Starting phenix.real_space_refine on Tue Mar 19 03:27:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tpq_10543/03_2024/6tpq_10543.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tpq_10543/03_2024/6tpq_10543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tpq_10543/03_2024/6tpq_10543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tpq_10543/03_2024/6tpq_10543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tpq_10543/03_2024/6tpq_10543.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tpq_10543/03_2024/6tpq_10543.pdb" } resolution = 3.07 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= 0.003 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 3047 5.49 5 Mg 219 5.21 5 S 88 5.16 5 C 45492 2.51 5 N 17033 2.21 5 O 25846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 5": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "b GLU 65": "OE1" <-> "OE2" Residue "b GLU 122": "OE1" <-> "OE2" Residue "W ARG 43": "NH1" <-> "NH2" Residue "W ARG 63": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W GLU 82": "OE1" <-> "OE2" Residue "W ARG 221": "NH1" <-> "NH2" Residue "X GLU 65": "OE1" <-> "OE2" Residue "X PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 27": "OE1" <-> "OE2" Residue "Z GLU 81": "OE1" <-> "OE2" Residue "Z ARG 92": "NH1" <-> "NH2" Residue "Z TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 134": "OE1" <-> "OE2" Residue "Z GLU 168": "OE1" <-> "OE2" Residue "a GLU 115": "OE1" <-> "OE2" Residue "a ARG 172": "NH1" <-> "NH2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 134": "OE1" <-> "OE2" Residue "e GLU 118": "OE1" <-> "OE2" Residue "f GLU 80": "OE1" <-> "OE2" Residue "f GLU 135": "OE1" <-> "OE2" Residue "h ARG 11": "NH1" <-> "NH2" Residue "h ARG 114": "NH1" <-> "NH2" Residue "i GLU 9": "OE1" <-> "OE2" Residue "i ARG 42": "NH1" <-> "NH2" Residue "i ARG 65": "NH1" <-> "NH2" Residue "i GLU 74": "OE1" <-> "OE2" Residue "i PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "k ARG 89": "NH1" <-> "NH2" Residue "l ARG 86": "NH1" <-> "NH2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "o ARG 28": "NH1" <-> "NH2" Residue "o ARG 84": "NH1" <-> "NH2" Residue "r ARG 12": "NH1" <-> "NH2" Residue "s ARG 8": "NH1" <-> "NH2" Residue "w GLU 5": "OE1" <-> "OE2" Residue "w GLU 17": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 91728 Number of models: 1 Model: "" Number of chains: 39 Chain: "B" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1425 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2628 Classifications: {'RNA': 123} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 58, 'rna3p_pyr': 53} Link IDs: {'rna2p': 12, 'rna3p': 110} Chain: "A" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 548 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 68} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "U" Number of atoms: 62790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2924, 62790 Classifications: {'RNA': 2924} Modifications used: {'rna2p_pur': 292, 'rna2p_pyr': 148, 'rna3p_pur': 1404, 'rna3p_pyr': 1080} Link IDs: {'rna2p': 440, 'rna3p': 2483} Chain: "W" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2111 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "X" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1575 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain: "Y" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "Z" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1404 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "a" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "c" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1124 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "d" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 921 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "e" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1082 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "f" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1097 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain: "g" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 954 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "h" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 913 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "i" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 937 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "j" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "k" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 787 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "l" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "m" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 752 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "n" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 762 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "o" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 630 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "p" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "q" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "r" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 368 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "s" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "t" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 289 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "u" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "v" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "w" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 456 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 214 Unusual residues: {' MG': 214} Classifications: {'undetermined': 214} Link IDs: {None: 213} Chain: "W" 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: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" 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 88322 SG CYS p 30 50.484 38.420 160.919 1.00136.97 S ATOM 88341 SG CYS p 33 48.331 40.919 162.453 1.00138.85 S ATOM 88419 SG CYS p 43 51.714 41.667 162.246 1.00136.19 S ATOM 88574 SG CYS q 9 105.794 175.931 112.685 1.00141.08 S ATOM 88596 SG CYS q 12 103.630 175.477 115.466 1.00145.90 S ATOM 88805 SG CYS q 36 102.215 175.019 112.309 1.00134.32 S ATOM 89864 SG CYS t 11 107.759 67.750 63.202 1.00144.12 S ATOM 89888 SG CYS t 14 105.588 68.306 65.765 1.00143.11 S ATOM 89992 SG CYS t 27 106.486 64.744 64.870 1.00144.70 S Time building chain proxies: 35.85, per 1000 atoms: 0.39 Number of scatterers: 91728 At special positions: 0 Unit cell: (183.06, 224.87, 253.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 88 16.00 P 3047 15.00 Mg 219 11.99 O 25846 8.00 N 17033 7.00 C 45492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.45 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN p 101 " pdb="ZN ZN p 101 " - pdb=" SG CYS p 30 " pdb="ZN ZN p 101 " - pdb=" SG CYS p 33 " pdb="ZN ZN p 101 " - pdb=" SG CYS p 43 " pdb=" ZN q 101 " pdb="ZN ZN q 101 " - pdb=" SG CYS q 12 " pdb="ZN ZN q 101 " - pdb=" SG CYS q 9 " pdb="ZN ZN q 101 " - pdb=" SG CYS q 36 " pdb=" ZN t 101 " pdb="ZN ZN t 101 " - pdb=" ND1 HIS t 32 " pdb="ZN ZN t 101 " - pdb=" SG CYS t 14 " pdb="ZN ZN t 101 " - pdb=" SG CYS t 11 " pdb="ZN ZN t 101 " - pdb=" SG CYS t 27 " Number of angles added : 3 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6088 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 44 sheets defined 31.1% alpha, 16.9% beta 992 base pairs and 1455 stacking pairs defined. Time for finding SS restraints: 31.76 Creating SS restraints... Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 58 through 72 Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 154 through 165 Processing helix chain 'B' and resid 169 through 185 Processing helix chain 'A' and resid 122 through 129 removed outlier: 3.509A pdb=" N LEU A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 removed outlier: 4.276A pdb=" N GLU A 146 " --> pdb=" O GLN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 166 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'b' and resid 5 through 20 removed outlier: 4.402A pdb=" N LYS b 9 " --> pdb=" O ILE b 5 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE b 15 " --> pdb=" O VAL b 11 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA b 16 " --> pdb=" O VAL b 12 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER b 17 " --> pdb=" O GLU b 13 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS b 20 " --> pdb=" O ALA b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 48 Processing helix chain 'b' and resid 60 through 67 Processing helix chain 'b' and resid 73 through 77 Processing helix chain 'b' and resid 94 through 104 Processing helix chain 'W' and resid 30 through 32 No H-bonds generated for 'chain 'W' and resid 30 through 32' Processing helix chain 'W' and resid 133 through 135 No H-bonds generated for 'chain 'W' and resid 133 through 135' Processing helix chain 'W' and resid 197 through 203 removed outlier: 3.776A pdb=" N GLU W 201 " --> pdb=" O GLU W 198 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE W 203 " --> pdb=" O HIS W 200 " (cutoff:3.500A) Processing helix chain 'W' and resid 207 through 213 removed outlier: 3.693A pdb=" N SER W 211 " --> pdb=" O LYS W 207 " (cutoff:3.500A) Processing helix chain 'W' and resid 221 through 225 removed outlier: 3.621A pdb=" N VAL W 224 " --> pdb=" O ARG W 221 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 270 Processing helix chain 'X' and resid 57 through 61 Processing helix chain 'X' and resid 62 through 71 removed outlier: 4.147A pdb=" N LYS X 71 " --> pdb=" O GLY X 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 98 through 102 removed outlier: 3.555A pdb=" N ILE X 101 " --> pdb=" O LYS X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 127 Processing helix chain 'Y' and resid 30 through 45 removed outlier: 3.552A pdb=" N PHE Y 34 " --> pdb=" O GLU Y 30 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP Y 35 " --> pdb=" O SER Y 31 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG Y 45 " --> pdb=" O ARG Y 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 102 through 120 removed outlier: 3.690A pdb=" N ASP Y 120 " --> pdb=" O SER Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 146 Processing helix chain 'Y' and resid 160 through 166 removed outlier: 3.946A pdb=" N SER Y 166 " --> pdb=" O ALA Y 162 " (cutoff:3.500A) Processing helix chain 'Y' and resid 179 through 181 No H-bonds generated for 'chain 'Y' and resid 179 through 181' Processing helix chain 'Y' and resid 182 through 189 removed outlier: 3.681A pdb=" N ASN Y 188 " --> pdb=" O LEU Y 184 " (cutoff:3.500A) Processing helix chain 'Y' and resid 196 through 206 removed outlier: 3.682A pdb=" N GLU Y 200 " --> pdb=" O LYS Y 196 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS Y 201 " --> pdb=" O ALA Y 197 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL Y 205 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU Y 206 " --> pdb=" O VAL Y 202 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 20 Proline residue: Z 14 - end of helix Processing helix chain 'Z' and resid 24 through 28 Processing helix chain 'Z' and resid 51 through 61 removed outlier: 4.033A pdb=" N GLU Z 55 " --> pdb=" O ASP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 93 through 107 removed outlier: 3.567A pdb=" N TYR Z 97 " --> pdb=" O GLY Z 93 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL Z 106 " --> pdb=" O LYS Z 102 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 174 removed outlier: 3.713A pdb=" N ALA Z 166 " --> pdb=" O THR Z 162 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL Z 173 " --> pdb=" O LEU Z 169 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 7 removed outlier: 4.081A pdb=" N LYS a 6 " --> pdb=" O ARG a 3 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS a 7 " --> pdb=" O VAL a 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 3 through 7' Processing helix chain 'a' and resid 20 through 24 removed outlier: 3.657A pdb=" N ASN a 23 " --> pdb=" O ASN a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 59 through 83 removed outlier: 4.052A pdb=" N GLY a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG a 70 " --> pdb=" O HIS a 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 138 through 151 Processing helix chain 'c' and resid 29 through 38 Processing helix chain 'c' and resid 59 through 63 removed outlier: 3.677A pdb=" N ILE c 63 " --> pdb=" O ALA c 60 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 