_final: 0.8439 (mttm) REVERT: R 87 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8172 (ttmt) REVERT: T 26 ASP cc_start: 0.7858 (m-30) cc_final: 0.7310 (t0) REVERT: U 39 ASN cc_start: 0.8298 (p0) cc_final: 0.8004 (p0) REVERT: V 73 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6543 (mm-30) REVERT: V 162 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8328 (mt) REVERT: V 166 VAL cc_start: 0.8317 (t) cc_final: 0.8000 (m) REVERT: c 47 GLU cc_start: 0.7723 (pm20) cc_final: 0.7258 (pp20) REVERT: c 126 ARG cc_start: 0.8118 (mpp80) cc_final: 0.7864 (mpp80) REVERT: c 134 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7628 (mmt-90) REVERT: d 52 GLU cc_start: 0.7504 (tp30) cc_final: 0.7261 (tt0) REVERT: e 180 ARG cc_start: 0.8389 (ttm110) cc_final: 0.7971 (mtm110) REVERT: f 84 SER cc_start: 0.9056 (m) cc_final: 0.8756 (p) REVERT: g 64 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6729 (ttp80) REVERT: g 131 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8699 (tm) REVERT: i 32 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7652 (mtm-85) REVERT: i 78 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7727 (mtp85) REVERT: k 40 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8705 (m) REVERT: l 70 GLU cc_start: 0.7520 (pm20) cc_final: 0.7241 (pm20) REVERT: m 79 ARG cc_start: 0.8330 (tpp80) cc_final: 0.7980 (ttm-80) REVERT: m 96 MET cc_start: 0.7985 (tpp) cc_final: 0.7712 (mmt) REVERT: p 6 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8688 (ptmt) REVERT: r 49 ARG cc_start: 0.8605 (mtt90) cc_final: 0.8245 (mtt90) outliers start: 159 outliers final: 94 residues processed: 772 average time/residue: 2.0901 time to fit residues: 2346.7566 Evaluate side-chains 800 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 685 time to evaluate : 5.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 17 ARG Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 34 VAL Chi-restraints excluded: chain 8 residue 29 LEU Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 10 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 5 ARG Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 56 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 69 ILE Chi-restraints excluded: chain V residue 73 GLU Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 132 GLU Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 162 LEU Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 65 GLU Chi-restraints excluded: chain Z residue 40 ASN Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 134 ARG Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain d residue 123 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 82 LYS Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 117 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 601 optimal weight: 3.9990 chunk 968 optimal weight: 5.9990 chunk 591 optimal weight: 0.9980 chunk 459 optimal weight: 10.0000 chunk 673 optimal weight: 10.0000 chunk 1016 optimal weight: 10.0000 chunk 935 optimal weight: 6.9990 chunk 809 optimal weight: 3.9990 chunk 84 optimal weight: 40.0000 chunk 625 optimal weight: 5.9990 chunk 496 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 HIS F 162 ASN J 94 GLN M 96 ASN U 70 ASN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 ASN W 40 GLN d 77 GLN d 121 ASN g 153 HIS l 105 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 160667 Z= 0.252 Angle : 0.568 13.795 241098 Z= 0.295 Chirality : 0.035 0.280 30849 Planarity : 0.005 0.128 12624 Dihedral : 22.778 178.542 82335 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.74 % Favored : 94.19 % Rotamer: Outliers : 2.79 % Allowed : 19.68 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.11), residues: 5526 helix: -0.04 (0.13), residues: 1641 sheet: -0.46 (0.16), residues: 1084 loop : -1.22 (0.11), residues: 2801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 201 HIS 0.006 0.001 HIS S 112 PHE 0.019 0.001 PHE i 85 TYR 0.015 0.001 TYR C 104 ARG 0.014 0.001 ARG h 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11052 Ramachandran restraints generated. 5526 Oldfield, 0 Emsley, 5526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 695 time to evaluate : 6.033 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: 0 30 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8115 (p) REVERT: 8 58 MET cc_start: 0.7879 (ptp) cc_final: 0.6984 (ppp) REVERT: 8 185 LEU cc_start: 0.8116 (tt) cc_final: 0.7794 (pt) REVERT: 8 199 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7714 (tp) REVERT: C 35 ARG cc_start: 0.7704 (mmt-90) cc_final: 0.7467 (mtt-85) REVERT: C 51 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8813 (p) REVERT: C 64 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.7020 (mtt) REVERT: F 10 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7994 (ptt-90) REVERT: F 52 ARG cc_start: 0.7429 (mpp-170) cc_final: 0.7216 (mtm-85) REVERT: G 17 VAL cc_start: 0.7589 (OUTLIER) cc_final: 0.7254 (t) REVERT: J 95 ARG cc_start: 0.7913 (mpp80) cc_final: 0.7406 (mtm180) REVERT: J 112 ASN cc_start: 0.8626 (p0) cc_final: 0.8377 (p0) REVERT: L 7 ASP cc_start: 0.8378 (m-30) cc_final: 0.8134 (m-30) REVERT: M 5 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7724 (ptm-80) REVERT: M 10 ARG cc_start: 0.8252 (mtp-110) cc_final: 0.7988 (mtm110) REVERT: M 45 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7132 (mtt90) REVERT: M 68 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8065 (mm) REVERT: M 83 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8298 (mmp) REVERT: N 21 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8335 (mt) REVERT: N 71 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8205 (mtt180) REVERT: O 60 SER cc_start: 0.9256 (t) cc_final: 0.8873 (t) REVERT: R 87 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8222 (ttmt) REVERT: T 26 ASP cc_start: 0.7868 (m-30) cc_final: 0.7307 (t0) REVERT: T 68 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7827 (ttm-80) REVERT: T 73 TYR cc_start: 0.8549 (m-10) cc_final: 0.8247 (m-10) REVERT: U 39 ASN cc_start: 0.8345 (p0) cc_final: 0.8049 (p0) REVERT: V 73 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6574 (mm-30) REVERT: V 162 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8337 (mt) REVERT: V 166 VAL cc_start: 0.8312 (t) cc_final: 0.7981 (m) REVERT: c 47 GLU cc_start: 0.7726 (pm20) cc_final: 0.7251 (pp20) REVERT: c 126 ARG cc_start: 0.8108 (mpp80) cc_final: 0.7862 (mpp80) REVERT: c 134 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7634 (mmt-90) REVERT: d 52 GLU cc_start: 0.7542 (tp30) cc_final: 0.7289 (tt0) REVERT: f 84 SER cc_start: 0.9061 (m) cc_final: 0.8681 (t) REVERT: g 64 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6732 (ttp80) REVERT: g 131 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8696 (tm) REVERT: i 32 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7714 (mtm-85) REVERT: i 78 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7722 (mtp85) REVERT: k 40 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8717 (m) REVERT: l 70 GLU cc_start: 0.7529 (pm20) cc_final: 0.7256 (pm20) REVERT: m 79 ARG cc_start: 0.8309 (tpp80) cc_final: 0.8043 (ttm-80) REVERT: m 96 MET cc_start: 0.8011 (tpp) cc_final: 0.7735 (mmt) REVERT: p 6 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8693 (ptmt) outliers start: 128 outliers final: 94 residues processed: 754 average time/residue: 2.1686 time to fit residues: 2371.0097 Evaluate side-chains 802 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 687 time to evaluate : 5.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 43 LEU Chi-restraints excluded: chain 2 residue 2 THR Chi-restraints excluded: chain 2 residue 17 ARG Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 34 VAL Chi-restraints excluded: chain 8 residue 29 LEU Chi-restraints excluded: chain 8 residue 199 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 10 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain M residue 5 ARG Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 91 ASP Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 73 GLU Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 132 GLU Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 162 LEU Chi-restraints excluded: chain W residue 57 ASP Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 65 GLU Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 134 ARG Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain d residue 123 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain e residue 162 ASP Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 64 ARG Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 82 LYS Chi-restraints excluded: chain i residue 32 ARG Chi-restraints excluded: chain k residue 36 THR Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 129 ASN Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 5 VAL Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 117 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 116 THR Chi-restraints excluded: chain q residue 131 LEU Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 642 optimal weight: 5.9990 chunk 861 optimal weight: 0.9990 chunk 247 optimal weight: 20.0000 chunk 746 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 810 optimal weight: 9.9990 chunk 339 optimal weight: 10.0000 chunk 832 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 HIS M 96 ASN S 71 ASN U 70 ASN W 12 ASN W 40 GLN d 77 GLN g 153 HIS l 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.073180 restraints weight = 220793.119| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.01 r_work: 0.2702 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 160667 Z= 0.473 Angle : 0.692 13.847 241098 Z= 0.348 Chirality : 0.042 0.307 30849 Planarity : 0.006 0.135 12624 Dihedral : 22.775 178.426 82335 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.41 % Favored : 93.50 % Rotamer: Outliers : 3.21 % Allowed : 19.35 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.24 (0.11), residues: 5526 helix: -0.22 (0.13), residues: 1633 sheet: -0.45 (0.16), residues: 1052 loop : -1.30 (0.11), residues: 2841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 22 HIS 0.010 0.002 HIS S 112 PHE 0.030 0.002 PHE i 85 TYR 0.021 0.002 TYR E 104 ARG 0.017 0.001 ARG g 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40059.31 seconds wall clock time: 698 minutes 5.21 seconds (41885.21 seconds total)