97 through 108 Processing helix chain 'c' and resid 113 through 120 Processing helix chain 'd' and resid 111 through 118 Processing helix chain 'e' and resid 2 through 6 removed outlier: 3.944A pdb=" N LEU e 6 " --> pdb=" O LEU e 3 " (cutoff:3.500A) Processing helix chain 'e' and resid 57 through 61 Processing helix chain 'e' and resid 78 through 84 removed outlier: 3.972A pdb=" N LEU e 82 " --> pdb=" O ASN e 78 " (cutoff:3.500A) Processing helix chain 'e' and resid 94 through 99 Processing helix chain 'e' and resid 129 through 139 removed outlier: 3.713A pdb=" N LYS e 133 " --> pdb=" O SER e 129 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU e 134 " --> pdb=" O ALA e 130 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 58 removed outlier: 3.822A pdb=" N GLU f 48 " --> pdb=" O ASN f 44 " (cutoff:3.500A) Processing helix chain 'f' and resid 110 through 123 removed outlier: 3.652A pdb=" N HIS f 123 " --> pdb=" O ARG f 119 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 28 Processing helix chain 'g' and resid 34 through 54 removed outlier: 4.794A pdb=" N SER g 42 " --> pdb=" O LYS g 38 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL g 43 " --> pdb=" O GLU g 39 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS g 46 " --> pdb=" O SER g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 55 through 64 Processing helix chain 'g' and resid 73 through 76 Processing helix chain 'g' and resid 79 through 91 Processing helix chain 'h' and resid 6 through 21 removed outlier: 3.583A pdb=" N ALA h 10 " --> pdb=" O SER h 6 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS h 21 " --> pdb=" O ARG h 17 " (cutoff:3.500A) Processing helix chain 'h' and resid 71 through 88 Processing helix chain 'h' and resid 103 through 116 Processing helix chain 'i' and resid 6 through 14 Processing helix chain 'i' and resid 56 through 59 Processing helix chain 'i' and resid 100 through 105 removed outlier: 3.632A pdb=" N GLU i 105 " --> pdb=" O TYR i 102 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 19 removed outlier: 4.319A pdb=" N ARG j 14 " --> pdb=" O THR j 10 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL j 17 " --> pdb=" O ARG j 13 " (cutoff:3.500A) Processing helix chain 'j' and resid 25 through 30 removed outlier: 3.625A pdb=" N HIS j 29 " --> pdb=" O GLY j 26 " (cutoff:3.500A) Processing helix chain 'j' and resid 32 through 70 removed outlier: 3.580A pdb=" N GLY j 43 " --> pdb=" O VAL j 39 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN j 44 " --> pdb=" O MET j 40 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA j 46 " --> pdb=" O SER j 42 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG j 51 " --> pdb=" O PHE j 47 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS j 54 " --> pdb=" O ARG j 50 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG j 55 " --> pdb=" O ARG j 51 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG j 58 " --> pdb=" O LYS j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 71 through 73 No H-bonds generated for 'chain 'j' and resid 71 through 73' Processing helix chain 'j' and resid 75 through 86 Processing helix chain 'j' and resid 92 through 99 Processing helix chain 'j' and resid 102 through 117 removed outlier: 3.833A pdb=" N PHE j 106 " --> pdb=" O ASP j 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 13 through 23 removed outlier: 3.703A pdb=" N LEU l 19 " --> pdb=" O ARG l 15 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL l 20 " --> pdb=" O LYS l 16 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU l 23 " --> pdb=" O LEU l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 28 through 38 removed outlier: 3.885A pdb=" N SER l 34 " --> pdb=" O GLY l 30 " (cutoff:3.500A) Processing helix chain 'l' and resid 43 through 61 Processing helix chain 'l' and resid 65 through 67 No H-bonds generated for 'chain 'l' and resid 65 through 67' Processing helix chain 'l' and resid 89 through 91 No H-bonds generated for 'chain 'l' and resid 89 through 91' Processing helix chain 'm' and resid 3 through 7 removed outlier: 3.757A pdb=" N VAL m 7 " --> pdb=" O ASP m 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 3 through 7' Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.052A pdb=" N THR m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 35 through 48 Processing helix chain 'p' and resid 9 through 17 removed outlier: 3.703A pdb=" N ARG p 17 " --> pdb=" O LYS p 13 " (cutoff:3.500A) Processing helix chain 'p' and resid 18 through 20 No H-bonds generated for 'chain 'p' and resid 18 through 20' Processing helix chain 'r' and resid 8 through 17 removed outlier: 3.742A pdb=" N ARG r 12 " --> pdb=" O ASN r 8 " (cutoff:3.500A) Processing helix chain 'r' and resid 17 through 22 Processing helix chain 'r' and resid 24 through 38 Processing helix chain 's' and resid 7 through 11 Processing helix chain 's' and resid 32 through 36 removed outlier: 3.576A pdb=" N ASN s 35 " --> pdb=" O LEU s 32 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS s 36 " --> pdb=" O PHE s 33 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 32 through 36' Processing helix chain 's' and resid 37 through 45 removed outlier: 3.731A pdb=" N ARG s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) Processing helix chain 's' and resid 51 through 59 Processing helix chain 't' and resid 29 through 33 Processing helix chain 'u' and resid 52 through 56 removed outlier: 3.709A pdb=" N SER u 56 " --> pdb=" O ALA u 53 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 8 Processing helix chain 'v' and resid 10 through 35 removed outlier: 4.223A pdb=" N ILE v 14 " --> pdb=" O THR v 10 " (cutoff:3.500A) Processing helix chain 'v' and resid 40 through 63 removed outlier: 4.094A pdb=" N ARG v 44 " --> pdb=" O THR v 40 " (cutoff:3.500A) Processing helix chain 'w' and resid 16 through 26 Processing helix chain 'w' and resid 40 through 50 removed outlier: 3.542A pdb=" N ARG w 44 " --> pdb=" O ASN w 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.170A pdb=" N ILE B 7 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 6 " --> pdb=" O ILE B 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 23 through 24 removed outlier: 4.047A pdb=" N LYS b 23 " --> pdb=" O GLU b 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'W' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'W' and resid 34 through 35 Processing sheet with id=AA5, first strand: chain 'W' and resid 100 through 105 removed outlier: 3.843A pdb=" N GLU W 100 " --> pdb=" O TYR W 96 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE W 91 " --> pdb=" O VAL W 81 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL W 81 " --> pdb=" O ILE W 91 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU W 93 " --> pdb=" O ALA W 79 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE W 116 " --> pdb=" O GLY W 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'W' and resid 129 through 131 removed outlier: 5.807A pdb=" N LEU W 173 " --> pdb=" O LEU W 165 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LYS W 167 " --> pdb=" O TYR W 171 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N TYR W 171 " --> pdb=" O LYS W 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 4 through 17 removed outlier: 5.484A pdb=" N LYS X 9 " --> pdb=" O GLU X 29 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU X 29 " --> pdb=" O LYS X 9 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY X 11 " --> pdb=" O VAL X 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP X 21 " --> pdb=" O ALA X 17 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU X 185 " --> pdb=" O VAL X 179 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL X 179 " --> pdb=" O LEU X 185 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU X 187 " --> pdb=" O VAL X 177 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLU X 175 " --> pdb=" O LYS X 189 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N THR X 170 " --> pdb=" O GLY X 112 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLY X 112 " --> pdb=" O THR X 170 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLN X 172 " --> pdb=" O VAL X 110 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL X 110 " --> pdb=" O GLN X 172 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL X 113 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU X 199 " --> pdb=" O VAL X 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 79 through 83 removed outlier: 6.696A pdb=" N ALA X 48 " --> pdb=" O LYS X 38 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS X 38 " --> pdb=" O ALA X 48 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN X 50 " --> pdb=" O LEU X 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'X' and resid 119 through 120 Processing sheet with id=AB1, first strand: chain 'Y' and resid 16 through 18 removed outlier: 9.875A pdb=" N ILE Y 123 " --> pdb=" O LYS Y 3 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA Y 5 " --> pdb=" O ILE Y 123 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL Y 125 " --> pdb=" O ALA Y 5 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE Y 154 " --> pdb=" O VAL Y 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Z' and resid 66 through 67 removed outlier: 4.152A pdb=" N LYS Z 33 " --> pdb=" O VAL Z 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL Z 157 " --> pdb=" O LYS Z 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 26 through 29 removed outlier: 3.540A pdb=" N GLY a 32 " --> pdb=" O GLY a 29 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'a' and resid 122 through 128 removed outlier: 5.198A pdb=" N ILE a 124 " --> pdb=" O LYS a 135 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS a 135 " --> pdb=" O ILE a 124 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL a 126 " --> pdb=" O VAL a 133 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL a 133 " --> pdb=" O VAL a 126 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER a 128 " --> pdb=" O LYS a 131 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG a 86 " --> pdb=" O VAL a 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 96 through 100 removed outlier: 3.516A pdb=" N ARG a 96 " --> pdb=" O ASN a 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 123 through 125 removed outlier: 3.551A pdb=" N ILE c 58 " --> pdb=" O VAL c 19 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 74 through 78 Processing sheet with id=AB9, first strand: chain 'd' and resid 2 through 3 Processing sheet with id=AC1, first strand: chain 'd' and resid 7 through 10 removed outlier: 6.495A pdb=" N ARG d 17 " --> pdb=" O VAL d 10 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLN d 45 " --> pdb=" O ARG d 17 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL d 19 " --> pdb=" O VAL d 43 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL d 43 " --> pdb=" O VAL d 19 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR d 21 " --> pdb=" O CYS d 41 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS d 41 " --> pdb=" O THR d 21 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS d 23 " --> pdb=" O ILE d 39 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ILE d 39 " --> pdb=" O LYS d 23 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS d 59 " --> pdb=" O ILE d 87 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA d 83 " --> pdb=" O VAL d 63 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N CYS d 84 " --> pdb=" O ARG d 7 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS d 9 " --> pdb=" O CYS d 84 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ILE d 86 " --> pdb=" O LYS d 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'd' and resid 76 through 78 removed outlier: 3.535A pdb=" N THR i 76 " --> pdb=" O TYR d 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL i 71 " --> pdb=" O SER i 68 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR i 61 " --> pdb=" O ARG i 53 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG i 53 " --> pdb=" O THR i 61 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR i 63 " --> pdb=" O ILE i 51 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE i 67 " --> pdb=" O GLU i 47 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N GLU i 47 " --> pdb=" O ILE i 67 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY i 48 " --> pdb=" O LEU i 29 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG i 30 " --> pdb=" O ILE i 87 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE i 87 " --> pdb=" O ARG i 30 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N HIS i 32 " --> pdb=" O ALA i 85 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'e' and resid 75 through 77 removed outlier: 5.828A pdb=" N ALA e 75 " --> pdb=" O LYS e 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS e 127 " --> pdb=" O VAL e 109 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 123 through 125 removed outlier: 6.412A pdb=" N VAL e 123 " --> pdb=" O GLU e 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'f' and resid 63 through 66 removed outlier: 3.500A pdb=" N GLU f 105 " --> pdb=" O TRP f 65 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE f 104 " --> pdb=" O ILE f 34 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE f 34 " --> pdb=" O PHE f 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 40 through 43 removed outlier: 5.854A pdb=" N ALA f 76 " --> pdb=" O PRO f 90 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR f 74 " --> pdb=" O GLY f 92 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS f 72 " --> pdb=" O VAL f 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 29 through 33 removed outlier: 4.502A pdb=" N MET g 114 " --> pdb=" O LEU g 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'g' and resid 70 through 72 removed outlier: 3.530A pdb=" N ASN g 72 " --> pdb=" O GLN g 77 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 30 through 35 removed outlier: 7.140A pdb=" N ILE h 40 " --> pdb=" O SER h 57 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER h 57 " --> pdb=" O ILE h 40 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA h 42 " --> pdb=" O SER h 55 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER h 55 " --> pdb=" O ALA h 42 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE h 44 " --> pdb=" O LEU h 53 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL h 51 " --> pdb=" O ASP h 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'k' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'k' and resid 19 through 22 removed outlier: 6.939A pdb=" N LYS k 94 " --> pdb=" O GLU k 63 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR k 59 " --> pdb=" O GLU k 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'k' and resid 71 through 77 removed outlier: 4.756A pdb=" N VAL k 82 " --> pdb=" O LYS k 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'l' and resid 3 through 7 removed outlier: 6.541A pdb=" N SER l 108 " --> pdb=" O ILE l 71 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE l 71 " --> pdb=" O SER l 108 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'l' and resid 82 through 87 Processing sheet with id=AD6, first strand: chain 'm' and resid 8 through 11 removed outlier: 3.676A pdb=" N LYS m 53 " --> pdb=" O LYS m 82 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'm' and resid 65 through 66 Processing sheet with id=AD8, first strand: chain 'n' and resid 9 through 11 Processing sheet with id=AD9, first strand: chain 'n' and resid 23 through 27 removed outlier: 6.967A pdb=" N LEU n 34 " --> pdb=" O LEU n 24 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ALA n 26 " --> pdb=" O ARG n 32 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG n 32 " --> pdb=" O ALA n 26 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'n' and resid 40 through 45 Processing sheet with id=AE2, first strand: chain 'o' and resid 30 through 31 removed outlier: 6.576A pdb=" N LEU o 67 " --> pdb=" O LEU o 45 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE o 68 " --> pdb=" O GLY o 60 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'o' and resid 38 through 39 removed outlier: 3.596A pdb=" N ARG o 84 " --> pdb=" O PHE o 80 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'q' and resid 15 through 22 removed outlier: 6.265A pdb=" N ARG q 15 " --> pdb=" O CYS q 9 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS q 9 " --> pdb=" O ARG q 15 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR q 17 " --> pdb=" O LEU q 7 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 't' and resid 3 through 4 removed outlier: 3.568A pdb=" N ARG t 4 " --> pdb=" O LYS t 35 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL t 23 " --> pdb=" O GLN t 36 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'u' and resid 13 through 15 Processing sheet with id=AE7, first strand: chain 'u' and resid 33 through 40 Processing sheet with id=AE8, first strand: chain 'w' and resid 34 through 38 896 hydrogen bonds defined for protein. 2472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2534 hydrogen bonds 4146 hydrogen bond angles 0 basepair planarities 992 basepair parallelities 1455 stacking parallelities Total time for adding SS restraints: 154.01 Time building geometry restraints manager: 42.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 12345 1.33 - 1.45: 43018 1.45 - 1.57: 38074 1.57 - 1.69: 6092 1.69 - 1.82: 161 Bond restraints: 99690 Sorted by residual: bond pdb=" CA LYS j 28 " pdb=" C LYS j 28 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.80e-02 3.09e+03 1.56e+01 bond pdb=" C LYS c 42 " pdb=" N PRO c 43 " ideal model delta sigma weight residual 1.337 1.306 0.030 9.80e-03 1.04e+04 9.54e+00 bond pdb=" C VAL f 97 " pdb=" N LYS f 98 " ideal model delta sigma weight residual 1.329 1.245 0.084 3.03e-02 1.09e+03 7.60e+00 bond pdb=" C GLN c 80 " pdb=" N HIS c 81 " ideal model delta sigma weight residual 1.339 1.220 0.119 5.57e-02 3.22e+02 4.58e+00 bond pdb=" C TYR W 6 " pdb=" N LYS W 7 " ideal model delta sigma weight residual 1.331 1.288 0.043 2.07e-02 2.33e+03 4.41e+00 ... (remaining 99685 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.46: 18154 106.46 - 113.40: 60691 113.40 - 120.35: 36544 120.35 - 127.29: 27618 127.29 - 134.23: 6665 Bond angle restraints: 149672 Sorted by residual: angle pdb=" N VAL b 50 " pdb=" CA VAL b 50 " pdb=" C VAL b 50 " ideal model delta sigma weight residual 113.20 108.27 4.93 9.60e-01 1.09e+00 2.64e+01 angle pdb=" O4' G U1243 " pdb=" C1' G U1243 " pdb=" N9 G U1243 " ideal model delta sigma weight residual 108.20 115.43 -7.23 1.50e+00 4.44e-01 2.32e+01 angle pdb=" C4' G U1243 " pdb=" C3' G U1243 " pdb=" O3' G U1243 " ideal model delta sigma weight residual 109.40 115.20 -5.80 1.50e+00 4.44e-01 1.50e+01 angle pdb=" C3' G U 556 " pdb=" O3' G U 556 " pdb=" P A U 557 " ideal model delta sigma weight residual 120.20 125.95 -5.75 1.50e+00 4.44e-01 1.47e+01 angle pdb=" C2' A U1024 " pdb=" C1' A U1024 " pdb=" N9 A U1024 " ideal model delta sigma weight residual 112.00 117.31 -5.31 1.50e+00 4.44e-01 1.25e+01 ... (remaining 149667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 56176 35.68 - 71.36: 6811 71.36 - 107.04: 885 107.04 - 142.72: 21 142.72 - 178.40: 36 Dihedral angle restraints: 63929 sinusoidal: 54453 harmonic: 9476 Sorted by residual: dihedral pdb=" O4' C U 480 " pdb=" C1' C U 480 " pdb=" N1 C U 480 " pdb=" C2 C U 480 " ideal model delta sinusoidal sigma weight residual 200.00 21.60 178.40 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U U 649 " pdb=" C1' U U 649 " pdb=" N1 U U 649 " pdb=" C2 U U 649 " ideal model delta sinusoidal sigma weight residual -160.00 17.98 -177.98 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C U1279 " pdb=" C1' C U1279 " pdb=" N1 C U1279 " pdb=" C2 C U1279 " ideal model delta sinusoidal sigma weight residual 200.00 27.84 172.16 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 63926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 17212 0.064 - 0.129: 1777 0.129 - 0.193: 166 0.193 - 0.257: 29 0.257 - 0.321: 7 Chirality restraints: 19191 Sorted by residual: chirality pdb=" C1' A U1027 " pdb=" O4' A U1027 " pdb=" C2' A U1027 " pdb=" N9 A U1027 " both_signs ideal model delta sigma weight residual False 2.46 2.14 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C1' A U1242 " pdb=" O4' A U1242 " pdb=" C2' A U1242 " pdb=" N9 A U1242 " both_signs ideal model delta sigma weight residual False 2.46 2.15 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C1' A U1024 " pdb=" O4' A U1024 " pdb=" C2' A U1024 " pdb=" N9 A U1024 " both_signs ideal model delta sigma weight residual False 2.46 2.16 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 19188 not shown) Planarity restraints: 7613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G U2243 " 0.027 2.00e-02 2.50e+03 2.39e-02 1.71e+01 pdb=" N9 G U2243 " -0.035 2.00e-02 2.50e+03 pdb=" C8 G U2243 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G U2243 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G U2243 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G U2243 " 0.015 2.00e-02 2.50e+03 pdb=" O6 G U2243 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G U2243 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G U2243 " 0.054 2.00e-02 2.50e+03 pdb=" N2 G U2243 " -0.039 2.00e-02 2.50e+03 pdb=" N3 G U2243 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G U2243 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G U1243 " -0.046 2.00e-02 2.50e+03 2.17e-02 1.41e+01 pdb=" N9 G U1243 " 0.057 2.00e-02 2.50e+03 pdb=" C8 G U1243 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G U1243 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G U1243 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G U1243 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G U1243 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G U1243 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G U1243 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G U1243 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G U1243 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G U1243 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A U 8 " -0.048 2.00e-02 2.50e+03 2.15e-02 1.28e+01 pdb=" N9 A U 8 " 0.047 2.00e-02 2.50e+03 pdb=" C8 A U 8 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A U 8 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A U 8 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A U 8 " -0.017 2.00e-02 2.50e+03 pdb=" N6 A U 8 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A U 8 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A U 8 " 0.008 2.00e-02 2.50e+03 pdb=" N3 A U 8 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A U 8 " 0.008 2.00e-02 2.50e+03 ... (remaining 7610 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.92: 19 1.92 - 2.67: 5914 2.67 - 3.41: 120314 3.41 - 4.16: 293010 4.16 - 4.90: 404852 Nonbonded interactions: 824109 Sorted by model distance: nonbonded pdb="MG MG U3108 " pdb="MG MG U3113 " model vdw 1.176 1.300 nonbonded pdb=" O4 U U 636 " pdb="MG MG U3051 " model vdw 1.824 2.170 nonbonded pdb=" OP2 C U1840 " pdb="MG MG U3136 " model vdw 1.828 2.170 nonbonded pdb=" OP1 G U2619 " pdb="MG MG U3175 " model vdw 1.855 2.170 nonbonded pdb=" OP2 A U1200 " pdb="MG MG U3100 " model vdw 1.870 2.170 ... (remaining 824104 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=1.00 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 13.000 Check model and map are aligned: 1.050 Set scattering table: 0.680 Process input model: 336.890 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.220 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 358.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 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 : 0.008 0.119 99690 Z= 0.454 Angle : 0.682 11.300 149672 Z= 0.358 Chirality : 0.041 0.321 19191 Planarity : 0.004 0.060 7613 Dihedral : 23.629 178.403 57841 Min Nonbonded Distance : 1.176 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 0.04 % Allowed : 8.53 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.12), residues: 3288 helix: -1.62 (0.15), residues: 908 sheet: -3.04 (0.17), residues: 624 loop : -3.35 (0.12), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP W 213 HIS 0.006 0.001 HIS W 232 PHE 0.016 0.002 PHE Z 59 TYR 0.016 0.001 TYR m 59 ARG 0.012 0.000 ARG j 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 850 time to evaluate : 4.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.9164 (pp) cc_final: 0.8667 (pp) REVERT: B 54 PHE cc_start: 0.8814 (t80) cc_final: 0.8567 (t80) REVERT: B 117 TRP cc_start: 0.8390 (m100) cc_final: 0.8097 (t-100) REVERT: B 172 PHE cc_start: 0.9179 (m-10) cc_final: 0.8973 (m-80) REVERT: A 156 ARG cc_start: 0.8833 (tpm170) cc_final: 0.8494 (mmm160) REVERT: A 157 GLN cc_start: 0.8846 (mm110) cc_final: 0.8557 (mm-40) REVERT: A 160 LYS cc_start: 0.9224 (mtmm) cc_final: 0.8878 (mttt) REVERT: A 178 GLN cc_start: 0.9151 (tp-100) cc_final: 0.8822 (tp-100) REVERT: b 126 LEU cc_start: 0.8774 (mm) cc_final: 0.8414 (pt) REVERT: W 28 LYS cc_start: 0.9209 (mmmm) cc_final: 0.8868 (mmmm) REVERT: W 111 GLN cc_start: 0.9244 (pm20) cc_final: 0.8978 (pm20) REVERT: X 29 GLU cc_start: 0.9006 (pp20) cc_final: 0.8623 (pp20) REVERT: X 89 ASP cc_start: 0.8696 (m-30) cc_final: 0.8417 (m-30) REVERT: Y 7 TYR cc_start: 0.9306 (m-10) cc_final: 0.8982 (m-10) REVERT: Y 50 LYS cc_start: 0.9383 (tttt) cc_final: 0.9167 (tttt) REVERT: Y 128 ASP cc_start: 0.9115 (p0) cc_final: 0.8861 (p0) REVERT: Z 38 MET cc_start: 0.9003 (tpp) cc_final: 0.8697 (tpp) REVERT: Z 83 MET cc_start: 0.9109 (mpp) cc_final: 0.8652 (mpp) REVERT: a 42 MET cc_start: 0.9004 (tpp) cc_final: 0.8782 (tpp) REVERT: a 59 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8897 (mm-40) REVERT: a 107 ASN cc_start: 0.8892 (m-40) cc_final: 0.8547 (m-40) REVERT: a 122 ILE cc_start: 0.9541 (mp) cc_final: 0.9302 (tp) REVERT: a 129 GLN cc_start: 0.9300 (pp30) cc_final: 0.8794 (pp30) REVERT: a 148 ASN cc_start: 0.9249 (m-40) cc_final: 0.8930 (m110) REVERT: c 75 TYR cc_start: 0.9568 (m-80) cc_final: 0.9302 (m-80) REVERT: c 118 GLN cc_start: 0.9585 (tm-30) cc_final: 0.9319 (tp40) REVERT: d 9 LYS cc_start: 0.9317 (ptmm) cc_final: 0.8877 (ptmm) REVERT: d 12 ASP cc_start: 0.8809 (p0) cc_final: 0.8571 (p0) REVERT: d 21 THR cc_start: 0.9663 (m) cc_final: 0.9217 (p) REVERT: d 66 LYS cc_start: 0.9202 (mtpp) cc_final: 0.8890 (ttpp) REVERT: d 87 ILE cc_start: 0.9299 (mm) cc_final: 0.8926 (tp) REVERT: d 105 GLU cc_start: 0.9123 (mp0) cc_final: 0.8522 (mp0) REVERT: e 17 ASN cc_start: 0.9138 (t0) cc_final: 0.8797 (t0) REVERT: e 58 PHE cc_start: 0.9348 (p90) cc_final: 0.9110 (p90) REVERT: e 106 ASN cc_start: 0.9248 (m-40) cc_final: 0.8390 (p0) REVERT: f 9 TYR cc_start: 0.9101 (m-80) cc_final: 0.8540 (m-80) REVERT: f 43 THR cc_start: 0.9569 (m) cc_final: 0.9128 (p) REVERT: f 74 TYR cc_start: 0.9363 (p90) cc_final: 0.8851 (p90) REVERT: f 79 LEU cc_start: 0.9303 (pt) cc_final: 0.8918 (pt) REVERT: g 28 GLU cc_start: 0.8624 (mt-10) cc_final: 0.7932 (mp0) REVERT: g 45 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8301 (mm-30) REVERT: h 44 ILE cc_start: 0.9537 (mm) cc_final: 0.9319 (mm) REVERT: h 60 ASP cc_start: 0.7938 (p0) cc_final: 0.7700 (p0) REVERT: i 34 LYS cc_start: 0.9511 (mtmt) cc_final: 0.9297 (mtmm) REVERT: i 114 LYS cc_start: 0.9105 (ptpp) cc_final: 0.8854 (ptpp) REVERT: k 23 GLU cc_start: 0.8696 (tp30) cc_final: 0.8115 (tp30) REVERT: l 28 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8075 (mm-40) REVERT: l 48 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8457 (tm-30) REVERT: l 69 LEU cc_start: 0.9798 (mt) cc_final: 0.9584 (mt) REVERT: m 31 ASP cc_start: 0.9157 (t70) cc_final: 0.8757 (t0) REVERT: m 33 ARG cc_start: 0.8948 (mtm180) cc_final: 0.8687 (mtm-85) REVERT: n 7 ASP cc_start: 0.8219 (m-30) cc_final: 0.7911 (m-30) REVERT: n 48 THR cc_start: 0.9414 (t) cc_final: 0.8600 (t) REVERT: o 46 TYR cc_start: 0.9454 (t80) cc_final: 0.8982 (t80) REVERT: o 52 LYS cc_start: 0.9541 (mttt) cc_final: 0.9069 (mttp) REVERT: o 82 ARG cc_start: 0.8633 (mtp85) cc_final: 0.7396 (mmm-85) REVERT: o 85 LYS cc_start: 0.9277 (mttp) cc_final: 0.8834 (mtpt) REVERT: p 12 LYS cc_start: 0.9321 (mmtt) cc_final: 0.8811 (mmtp) REVERT: p 37 LYS cc_start: 0.8962 (pttt) cc_final: 0.8545 (pttp) REVERT: q 14 GLU cc_start: 0.8374 (pt0) cc_final: 0.7466 (pm20) REVERT: q 38 ARG cc_start: 0.8750 (ttp-170) cc_final: 0.8336 (ptm160) REVERT: q 41 LYS cc_start: 0.9597 (ptpt) cc_final: 0.9368 (ptpp) REVERT: r 25 LYS cc_start: 0.8601 (tmmt) cc_final: 0.8055 (tmmt) REVERT: r 29 LEU cc_start: 0.9743 (mm) cc_final: 0.9233 (mm) REVERT: s 38 GLN cc_start: 0.9332 (tp40) cc_final: 0.9080 (tp-100) REVERT: s 60 GLN cc_start: 0.9476 (tp-100) cc_final: 0.9253 (tp-100) REVERT: u 17 ASN cc_start: 0.9216 (t0) cc_final: 0.8785 (t0) REVERT: u 35 LYS cc_start: 0.9474 (ttmt) cc_final: 0.9216 (ttmm) REVERT: u 43 LYS cc_start: 0.9136 (mttt) cc_final: 0.8926 (mmmt) REVERT: u 46 LYS cc_start: 0.9397 (ptmt) cc_final: 0.8890 (mtpp) REVERT: v 1 MET cc_start: 0.8890 (ptm) cc_final: 0.8419 (ptm) REVERT: v 5 GLU cc_start: 0.9540 (mp0) cc_final: 0.9047 (mp0) REVERT: v 8 ASP cc_start: 0.9063 (m-30) cc_final: 0.7978 (m-30) REVERT: v 15 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9241 (mm-30) REVERT: v 23 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8271 (tm-30) REVERT: v 29 ARG cc_start: 0.9134 (mtt-85) cc_final: 0.8907 (mtm-85) REVERT: w 17 GLU cc_start: 0.8672 (tp30) cc_final: 0.8232 (tp30) REVERT: w 29 LYS cc_start: 0.9442 (ptpt) cc_final: 0.9179 (ptpp) REVERT: w 30 LYS cc_start: 0.9359 (mtpt) cc_final: 0.8966 (ttpp) REVERT: w 57 LYS cc_start: 0.9215 (tmmt) cc_final: 0.8867 (tmtt) outliers start: 1 outliers final: 0 residues processed: 851 average time/residue: 0.9131 time to fit residues: 1299.0736 Evaluate side-chains 745 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 745 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 5.9990 chunk 472 optimal weight: 6.9990 chunk 262 optimal weight: 50.0000 chunk 161 optimal weight: 40.0000 chunk 319 optimal weight: 8.9990 chunk 252 optimal weight: 6.9990 chunk 489 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 364 optimal weight: 10.0000 chunk 566 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN B 109 ASN A 142 GLN ** b 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 11 ASN W 45 ASN W 58 HIS W 230 HIS W 232 HIS X 33 ASN X 173 ASN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 46 ASN Z 161 ASN a 62 HIS ** a 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 48 HIS c 81 HIS e 78 ASN e 126 ASN f 13 HIS f 123 HIS g 75 ASN g 81 GLN h 37 ASN h 43 GLN ** i 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 39 ASN j 37 GLN j 72 ASN j 91 ASN j 118 ASN l 102 HIS m 35 ASN m 55 ASN n 64 HIS p 40 HIS q 16 ASN ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 45 HIS r 6 GLN s 64 ASN v 65 ASN w 32 ASN w 33 GLN w 37 HIS w 40 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.0619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 99690 Z= 0.409 Angle : 0.675 13.053 149672 Z= 0.344 Chirality : 0.040 0.319 19191 Planarity : 0.005 0.057 7613 Dihedral : 24.081 178.766 51131 Min Nonbonded Distance : 1.104 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.36 % Favored : 91.61 % Rotamer: Outliers : 3.36 % Allowed : 18.84 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.13), residues: 3288 helix: -0.36 (0.17), residues: 923 sheet: -2.34 (0.18), residues: 636 loop : -2.88 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP W 213 HIS 0.006 0.001 HIS Y 189 PHE 0.020 0.002 PHE b 84 TYR 0.018 0.002 TYR Z 97 ARG 0.009 0.001 ARG w 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 788 time to evaluate : 4.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 PHE cc_start: 0.8881 (t80) cc_final: 0.8596 (t80) REVERT: B 117 TRP cc_start: 0.8358 (m100) cc_final: 0.8126 (t-100) REVERT: A 157 GLN cc_start: 0.8781 (mm110) cc_final: 0.8236 (mm-40) REVERT: A 160 LYS cc_start: 0.9183 (mtmm) cc_final: 0.8815 (mttt) REVERT: b 31 ARG cc_start: 0.8684 (mpt-90) cc_final: 0.8466 (mmm-85) REVERT: b 126 LEU cc_start: 0.8798 (mm) cc_final: 0.8427 (pt) REVERT: W 28 LYS cc_start: 0.9208 (mmmm) cc_final: 0.8876 (mmmm) REVERT: W 111 GLN cc_start: 0.9231 (pm20) cc_final: 0.8937 (pm20) REVERT: X 29 GLU cc_start: 0.8966 (pp20) cc_final: 0.8705 (pp20) REVERT: X 89 ASP cc_start: 0.8717 (m-30) cc_final: 0.8411 (m-30) REVERT: X 140 HIS cc_start: 0.8642 (OUTLIER) cc_final: 0.7138 (p-80) REVERT: X 175 GLU cc_start: 0.8606 (tt0) cc_final: 0.8365 (tm-30) REVERT: X 201 THR cc_start: 0.9521 (m) cc_final: 0.9070 (p) REVERT: Y 7 TYR cc_start: 0.9282 (m-10) cc_final: 0.8956 (m-10) REVERT: Y 50 LYS cc_start: 0.9351 (tttt) cc_final: 0.9128 (tttt) REVERT: Y 128 ASP cc_start: 0.9123 (p0) cc_final: 0.8871 (p0) REVERT: Z 26 MET cc_start: 0.9280 (mtp) cc_final: 0.9080 (mtp) REVERT: Z 38 MET cc_start: 0.9049 (tpp) cc_final: 0.8828 (tpp) REVERT: Z 83 MET cc_start: 0.9101 (mpp) cc_final: 0.8660 (mpp) REVERT: Z 96 MET cc_start: 0.9161 (tmm) cc_final: 0.8698 (ptm) REVERT: a 59 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8901 (mm-40) REVERT: a 107 ASN cc_start: 0.8934 (m-40) cc_final: 0.8622 (m-40) REVERT: a 110 TYR cc_start: 0.9121 (m-10) cc_final: 0.8920 (m-10) REVERT: a 122 ILE cc_start: 0.9554 (mp) cc_final: 0.9304 (tp) REVERT: a 148 ASN cc_start: 0.9265 (m-40) cc_final: 0.8858 (m-40) REVERT: a 165 TYR cc_start: 0.9255 (OUTLIER) cc_final: 0.9046 (m-80) REVERT: c 118 GLN cc_start: 0.9583 (tm-30) cc_final: 0.9021 (tm-30) REVERT: d 3 GLN cc_start: 0.9012 (pt0) cc_final: 0.8790 (pt0) REVERT: d 9 LYS cc_start: 0.9345 (ptmm) cc_final: 0.9124 (ptmm) REVERT: d 21 THR cc_start: 0.9698 (m) cc_final: 0.9286 (p) REVERT: d 66 LYS cc_start: 0.9220 (mtpp) cc_final: 0.8828 (ttpp) REVERT: d 81 GLU cc_start: 0.7929 (pm20) cc_final: 0.7702 (pm20) REVERT: d 87 ILE cc_start: 0.9316 (mm) cc_final: 0.8895 (tp) REVERT: d 90 ASP cc_start: 0.8353 (t0) cc_final: 0.8138 (t0) REVERT: d 105 GLU cc_start: 0.9170 (mp0) cc_final: 0.8913 (mp0) REVERT: e 17 ASN cc_start: 0.9215 (t0) cc_final: 0.8907 (t0) REVERT: e 106 ASN cc_start: 0.9254 (m-40) cc_final: 0.8326 (p0) REVERT: f 9 TYR cc_start: 0.9111 (m-80) cc_final: 0.8532 (m-80) REVERT: f 37 LEU cc_start: 0.9529 (mt) cc_final: 0.9285 (mt) REVERT: f 43 THR cc_start: 0.9570 (m) cc_final: 0.9159 (p) REVERT: f 74 TYR cc_start: 0.9222 (p90) cc_final: 0.8932 (p90) REVERT: g 28 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7992 (mp0) REVERT: g 31 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8142 (pp20) REVERT: g 45 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8005 (mt-10) REVERT: g 92 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8355 (pp20) REVERT: g 93 GLU cc_start: 0.8840 (pm20) cc_final: 0.8053 (pm20) REVERT: i 9 GLU cc_start: 0.9085 (tp30) cc_final: 0.8621 (tm-30) REVERT: i 105 GLU cc_start: 0.9093 (mp0) cc_final: 0.8847 (mp0) REVERT: i 114 LYS cc_start: 0.9078 (ptpp) cc_final: 0.8812 (ptpp) REVERT: k 36 GLU cc_start: 0.8710 (pm20) cc_final: 0.8485 (mp0) REVERT: k 39 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8464 (pp) REVERT: l 48 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8475 (tm-30) REVERT: l 52 LYS cc_start: 0.9502 (mtpt) cc_final: 0.9237 (mtpp) REVERT: m 31 ASP cc_start: 0.9171 (t70) cc_final: 0.8782 (t0) REVERT: m 33 ARG cc_start: 0.8883 (mtm180) cc_final: 0.8642 (mtm-85) REVERT: n 7 ASP cc_start: 0.8210 (m-30) cc_final: 0.7923 (m-30) REVERT: n 77 GLU cc_start: 0.8717 (tp30) cc_final: 0.8458 (mm-30) REVERT: o 52 LYS cc_start: 0.9534 (mttt) cc_final: 0.9047 (ttmm) REVERT: o 82 ARG cc_start: 0.8711 (mtp85) cc_final: 0.7467 (mmm-85) REVERT: o 85 LYS cc_start: 0.9297 (mttp) cc_final: 0.9051 (mttm) REVERT: p 12 LYS cc_start: 0.9319 (mmtt) cc_final: 0.8871 (mmtm) REVERT: p 28 THR cc_start: 0.8771 (p) cc_final: 0.8405 (p) REVERT: q 14 GLU cc_start: 0.8491 (pt0) cc_final: 0.7673 (pm20) REVERT: q 38 ARG cc_start: 0.8775 (ttp-170) cc_final: 0.8410 (ptm160) REVERT: q 41 LYS cc_start: 0.9627 (ptpt) cc_final: 0.9391 (ptpp) REVERT: r 6 GLN cc_start: 0.9315 (mm110) cc_final: 0.8960 (mm110) REVERT: s 38 GLN cc_start: 0.9251 (tp40) cc_final: 0.8954 (tp-100) REVERT: u 17 ASN cc_start: 0.9209 (t0) cc_final: 0.8725 (t0) REVERT: u 35 LYS cc_start: 0.9488 (ttmt) cc_final: 0.9241 (ttmm) REVERT: u 43 LYS cc_start: 0.9117 (mttt) cc_final: 0.8807 (mmmt) REVERT: u 46 LYS cc_start: 0.9494 (ptmt) cc_final: 0.9083 (mtpp) REVERT: v 1 MET cc_start: 0.8835 (ptm) cc_final: 0.8354 (ptm) REVERT: v 5 GLU cc_start: 0.9335 (mp0) cc_final: 0.8736 (mp0) REVERT: v 8 ASP cc_start: 0.9204 (m-30) cc_final: 0.8982 (m-30) REVERT: v 15 GLU cc_start: 0.9485 (mm-30) cc_final: 0.9212 (mm-30) REVERT: v 23 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8259 (tm-30) REVERT: w 9 LYS cc_start: 0.9343 (ptmm) cc_final: 0.8892 (ptpp) REVERT: w 17 GLU cc_start: 0.8561 (tp30) cc_final: 0.8161 (tp30) REVERT: w 29 LYS cc_start: 0.9433 (ptpt) cc_final: 0.9199 (ptpp) REVERT: w 32 ASN cc_start: 0.9482 (OUTLIER) cc_final: 0.9156 (t0) REVERT: w 37 HIS cc_start: 0.9181 (OUTLIER) cc_final: 0.8401 (m-70) REVERT: w 57 LYS cc_start: 0.9172 (tmmt) cc_final: 0.8813 (tmtt) outliers start: 93 outliers final: 63 residues processed: 816 average time/residue: 0.8864 time to fit residues: 1224.5635 Evaluate side-chains 814 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 746 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 55 TYR Chi-restraints excluded: chain b residue 80 ASN Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain X residue 21 ASP Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain Y residue 120 ASP Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Z residue 17 MET Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 165 TYR Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 144 ARG Chi-restraints excluded: chain d residue 80 ASP Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 76 VAL Chi-restraints excluded: chain f residue 127 ILE Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 117 ILE Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 106 VAL Chi-restraints excluded: chain i residue 47 GLU Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 8 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 17 VAL Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 50 ASN Chi-restraints excluded: chain l residue 24 ILE Chi-restraints excluded: chain l residue 65 ASP Chi-restraints excluded: chain l residue 67 ASN Chi-restraints excluded: chain m residue 6 ASP Chi-restraints excluded: chain m residue 22 THR Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain o residue 92 VAL Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 64 ASN Chi-restraints excluded: chain t residue 4 ARG Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain v residue 4 ASN Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain v residue 62 ILE Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 32 ASN Chi-restraints excluded: chain w residue 37 HIS Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 471 optimal weight: 3.9990 chunk 385 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 567 optimal weight: 9.9990 chunk 613 optimal weight: 8.9990 chunk 505 optimal weight: 0.0980 chunk 562 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 455 optimal weight: 3.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 70 ASN b 97 ASN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 99690 Z= 0.234 Angle : 0.591 10.825 149672 Z= 0.305 Chirality : 0.036 0.314 19191 Planarity : 0.004 0.051 7613 Dihedral : 23.985 179.338 51131 Min Nonbonded Distance : 1.143 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.40 % Allowed : 21.33 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.14), residues: 3288 helix: 0.34 (0.18), residues: 908 sheet: -1.90 (0.19), residues: 642 loop : -2.55 (0.13), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP W 213 HIS 0.019 0.001 HIS w 37 PHE 0.026 0.001 PHE Z 138 TYR 0.017 0.001 TYR f 74 ARG 0.008 0.000 ARG Y 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 811 time to evaluate : 4.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 PHE cc_start: 0.8859 (t80) cc_final: 0.8581 (t80) REVERT: B 172 PHE cc_start: 0.9135 (m-80) cc_final: 0.8801 (m-80) REVERT: B 180 MET cc_start: 0.9327 (ppp) cc_final: 0.9110 (ppp) REVERT: A 123 PHE cc_start: 0.8851 (t80) cc_final: 0.8211 (t80) REVERT: A 140 ARG cc_start: 0.9178 (ttm-80) cc_final: 0.8813 (ttp-110) REVERT: A 159 HIS cc_start: 0.9226 (t-90) cc_final: 0.8990 (t-170) REVERT: A 163 LYS cc_start: 0.9768 (tmtt) cc_final: 0.9441 (mtmt) REVERT: A 178 GLN cc_start: 0.9219 (tp-100) cc_final: 0.8940 (tp-100) REVERT: b 126 LEU cc_start: 0.8724 (mm) cc_final: 0.8394 (pt) REVERT: W 28 LYS cc_start: 0.9199 (mmmm) cc_final: 0.8876 (mmmm) REVERT: W 111 GLN cc_start: 0.9205 (pm20) cc_final: 0.8929 (pm20) REVERT: W 219 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9159 (p) REVERT: W 247 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8625 (mtp) REVERT: X 89 ASP cc_start: 0.8577 (m-30) cc_final: 0.8004 (m-30) REVERT: X 140 HIS cc_start: 0.8559 (OUTLIER) cc_final: 0.7037 (p-80) REVERT: X 201 THR cc_start: 0.9508 (m) cc_final: 0.9073 (p) REVERT: Y 7 TYR cc_start: 0.9243 (m-10) cc_final: 0.8880 (m-10) REVERT: Y 128 ASP cc_start: 0.9127 (p0) cc_final: 0.8899 (p0) REVERT: Z 38 MET cc_start: 0.9077 (tpp) cc_final: 0.8814 (tpp) REVERT: Z 83 MET cc_start: 0.9122 (mpp) cc_final: 0.8662 (mpp) REVERT: Z 96 MET cc_start: 0.9149 (tmm) cc_final: 0.8723 (ptm) REVERT: Z 122 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.7146 (m-10) REVERT: Z 128 TYR cc_start: 0.8979 (t80) cc_final: 0.8697 (t80) REVERT: a 59 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8904 (mp10) REVERT: a 107 ASN cc_start: 0.8919 (m-40) cc_final: 0.8593 (m-40) REVERT: a 110 TYR cc_start: 0.9127 (m-10) cc_final: 0.8854 (m-10) REVERT: a 122 ILE cc_start: 0.9528 (mp) cc_final: 0.9323 (tp) REVERT: a 148 ASN cc_start: 0.9247 (m-40) cc_final: 0.8840 (m110) REVERT: c 109 MET cc_start: 0.9390 (mtt) cc_final: 0.9153 (mtt) REVERT: c 118 GLN cc_start: 0.9593 (tm-30) cc_final: 0.9063 (tm-30) REVERT: d 53 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8956 (mmmt) REVERT: d 66 LYS cc_start: 0.9178 (mtpp) cc_final: 0.8788 (ttpp) REVERT: d 81 GLU cc_start: 0.7943 (pm20) cc_final: 0.7700 (pm20) REVERT: d 105 GLU cc_start: 0.9128 (mp0) cc_final: 0.8850 (mp0) REVERT: e 17 ASN cc_start: 0.9200 (t0) cc_final: 0.8908 (t0) REVERT: e 106 ASN cc_start: 0.9202 (m-40) cc_final: 0.8305 (p0) REVERT: f 9 TYR cc_start: 0.9097 (m-80) cc_final: 0.8543 (m-80) REVERT: f 37 LEU cc_start: 0.9534 (mt) cc_final: 0.9314 (mt) REVERT: f 43 THR cc_start: 0.9449 (m) cc_final: 0.9038 (p) REVERT: g 28 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8061 (mp0) REVERT: g 45 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8238 (mm-30) REVERT: g 75 ASN cc_start: 0.8503 (m-40) cc_final: 0.7996 (m-40) REVERT: g 77 GLN cc_start: 0.8913 (tt0) cc_final: 0.8653 (tt0) REVERT: g 92 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8333 (pp20) REVERT: g 93 GLU cc_start: 0.8833 (pm20) cc_final: 0.8020 (pm20) REVERT: g 114 MET cc_start: 0.8911 (mmm) cc_final: 0.8709 (mmm) REVERT: i 9 GLU cc_start: 0.9076 (tp30) cc_final: 0.8564 (tm-30) REVERT: i 105 GLU cc_start: 0.9084 (mp0) cc_final: 0.8840 (mp0) REVERT: i 114 LYS cc_start: 0.8968 (ptpp) cc_final: 0.8767 (ptpp) REVERT: j 19 LYS cc_start: 0.9145 (mmtt) cc_final: 0.8922 (mmmt) REVERT: j 108 GLN cc_start: 0.9335 (tp40) cc_final: 0.9072 (tp40) REVERT: k 36 GLU cc_start: 0.8758 (pm20) cc_final: 0.8548 (mp0) REVERT: k 39 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8426 (pp) REVERT: k 45 ASN cc_start: 0.8375 (p0) cc_final: 0.8070 (p0) REVERT: k 47 LYS cc_start: 0.8524 (tmmt) cc_final: 0.8320 (tmmt) REVERT: l 28 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7912 (mt0) REVERT: l 48 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8197 (tm-30) REVERT: l 52 LYS cc_start: 0.9499 (mtpt) cc_final: 0.8958 (mmtp) REVERT: m 31 ASP cc_start: 0.9147 (t70) cc_final: 0.8750 (t0) REVERT: m 33 ARG cc_start: 0.8864 (mtm180) cc_final: 0.8634 (mtm-85) REVERT: m 76 ARG cc_start: 0.9010 (mtm180) cc_final: 0.8478 (mtm-85) REVERT: n 7 ASP cc_start: 0.8208 (m-30) cc_final: 0.7941 (m-30) REVERT: n 39 ASN cc_start: 0.9556 (t0) cc_final: 0.9122 (t0) REVERT: n 77 GLU cc_start: 0.8731 (tp30) cc_final: 0.8382 (mm-30) REVERT: o 52 LYS cc_start: 0.9505 (mttt) cc_final: 0.9027 (mtpp) REVERT: o 76 LYS cc_start: 0.8885 (mmtp) cc_final: 0.8635 (mmmm) REVERT: o 82 ARG cc_start: 0.8788 (mtp85) cc_final: 0.7552 (mmm-85) REVERT: o 85 LYS cc_start: 0.9263 (mttp) cc_final: 0.8994 (mttm) REVERT: o 86 LYS cc_start: 0.9037 (ttpp) cc_final: 0.8509 (ttmm) REVERT: p 28 THR cc_start: 0.8494 (p) cc_final: 0.8169 (p) REVERT: p 53 ASP cc_start: 0.8745 (t0) cc_final: 0.8474 (t0) REVERT: q 14 GLU cc_start: 0.8460 (pt0) cc_final: 0.7583 (pm20) REVERT: q 38 ARG cc_start: 0.8734 (ttp-170) cc_final: 0.8467 (ptm160) REVERT: s 38 GLN cc_start: 0.9187 (tp40) cc_final: 0.8975 (tp-100) REVERT: u 17 ASN cc_start: 0.9125 (t0) cc_final: 0.8626 (t0) REVERT: u 35 LYS cc_start: 0.9474 (ttmt) cc_final: 0.9234 (ttmm) REVERT: u 36 VAL cc_start: 0.8877 (m) cc_final: 0.8605 (p) REVERT: u 46 LYS cc_start: 0.9479 (ptmt) cc_final: 0.9082 (mtpp) REVERT: v 1 MET cc_start: 0.8877 (ptm) cc_final: 0.8306 (ptm) REVERT: v 5 GLU cc_start: 0.9330 (mp0) cc_final: 0.8609 (mp0) REVERT: v 15 GLU cc_start: 0.9467 (mm-30) cc_final: 0.9180 (mm-30) REVERT: v 23 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8177 (tm-30) REVERT: w 9 LYS cc_start: 0.9325 (ptmm) cc_final: 0.8867 (ptpp) REVERT: w 17 GLU cc_start: 0.8580 (tp30) cc_final: 0.8373 (tp30) REVERT: w 57 LYS cc_start: 0.9090 (tmmt) cc_final: 0.8758 (tmtt) outliers start: 94 outliers final: 67 residues processed: 847 average time/residue: 0.8802 time to fit residues: 1264.5948 Evaluate side-chains 829 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 757 time to evaluate : 3.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 25 THR Chi-restraints excluded: chain b residue 55 TYR Chi-restraints excluded: chain b residue 70 ASN Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 203 ILE Chi-restraints excluded: chain W residue 219 THR Chi-restraints excluded: chain W residue 247 MET Chi-restraints excluded: chain W residue 254 THR Chi-restraints excluded: chain X residue 21 ASP Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain Y residue 120 ASP Chi-restraints excluded: chain Y residue 130 THR Chi-restraints excluded: chain Y residue 183 VAL Chi-restraints excluded: chain Z residue 17 MET Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 122 PHE Chi-restraints excluded: chain Z residue 141 ILE Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 173 VAL Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 53 ASP Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 80 ASP Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain g residue 117 ILE Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 3 THR Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 47 GLU Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 50 ASN Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 100 ILE Chi-restraints excluded: chain l residue 24 ILE Chi-restraints excluded: chain l residue 46 ILE Chi-restraints excluded: chain l residue 65 ASP Chi-restraints excluded: chain l residue 67 ASN Chi-restraints excluded: chain m residue 6 ASP Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain q residue 21 LYS Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain t residue 25 VAL Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain v residue 4 ASN Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain v residue 62 ILE Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 6.9990 chunk 426 optimal weight: 7.9990 chunk 294 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 270 optimal weight: 20.0000 chunk 381 optimal weight: 4.9990 chunk 569 optimal weight: 10.0000 chunk 603 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 chunk 539 optimal weight: 9.9990 chunk 162 optimal weight: 40.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS b 70 ASN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 64 ASN w 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 99690 Z= 0.430 Angle : 0.671 11.095 149672 Z= 0.341 Chirality : 0.040 0.308 19191 Planarity : 0.005 0.051 7613 Dihedral : 23.953 179.419 51131 Min Nonbonded Distance : 1.102 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 5.17 % Allowed : 23.36 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.14), residues: 3288 helix: 0.28 (0.18), residues: 916 sheet: -1.70 (0.19), residues: 653 loop : -2.45 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP W 213 HIS 0.006 0.001 HIS w 37 PHE 0.019 0.002 PHE B 172 TYR 0.023 0.002 TYR a 95 ARG 0.007 0.000 ARG m 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 758 time to evaluate : 5.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 PHE cc_start: 0.8858 (t80) cc_final: 0.8607 (t80) REVERT: B 172 PHE cc_start: 0.9155 (m-80) cc_final: 0.8774 (m-80) REVERT: B 180 MET cc_start: 0.9354 (ppp) cc_final: 0.9140 (ppp) REVERT: A 156 ARG cc_start: 0.9103 (mmm160) cc_final: 0.8344 (mmm160) REVERT: A 172 PHE cc_start: 0.9458 (t80) cc_final: 0.9147 (t80) REVERT: A 178 GLN cc_start: 0.9206 (tp-100) cc_final: 0.8926 (tp-100) REVERT: b 126 LEU cc_start: 0.8725 (mm) cc_final: 0.8419 (pt) REVERT: W 28 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8915 (mmmm) REVERT: W 111 GLN cc_start: 0.9242 (pm20) cc_final: 0.8945 (pm20) REVERT: W 219 THR cc_start: 0.9503 (OUTLIER) cc_final: 0.9251 (p) REVERT: X 89 ASP cc_start: 0.8465 (m-30) cc_final: 0.7913 (m-30) REVERT: X 140 HIS cc_start: 0.8603 (OUTLIER) cc_final: 0.7049 (p-80) REVERT: X 201 THR cc_start: 0.9514 (m) cc_final: 0.9059 (p) REVERT: Y 128 ASP cc_start: 0.9158 (p0) cc_final: 0.8888 (p0) REVERT: Z 38 MET cc_start: 0.9021 (tpp) cc_final: 0.8672 (tpp) REVERT: Z 83 MET cc_start: 0.9062 (mpp) cc_final: 0.8577 (mpp) REVERT: Z 96 MET cc_start: 0.9235 (tmm) cc_final: 0.8505 (ptm) REVERT: Z 122 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.6730 (m-10) REVERT: Z 128 TYR cc_start: 0.8915 (t80) cc_final: 0.8543 (t80) REVERT: a 59 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8919 (mm-40) REVERT: a 107 ASN cc_start: 0.9007 (m-40) cc_final: 0.8651 (m-40) REVERT: a 122 ILE cc_start: 0.9566 (mp) cc_final: 0.9344 (tp) REVERT: a 148 ASN cc_start: 0.9272 (m-40) cc_final: 0.8866 (m110) REVERT: c 118 GLN cc_start: 0.9568 (tm-30) cc_final: 0.9062 (tm-30) REVERT: d 53 LYS cc_start: 0.9252 (mmmm) cc_final: 0.8960 (mmmt) REVERT: d 66 LYS cc_start: 0.9201 (mtpp) cc_final: 0.8820 (ttpp) REVERT: d 81 GLU cc_start: 0.7930 (pm20) cc_final: 0.7688 (pm20) REVERT: d 105 GLU cc_start: 0.9157 (mp0) cc_final: 0.8855 (mp0) REVERT: e 17 ASN cc_start: 0.9231 (t0) cc_final: 0.8956 (t0) REVERT: e 106 ASN cc_start: 0.9242 (m-40) cc_final: 0.8314 (p0) REVERT: f 9 TYR cc_start: 0.9142 (m-80) cc_final: 0.8426 (m-80) REVERT: f 43 THR cc_start: 0.9463 (m) cc_final: 0.9059 (p) REVERT: f 80 GLU cc_start: 0.8333 (mp0) cc_final: 0.8113 (mp0) REVERT: g 31 GLU cc_start: 0.8425 (pp20) cc_final: 0.8128 (pm20) REVERT: g 45 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8293 (mm-30) REVERT: g 92 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8105 (pp20) REVERT: g 93 GLU cc_start: 0.8831 (pm20) cc_final: 0.7780 (pm20) REVERT: g 118 GLU cc_start: 0.8828 (pm20) cc_final: 0.8360 (pm20) REVERT: i 9 GLU cc_start: 0.9081 (tp30) cc_final: 0.8626 (tm-30) REVERT: i 114 LYS cc_start: 0.8972 (ptpp) cc_final: 0.8718 (ptpp) REVERT: j 19 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8958 (mmmt) REVERT: j 108 GLN cc_start: 0.9380 (tp40) cc_final: 0.9146 (tp40) REVERT: k 39 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8395 (pp) REVERT: k 45 ASN cc_start: 0.8466 (p0) cc_final: 0.8220 (p0) REVERT: l 48 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8468 (tm-30) REVERT: m 1 MET cc_start: 0.9197 (tmm) cc_final: 0.8916 (tmm) REVERT: m 31 ASP cc_start: 0.9167 (t70) cc_final: 0.8809 (t0) REVERT: m 33 ARG cc_start: 0.8925 (mtm180) cc_final: 0.8683 (mtm-85) REVERT: n 7 ASP cc_start: 0.8264 (m-30) cc_final: 0.7910 (m-30) REVERT: n 39 ASN cc_start: 0.9603 (t0) cc_final: 0.9203 (t0) REVERT: o 52 LYS cc_start: 0.9517 (mttt) cc_final: 0.9057 (mttp) REVERT: o 82 ARG cc_start: 0.8732 (mtp85) cc_final: 0.7517 (mmm-85) REVERT: o 85 LYS cc_start: 0.9275 (mttp) cc_final: 0.9015 (mttm) REVERT: s 38 GLN cc_start: 0.9266 (tp40) cc_final: 0.9007 (tp-100) REVERT: u 17 ASN cc_start: 0.9228 (t0) cc_final: 0.8788 (t0) REVERT: u 22 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7603 (mmm) REVERT: u 35 LYS cc_start: 0.9490 (ttmt) cc_final: 0.9227 (ttmm) REVERT: u 36 VAL cc_start: 0.8885 (m) cc_final: 0.8629 (p) REVERT: u 43 LYS cc_start: 0.9104 (mttt) cc_final: 0.8742 (mmmt) REVERT: u 46 LYS cc_start: 0.9505 (ptmt) cc_final: 0.9104 (mtpp) REVERT: v 1 MET cc_start: 0.8835 (ptm) cc_final: 0.8263 (ptm) REVERT: v 5 GLU cc_start: 0.9306 (mp0) cc_final: 0.8660 (mp0) REVERT: v 15 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9211 (mm-30) REVERT: v 23 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8291 (tm-30) REVERT: w 9 LYS cc_start: 0.9315 (ptmm) cc_final: 0.8851 (ptpp) REVERT: w 32 ASN cc_start: 0.9417 (OUTLIER) cc_final: 0.9071 (t0) REVERT: w 57 LYS cc_start: 0.9134 (tmmt) cc_final: 0.8854 (tmtt) outliers start: 143 outliers final: 110 residues processed: 830 average time/residue: 0.8997 time to fit residues: 1271.7339 Evaluate side-chains 856 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 740 time to evaluate : 3.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 25 THR Chi-restraints excluded: chain b residue 55 TYR Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 203 ILE Chi-restraints excluded: chain W residue 219 THR Chi-restraints excluded: chain W residue 254 THR Chi-restraints excluded: chain X residue 21 ASP Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain X residue 192 VAL Chi-restraints excluded: chain Y residue 120 ASP Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Z residue 17 MET Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 122 PHE Chi-restraints excluded: chain Z residue 144 ASP Chi-restraints excluded: chain Z residue 159 THR Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 173 VAL Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 53 ASP Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 144 ARG Chi-restraints excluded: chain d residue 18 GLU Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 80 ASP Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 76 VAL Chi-restraints excluded: chain f residue 127 ILE Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 9 THR Chi-restraints excluded: chain g residue 20 LEU Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain g residue 89 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 3 THR Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 106 VAL Chi-restraints excluded: chain i residue 13 LYS Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 47 GLU Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 71 VAL Chi-restraints excluded: chain i residue 88 GLU Chi-restraints excluded: chain i residue 116 ILE Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 17 VAL Chi-restraints excluded: chain j residue 42 SER Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 50 ASN Chi-restraints excluded: chain k residue 53 VAL Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain l residue 65 ASP Chi-restraints excluded: chain l residue 67 ASN Chi-restraints excluded: chain m residue 6 ASP Chi-restraints excluded: chain m residue 22 THR Chi-restraints excluded: chain m residue 35 ASN Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 48 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 80 PHE Chi-restraints excluded: chain o residue 92 VAL Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain q residue 21 LYS Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain t residue 4 ARG Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 25 VAL Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 22 MET Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain v residue 4 ASN Chi-restraints excluded: chain v residue 8 ASP Chi-restraints excluded: chain v residue 21 LEU Chi-restraints excluded: chain v residue 34 THR Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 32 ASN Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 2.9990 chunk 342 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 449 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 514 optimal weight: 4.9990 chunk 416 optimal weight: 30.0000 chunk 0 optimal weight: 70.0000 chunk 307 optimal weight: 10.0000 chunk 541 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 59 GLN g 76 ASN ** i 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 99690 Z= 0.367 Angle : 0.647 11.823 149672 Z= 0.330 Chirality : 0.039 0.316 19191 Planarity : 0.004 0.051 7613 Dihedral : 23.940 179.817 51131 Min Nonbonded Distance : 1.113 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 5.75 % Allowed : 24.95 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.14), residues: 3288 helix: 0.30 (0.18), residues: 923 sheet: -1.57 (0.20), residues: 647 loop : -2.38 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP W 213 HIS 0.009 0.001 HIS w 52 PHE 0.021 0.002 PHE Z 59 TYR 0.017 0.002 TYR g 65 ARG 0.010 0.000 ARG Y 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 769 time to evaluate : 4.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 PHE cc_start: 0.8845 (t80) cc_final: 0.8582 (t80) REVERT: B 172 PHE cc_start: 0.9193 (m-80) cc_final: 0.8839 (m-80) REVERT: B 180 MET cc_start: 0.9377 (ppp) cc_final: 0.9169 (ppp) REVERT: A 123 PHE cc_start: 0.8997 (t80) cc_final: 0.8539 (t80) REVERT: A 156 ARG cc_start: 0.9033 (mmm160) cc_final: 0.8628 (mmm160) REVERT: A 172 PHE cc_start: 0.9459 (t80) cc_final: 0.9148 (t80) REVERT: A 178 GLN cc_start: 0.9228 (tp-100) cc_final: 0.8943 (tp-100) REVERT: b 59 MET cc_start: 0.6783 (tpp) cc_final: 0.6314 (ppp) REVERT: b 126 LEU cc_start: 0.8742 (mm) cc_final: 0.8415 (pt) REVERT: W 28 LYS cc_start: 0.9223 (mmmm) cc_final: 0.8894 (mmmm) REVERT: W 111 GLN cc_start: 0.9225 (pm20) cc_final: 0.8933 (pm20) REVERT: W 219 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.9207 (p) REVERT: X 89 ASP cc_start: 0.8553 (m-30) cc_final: 0.8166 (m-30) REVERT: X 140 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.6967 (p-80) REVERT: X 201 THR cc_start: 0.9509 (m) cc_final: 0.9062 (p) REVERT: Y 128 ASP cc_start: 0.9165 (p0) cc_final: 0.8894 (p0) REVERT: Y 132 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7607 (p0) REVERT: Z 38 MET cc_start: 0.9009 (tpp) cc_final: 0.8662 (tpp) REVERT: Z 83 MET cc_start: 0.9064 (mpp) cc_final: 0.8565 (mpp) REVERT: Z 96 MET cc_start: 0.9246 (tmm) cc_final: 0.8455 (ptm) REVERT: Z 122 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6456 (m-10) REVERT: Z 127 ASN cc_start: 0.8318 (p0) cc_final: 0.7961 (p0) REVERT: Z 128 TYR cc_start: 0.8898 (t80) cc_final: 0.8431 (t80) REVERT: a 59 GLN cc_start: 0.9292 (mm-40) cc_final: 0.8924 (mm-40) REVERT: a 107 ASN cc_start: 0.9000 (m-40) cc_final: 0.8682 (m-40) REVERT: a 122 ILE cc_start: 0.9561 (mp) cc_final: 0.9340 (tp) REVERT: a 148 ASN cc_start: 0.9280 (m-40) cc_final: 0.8862 (m110) REVERT: c 118 GLN cc_start: 0.9572 (tm-30) cc_final: 0.9352 (tm-30) REVERT: d 66 LYS cc_start: 0.9224 (mtpp) cc_final: 0.8848 (ttpp) REVERT: d 81 GLU cc_start: 0.8046 (pm20) cc_final: 0.7766 (pm20) REVERT: d 105 GLU cc_start: 0.9161 (mp0) cc_final: 0.8861 (mp0) REVERT: e 17 ASN cc_start: 0.9233 (t0) cc_final: 0.8980 (t0) REVERT: e 106 ASN cc_start: 0.9229 (m-40) cc_final: 0.8306 (p0) REVERT: f 9 TYR cc_start: 0.9166 (m-80) cc_final: 0.8588 (m-80) REVERT: f 37 LEU cc_start: 0.9523 (mt) cc_final: 0.9289 (mt) REVERT: f 43 THR cc_start: 0.9447 (m) cc_final: 0.9081 (p) REVERT: g 45 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8275 (mm-30) REVERT: g 92 GLU cc_start: 0.8799 (tm-30) cc_final: 0.7918 (pp20) REVERT: g 93 GLU cc_start: 0.8815 (pm20) cc_final: 0.7763 (pm20) REVERT: g 118 GLU cc_start: 0.8836 (pm20) cc_final: 0.8341 (pm20) REVERT: h 60 ASP cc_start: 0.7873 (t70) cc_final: 0.6837 (t70) REVERT: h 62 ASP cc_start: 0.9161 (t0) cc_final: 0.8723 (p0) REVERT: h 63 LEU cc_start: 0.8665 (mp) cc_final: 0.7756 (pp) REVERT: i 9 GLU cc_start: 0.9087 (tp30) cc_final: 0.8636 (tm-30) REVERT: i 69 TYR cc_start: 0.9339 (m-80) cc_final: 0.9100 (m-80) REVERT: i 114 LYS cc_start: 0.8973 (ptpp) cc_final: 0.8749 (ptpp) REVERT: j 108 GLN cc_start: 0.9365 (tp40) cc_final: 0.9146 (tp40) REVERT: k 45 ASN cc_start: 0.8497 (p0) cc_final: 0.8279 (p0) REVERT: k 63 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8890 (mm-30) REVERT: l 48 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8168 (tm-30) REVERT: l 52 LYS cc_start: 0.9493 (mtpp) cc_final: 0.8797 (mmtp) REVERT: m 31 ASP cc_start: 0.9158 (t70) cc_final: 0.8785 (t0) REVERT: m 33 ARG cc_start: 0.8916 (mtm180) cc_final: 0.8666 (mtm-85) REVERT: n 7 ASP cc_start: 0.8263 (m-30) cc_final: 0.7904 (m-30) REVERT: o 46 TYR cc_start: 0.9243 (t80) cc_final: 0.9004 (t80) REVERT: o 52 LYS cc_start: 0.9504 (mttt) cc_final: 0.9025 (mttp) REVERT: o 82 ARG cc_start: 0.8787 (mtp85) cc_final: 0.7556 (mmm-85) REVERT: o 85 LYS cc_start: 0.9261 (mttp) cc_final: 0.8988 (mttm) REVERT: o 86 LYS cc_start: 0.9138 (ttpp) cc_final: 0.8473 (ttmm) REVERT: p 53 ASP cc_start: 0.8839 (t0) cc_final: 0.8597 (t0) REVERT: q 14 GLU cc_start: 0.8979 (pt0) cc_final: 0.8630 (pm20) REVERT: q 31 GLU cc_start: 0.8937 (pm20) cc_final: 0.8697 (pm20) REVERT: s 38 GLN cc_start: 0.9250 (tp40) cc_final: 0.8995 (tp-100) REVERT: t 24 MET cc_start: 0.8629 (mtp) cc_final: 0.8216 (mtt) REVERT: u 17 ASN cc_start: 0.9132 (t0) cc_final: 0.8666 (t0) REVERT: u 22 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7663 (mmm) REVERT: u 35 LYS cc_start: 0.9480 (ttmt) cc_final: 0.9231 (ttmm) REVERT: u 36 VAL cc_start: 0.8870 (m) cc_final: 0.8626 (p) REVERT: u 43 LYS cc_start: 0.9079 (mttt) cc_final: 0.8750 (mmmt) REVERT: u 46 LYS cc_start: 0.9506 (ptmt) cc_final: 0.9140 (mtpp) REVERT: v 5 GLU cc_start: 0.9276 (mp0) cc_final: 0.8701 (mp0) REVERT: v 15 GLU cc_start: 0.9480 (mm-30) cc_final: 0.9191 (mm-30) REVERT: v 23 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8244 (tm-30) REVERT: w 32 ASN cc_start: 0.9395 (t0) cc_final: 0.9027 (t0) REVERT: w 57 LYS cc_start: 0.9135 (tmmt) cc_final: 0.8843 (tmtt) outliers start: 159 outliers final: 127 residues processed: 846 average time/residue: 0.9329 time to fit residues: 1347.7804 Evaluate side-chains 873 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 741 time to evaluate : 3.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 25 THR Chi-restraints excluded: chain b residue 55 TYR Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 203 ILE Chi-restraints excluded: chain W residue 219 THR Chi-restraints excluded: chain W residue 229 ASP Chi-restraints excluded: chain W residue 254 THR Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 21 ASP Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain Y residue 120 ASP Chi-restraints excluded: chain Y residue 130 THR Chi-restraints excluded: chain Y residue 132 ASP Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Z residue 17 MET Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 122 PHE Chi-restraints excluded: chain Z residue 144 ASP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 173 VAL Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 95 TYR Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 53 ASP Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 130 GLU Chi-restraints excluded: chain c residue 144 ARG Chi-restraints excluded: chain d residue 18 GLU Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 80 ASP Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 76 VAL Chi-restraints excluded: chain f residue 35 GLN Chi-restraints excluded: chain f residue 54 MET Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 20 LEU Chi-restraints excluded: chain g residue 22 THR Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 3 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 THR Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 106 VAL Chi-restraints excluded: chain i residue 13 LYS Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 47 GLU Chi-restraints excluded: chain i residue 60 GLU Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 71 VAL Chi-restraints excluded: chain i residue 116 ILE Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 8 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 17 VAL Chi-restraints excluded: chain j residue 42 SER Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 50 ASN Chi-restraints excluded: chain k residue 53 VAL Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain l residue 65 ASP Chi-restraints excluded: chain l residue 67 ASN Chi-restraints excluded: chain l residue 73 GLN Chi-restraints excluded: chain m residue 6 ASP Chi-restraints excluded: chain m residue 22 THR Chi-restraints excluded: chain m residue 35 ASN Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 48 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 80 PHE Chi-restraints excluded: chain o residue 92 VAL Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 21 LYS Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 64 ASN Chi-restraints excluded: chain t residue 25 VAL Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 22 MET Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain v residue 4 ASN Chi-restraints excluded: chain v residue 8 ASP Chi-restraints excluded: chain v residue 21 LEU Chi-restraints excluded: chain v residue 34 THR Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 29 LYS Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 10.0000 chunk 543 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 354 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 603 optimal weight: 9.9990 chunk 501 optimal weight: 1.9990 chunk 279 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 59 GLN ** i 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 32 HIS w 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 99690 Z= 0.388 Angle : 0.659 11.877 149672 Z= 0.336 Chirality : 0.039 0.315 19191 Planarity : 0.004 0.050 7613 Dihedral : 23.929 179.671 51131 Min Nonbonded Distance : 1.110 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 6.11 % Allowed : 25.38 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.14), residues: 3288 helix: 0.32 (0.18), residues: 930 sheet: -1.42 (0.20), residues: 623 loop : -2.31 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP W 213 HIS 0.008 0.001 HIS w 52 PHE 0.024 0.002 PHE B 172 TYR 0.023 0.002 TYR Z 97 ARG 0.009 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 771 time to evaluate : 4.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 PHE cc_start: 0.8874 (t80) cc_final: 0.8616 (t80) REVERT: B 172 PHE cc_start: 0.9267 (m-80) cc_final: 0.8923 (m-80) REVERT: A 156 ARG cc_start: 0.9205 (mmm160) cc_final: 0.8910 (mmm160) REVERT: A 157 GLN cc_start: 0.9337 (mm-40) cc_final: 0.9076 (mm-40) REVERT: A 172 PHE cc_start: 0.9452 (t80) cc_final: 0.9014 (t80) REVERT: A 173 TYR cc_start: 0.9245 (m-80) cc_final: 0.8684 (m-80) REVERT: A 178 GLN cc_start: 0.9227 (tp-100) cc_final: 0.8946 (tp-100) REVERT: b 59 MET cc_start: 0.6777 (tpp) cc_final: 0.6373 (ppp) REVERT: b 126 LEU cc_start: 0.8671 (mm) cc_final: 0.8396 (pt) REVERT: W 28 LYS cc_start: 0.9242 (mmmm) cc_final: 0.8901 (mmmm) REVERT: W 111 GLN cc_start: 0.9227 (pm20) cc_final: 0.8943 (pm20) REVERT: W 219 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.9214 (p) REVERT: X 89 ASP cc_start: 0.8572 (m-30) cc_final: 0.8193 (m-30) REVERT: X 140 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.6999 (p-80) REVERT: X 201 THR cc_start: 0.9512 (m) cc_final: 0.9062 (p) REVERT: Y 128 ASP cc_start: 0.9179 (p0) cc_final: 0.8905 (p0) REVERT: Y 132 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7514 (p0) REVERT: Z 38 MET cc_start: 0.8960 (tpp) cc_final: 0.8619 (tpp) REVERT: Z 83 MET cc_start: 0.9054 (mpp) cc_final: 0.8557 (mpp) REVERT: Z 96 MET cc_start: 0.9285 (tmm) cc_final: 0.8565 (ptm) REVERT: Z 122 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.6299 (m-10) REVERT: Z 127 ASN cc_start: 0.8393 (p0) cc_final: 0.7951 (p0) REVERT: Z 128 TYR cc_start: 0.8876 (t80) cc_final: 0.8419 (t80) REVERT: a 42 MET cc_start: 0.8682 (tpp) cc_final: 0.7739 (tpp) REVERT: a 59 GLN cc_start: 0.9295 (mm-40) cc_final: 0.8928 (mm-40) REVERT: a 107 ASN cc_start: 0.9010 (m-40) cc_final: 0.8703 (m-40) REVERT: a 110 TYR cc_start: 0.9192 (m-10) cc_final: 0.8763 (m-10) REVERT: a 122 ILE cc_start: 0.9568 (mp) cc_final: 0.9347 (tp) REVERT: a 148 ASN cc_start: 0.9294 (m-40) cc_final: 0.8870 (m110) REVERT: c 118 GLN cc_start: 0.9571 (tm-30) cc_final: 0.9351 (tm-30) REVERT: d 66 LYS cc_start: 0.9258 (mtpp) cc_final: 0.8930 (ttpp) REVERT: d 81 GLU cc_start: 0.8009 (pm20) cc_final: 0.7762 (pm20) REVERT: d 105 GLU cc_start: 0.9176 (mp0) cc_final: 0.8888 (mp0) REVERT: e 17 ASN cc_start: 0.9248 (t0) cc_final: 0.8995 (t0) REVERT: e 106 ASN cc_start: 0.9230 (m-40) cc_final: 0.8308 (p0) REVERT: f 9 TYR cc_start: 0.9172 (m-80) cc_final: 0.8457 (m-80) REVERT: f 37 LEU cc_start: 0.9516 (mt) cc_final: 0.9277 (mt) REVERT: f 43 THR cc_start: 0.9455 (m) cc_final: 0.9105 (p) REVERT: g 45 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8208 (mm-30) REVERT: g 73 GLU cc_start: 0.9136 (pm20) cc_final: 0.8691 (pm20) REVERT: g 92 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.7898 (pp20) REVERT: g 93 GLU cc_start: 0.8867 (pm20) cc_final: 0.7984 (pm20) REVERT: g 118 GLU cc_start: 0.8865 (pm20) cc_final: 0.8341 (pm20) REVERT: h 62 ASP cc_start: 0.9095 (t0) cc_final: 0.8771 (p0) REVERT: i 9 GLU cc_start: 0.9100 (tp30) cc_final: 0.8647 (tm-30) REVERT: i 114 LYS cc_start: 0.8986 (ptpp) cc_final: 0.8733 (ptpp) REVERT: j 108 GLN cc_start: 0.9377 (tp40) cc_final: 0.9168 (tp40) REVERT: k 39 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8338 (pp) REVERT: k 45 ASN cc_start: 0.8544 (p0) cc_final: 0.8342 (p0) REVERT: l 48 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8144 (tm-30) REVERT: l 52 LYS cc_start: 0.9527 (mtpp) cc_final: 0.8994 (mmtp) REVERT: m 31 ASP cc_start: 0.9172 (t70) cc_final: 0.8804 (t0) REVERT: m 33 ARG cc_start: 0.8914 (mtm180) cc_final: 0.8667 (mtm-85) REVERT: n 7 ASP cc_start: 0.8282 (m-30) cc_final: 0.7900 (m-30) REVERT: n 40 MET cc_start: 0.9055 (mmm) cc_final: 0.8326 (mmm) REVERT: n 77 GLU cc_start: 0.8855 (tp30) cc_final: 0.8295 (mm-30) REVERT: o 46 TYR cc_start: 0.9269 (t80) cc_final: 0.8945 (t80) REVERT: o 52 LYS cc_start: 0.9508 (mttt) cc_final: 0.9030 (mttp) REVERT: o 78 GLU cc_start: 0.8579 (pm20) cc_final: 0.8286 (mp0) REVERT: o 82 ARG cc_start: 0.8743 (mtp85) cc_final: 0.7509 (mmm-85) REVERT: o 85 LYS cc_start: 0.9256 (mttp) cc_final: 0.8978 (mttm) REVERT: o 86 LYS cc_start: 0.9159 (ttpp) cc_final: 0.8445 (ttmm) REVERT: p 36 MET cc_start: 0.9044 (tpp) cc_final: 0.8199 (mmm) REVERT: p 53 ASP cc_start: 0.8883 (t0) cc_final: 0.8645 (t0) REVERT: q 14 GLU cc_start: 0.8711 (pt0) cc_final: 0.8309 (pm20) REVERT: q 31 GLU cc_start: 0.8996 (pm20) cc_final: 0.8759 (pm20) REVERT: s 38 GLN cc_start: 0.9256 (tp40) cc_final: 0.9007 (tp-100) REVERT: t 24 MET cc_start: 0.8681 (mtp) cc_final: 0.8307 (mtp) REVERT: u 17 ASN cc_start: 0.9138 (t0) cc_final: 0.8691 (t0) REVERT: u 35 LYS cc_start: 0.9475 (ttmt) cc_final: 0.9223 (ttmm) REVERT: u 36 VAL cc_start: 0.8819 (m) cc_final: 0.8598 (p) REVERT: u 43 LYS cc_start: 0.9080 (mttt) cc_final: 0.8731 (mmmt) REVERT: u 46 LYS cc_start: 0.9553 (ptmt) cc_final: 0.9161 (mtpp) REVERT: v 5 GLU cc_start: 0.9245 (mp0) cc_final: 0.8682 (mp0) REVERT: v 15 GLU cc_start: 0.9483 (mm-30) cc_final: 0.9230 (tm-30) REVERT: v 23 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8261 (tm-30) REVERT: w 32 ASN cc_start: 0.9429 (OUTLIER) cc_final: 0.9033 (t0) REVERT: w 57 LYS cc_start: 0.9137 (tmmt) cc_final: 0.8871 (tmtt) outliers start: 169 outliers final: 139 residues processed: 855 average time/residue: 0.8846 time to fit residues: 1285.3196 Evaluate side-chains 892 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 746 time to evaluate : 3.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 25 THR Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 55 TYR Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 203 ILE Chi-restraints excluded: chain W residue 219 THR Chi-restraints excluded: chain W residue 229 ASP Chi-restraints excluded: chain W residue 254 THR Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 21 ASP Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain X residue 192 VAL Chi-restraints excluded: chain Y residue 35 ASP Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 120 ASP Chi-restraints excluded: chain Y residue 130 THR Chi-restraints excluded: chain Y residue 132 ASP Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 183 VAL Chi-restraints excluded: chain Z residue 17 MET Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 122 PHE Chi-restraints excluded: chain Z residue 144 ASP Chi-restraints excluded: chain Z residue 159 THR Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 173 VAL Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 95 TYR Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 53 ASP Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 130 GLU Chi-restraints excluded: chain d residue 18 GLU Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 80 ASP Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 76 VAL Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain f residue 54 MET Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 127 ILE Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 20 LEU Chi-restraints excluded: chain g residue 22 THR Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain g residue 92 GLU Chi-restraints excluded: chain g residue 99 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 3 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 THR Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 106 VAL Chi-restraints excluded: chain i residue 13 LYS Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 60 GLU Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 71 VAL Chi-restraints excluded: chain i residue 116 ILE Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 8 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 42 SER Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 50 ASN Chi-restraints excluded: chain k residue 53 VAL Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 100 ILE Chi-restraints excluded: chain l residue 65 ASP Chi-restraints excluded: chain l residue 67 ASN Chi-restraints excluded: chain l residue 73 GLN Chi-restraints excluded: chain m residue 6 ASP Chi-restraints excluded: chain m residue 35 ASN Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 48 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 80 PHE Chi-restraints excluded: chain o residue 92 VAL Chi-restraints excluded: chain p residue 11 MET Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain p residue 27 MET Chi-restraints excluded: chain q residue 23 LYS Chi-restraints excluded: chain q residue 39 ASP Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 64 ASN Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 25 VAL Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain v residue 4 ASN Chi-restraints excluded: chain v residue 8 ASP Chi-restraints excluded: chain v residue 21 LEU Chi-restraints excluded: chain v residue 34 THR Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 29 LYS Chi-restraints excluded: chain w residue 32 ASN Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 343 optimal weight: 6.9990 chunk 440 optimal weight: 5.9990 chunk 341 optimal weight: 6.9990 chunk 508 optimal weight: 5.9990 chunk 337 optimal weight: 10.0000 chunk 601 optimal weight: 5.9990 chunk 376 optimal weight: 4.9990 chunk 366 optimal weight: 4.9990 chunk 277 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 59 GLN ** i 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 99690 Z= 0.298 Angle : 0.621 12.907 149672 Z= 0.318 Chirality : 0.037 0.317 19191 Planarity : 0.004 0.052 7613 Dihedral : 23.901 179.310 51131 Min Nonbonded Distance : 1.127 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.36 % Favored : 92.61 % Rotamer: Outliers : 5.39 % Allowed : 27.55 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.14), residues: 3288 helix: 0.43 (0.18), residues: 928 sheet: -1.31 (0.20), residues: 628 loop : -2.26 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP W 213 HIS 0.015 0.001 HIS e 4 PHE 0.024 0.001 PHE B 172 TYR 0.020 0.001 TYR g 65 ARG 0.009 0.000 ARG j 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 793 time to evaluate : 4.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 PHE cc_start: 0.8886 (t80) cc_final: 0.8619 (t80) REVERT: B 172 PHE cc_start: 0.9304 (m-80) cc_final: 0.9031 (m-80) REVERT: A 122 THR cc_start: 0.8765 (t) cc_final: 0.8542 (p) REVERT: A 125 GLU cc_start: 0.9639 (mm-30) cc_final: 0.9300 (mp0) REVERT: A 172 PHE cc_start: 0.9465 (t80) cc_final: 0.9145 (t80) REVERT: A 178 GLN cc_start: 0.9256 (tp-100) cc_final: 0.8990 (tp-100) REVERT: b 59 MET cc_start: 0.6688 (tpp) cc_final: 0.6346 (ppp) REVERT: b 126 LEU cc_start: 0.8666 (mm) cc_final: 0.8403 (pt) REVERT: W 28 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8892 (mmmm) REVERT: W 111 GLN cc_start: 0.9200 (pm20) cc_final: 0.8927 (pm20) REVERT: W 219 THR cc_start: 0.9415 (OUTLIER) cc_final: 0.9185 (p) REVERT: X 88 MET cc_start: 0.8621 (mtt) cc_final: 0.8367 (mtt) REVERT: X 89 ASP cc_start: 0.8538 (m-30) cc_final: 0.8116 (m-30) REVERT: X 140 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.6851 (p-80) REVERT: X 201 THR cc_start: 0.9509 (m) cc_final: 0.9069 (p) REVERT: Y 7 TYR cc_start: 0.9101 (m-10) cc_final: 0.8808 (m-80) REVERT: Y 128 ASP cc_start: 0.9168 (p0) cc_final: 0.8892 (p0) REVERT: Y 132 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7571 (p0) REVERT: Z 38 MET cc_start: 0.8979 (tpp) cc_final: 0.8621 (tpp) REVERT: Z 83 MET cc_start: 0.9104 (mpp) cc_final: 0.8675 (mpp) REVERT: Z 96 MET cc_start: 0.9237 (tmm) cc_final: 0.8559 (ptm) REVERT: Z 122 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.6219 (m-10) REVERT: Z 127 ASN cc_start: 0.8418 (p0) cc_final: 0.7983 (p0) REVERT: Z 128 TYR cc_start: 0.8773 (t80) cc_final: 0.8419 (t80) REVERT: a 59 GLN cc_start: 0.9287 (mm-40) cc_final: 0.8911 (mm-40) REVERT: a 107 ASN cc_start: 0.8975 (m-40) cc_final: 0.8715 (m-40) REVERT: a 110 TYR cc_start: 0.9185 (m-10) cc_final: 0.8832 (m-10) REVERT: a 122 ILE cc_start: 0.9563 (mp) cc_final: 0.9362 (tp) REVERT: a 148 ASN cc_start: 0.9306 (m-40) cc_final: 0.8873 (m110) REVERT: c 118 GLN cc_start: 0.9583 (tm-30) cc_final: 0.9355 (tm-30) REVERT: d 53 LYS cc_start: 0.9327 (mmmm) cc_final: 0.9052 (mmmt) REVERT: d 66 LYS cc_start: 0.9252 (mtpp) cc_final: 0.8778 (ttpp) REVERT: d 81 GLU cc_start: 0.8040 (pm20) cc_final: 0.7749 (pm20) REVERT: d 105 GLU cc_start: 0.9175 (mp0) cc_final: 0.8884 (mp0) REVERT: e 17 ASN cc_start: 0.9258 (t0) cc_final: 0.9013 (t0) REVERT: e 73 GLU cc_start: 0.8336 (pm20) cc_final: 0.8132 (pm20) REVERT: e 106 ASN cc_start: 0.9210 (m-40) cc_final: 0.8312 (p0) REVERT: f 9 TYR cc_start: 0.9165 (m-80) cc_final: 0.8592 (m-80) REVERT: f 37 LEU cc_start: 0.9513 (mt) cc_final: 0.9290 (mt) REVERT: f 43 THR cc_start: 0.9452 (OUTLIER) cc_final: 0.9111 (p) REVERT: g 45 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8246 (mm-30) REVERT: g 72 ASN cc_start: 0.8904 (t0) cc_final: 0.8663 (t0) REVERT: g 92 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.7892 (pp20) REVERT: g 93 GLU cc_start: 0.8890 (pm20) cc_final: 0.8013 (pm20) REVERT: g 118 GLU cc_start: 0.8845 (pm20) cc_final: 0.8318 (pm20) REVERT: h 60 ASP cc_start: 0.8075 (t70) cc_final: 0.7094 (t70) REVERT: h 62 ASP cc_start: 0.9078 (t0) cc_final: 0.8664 (p0) REVERT: h 63 LEU cc_start: 0.8686 (mp) cc_final: 0.7743 (pp) REVERT: i 9 GLU cc_start: 0.9115 (tp30) cc_final: 0.8662 (tm-30) REVERT: i 114 LYS cc_start: 0.8919 (ptpp) cc_final: 0.8674 (ptpp) REVERT: j 108 GLN cc_start: 0.9356 (tp40) cc_final: 0.9144 (tp40) REVERT: k 39 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8333 (pp) REVERT: l 48 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8146 (tm-30) REVERT: l 52 LYS cc_start: 0.9525 (mtpp) cc_final: 0.8877 (mmtp) REVERT: m 5 ARG cc_start: 0.9584 (OUTLIER) cc_final: 0.9008 (mtt90) REVERT: m 31 ASP cc_start: 0.9168 (t70) cc_final: 0.8755 (t70) REVERT: m 33 ARG cc_start: 0.8885 (mtm180) cc_final: 0.8663 (mtm-85) REVERT: m 72 MET cc_start: 0.8946 (mtp) cc_final: 0.8681 (mmm) REVERT: n 7 ASP cc_start: 0.8239 (m-30) cc_final: 0.7890 (m-30) REVERT: n 77 GLU cc_start: 0.8833 (tp30) cc_final: 0.8312 (mm-30) REVERT: o 46 TYR cc_start: 0.9186 (t80) cc_final: 0.8922 (t80) REVERT: o 52 LYS cc_start: 0.9507 (mttt) cc_final: 0.9077 (mttp) REVERT: o 78 GLU cc_start: 0.8540 (pm20) cc_final: 0.8228 (mp0) REVERT: o 82 ARG cc_start: 0.8782 (mtp85) cc_final: 0.7531 (mmm-85) REVERT: o 85 LYS cc_start: 0.9246 (mttp) cc_final: 0.8978 (mttm) REVERT: o 86 LYS cc_start: 0.9157 (ttpp) cc_final: 0.8532 (ttmm) REVERT: p 53 ASP cc_start: 0.8854 (t0) cc_final: 0.8611 (t0) REVERT: q 14 GLU cc_start: 0.8717 (pt0) cc_final: 0.8014 (pm20) REVERT: q 31 GLU cc_start: 0.9010 (pm20) cc_final: 0.8775 (pm20) REVERT: s 38 GLN cc_start: 0.9230 (tp40) cc_final: 0.8983 (tp-100) REVERT: s 56 LYS cc_start: 0.9494 (ttpt) cc_final: 0.9287 (ttpt) REVERT: u 17 ASN cc_start: 0.9117 (t0) cc_final: 0.8691 (t0) REVERT: u 35 LYS cc_start: 0.9485 (ttmt) cc_final: 0.9251 (ttmm) REVERT: u 43 LYS cc_start: 0.9082 (mttt) cc_final: 0.8709 (mmmt) REVERT: u 46 LYS cc_start: 0.9536 (ptmt) cc_final: 0.9174 (mtpp) REVERT: v 5 GLU cc_start: 0.9233 (mp0) cc_final: 0.8660 (mp0) REVERT: v 8 ASP cc_start: 0.9560 (OUTLIER) cc_final: 0.9085 (t0) REVERT: v 15 GLU cc_start: 0.9472 (mm-30) cc_final: 0.9213 (tm-30) REVERT: v 23 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8320 (tm-30) REVERT: w 30 LYS cc_start: 0.9319 (mtpt) cc_final: 0.8859 (ttpp) REVERT: w 32 ASN cc_start: 0.9368 (OUTLIER) cc_final: 0.9018 (t0) REVERT: w 57 LYS cc_start: 0.9124 (tmmt) cc_final: 0.8859 (tmtt) outliers start: 149 outliers final: 123 residues processed: 866 average time/residue: 0.8872 time to fit residues: 1303.6528 Evaluate side-chains 888 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 755 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 25 THR Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 55 TYR Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 203 ILE Chi-restraints excluded: chain W residue 219 THR Chi-restraints excluded: chain W residue 229 ASP Chi-restraints excluded: chain W residue 254 THR Chi-restraints excluded: chain X residue 21 ASP Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain X residue 192 VAL Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 120 ASP Chi-restraints excluded: chain Y residue 130 THR Chi-restraints excluded: chain Y residue 132 ASP Chi-restraints excluded: chain Y residue 183 VAL Chi-restraints excluded: chain Z residue 17 MET Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 122 PHE Chi-restraints excluded: chain Z residue 141 ILE Chi-restraints excluded: chain Z residue 144 ASP Chi-restraints excluded: chain Z residue 159 THR Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 173 VAL Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 95 TYR Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 53 ASP Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 130 GLU Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 80 ASP Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 76 VAL Chi-restraints excluded: chain f residue 35 GLN Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 54 MET Chi-restraints excluded: chain f residue 127 ILE Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 22 THR Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain g residue 89 THR Chi-restraints excluded: chain g residue 92 GLU Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 3 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 THR Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 106 VAL Chi-restraints excluded: chain i residue 13 LYS Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 71 VAL Chi-restraints excluded: chain i residue 116 ILE Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 50 ASN Chi-restraints excluded: chain k residue 53 VAL Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain l residue 65 ASP Chi-restraints excluded: chain l residue 67 ASN Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 6 ASP Chi-restraints excluded: chain m residue 35 ASN Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 80 PHE Chi-restraints excluded: chain o residue 92 VAL Chi-restraints excluded: chain p residue 11 MET Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain q residue 11 GLU Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 23 LYS Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 64 ASN Chi-restraints excluded: chain t residue 25 VAL Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain v residue 4 ASN Chi-restraints excluded: chain v residue 8 ASP Chi-restraints excluded: chain v residue 34 THR Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 29 LYS Chi-restraints excluded: chain w residue 32 ASN Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 9.9990 chunk 240 optimal weight: 30.0000 chunk 359 optimal weight: 0.5980 chunk 181 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 382 optimal weight: 6.9990 chunk 409 optimal weight: 0.0570 chunk 297 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 472 optimal weight: 3.9990 overall best weight: 4.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 99690 Z= 0.247 Angle : 0.600 13.074 149672 Z= 0.307 Chirality : 0.036 0.309 19191 Planarity : 0.004 0.093 7613 Dihedral : 23.871 179.570 51131 Min Nonbonded Distance : 1.133 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 5.21 % Allowed : 28.27 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.14), residues: 3288 helix: 0.48 (0.18), residues: 930 sheet: -1.15 (0.21), residues: 610 loop : -2.19 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP W 213 HIS 0.013 0.001 HIS e 4 PHE 0.023 0.001 PHE Z 138 TYR 0.028 0.001 TYR Z 97 ARG 0.018 0.000 ARG m 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 787 time to evaluate : 4.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 PHE cc_start: 0.8891 (t80) cc_final: 0.8633 (t80) REVERT: B 172 PHE cc_start: 0.9301 (m-80) cc_final: 0.9067 (m-80) REVERT: A 125 GLU cc_start: 0.9641 (mm-30) cc_final: 0.9325 (mp0) REVERT: A 172 PHE cc_start: 0.9457 (t80) cc_final: 0.9038 (t80) REVERT: A 173 TYR cc_start: 0.9272 (m-80) cc_final: 0.8773 (m-80) REVERT: A 178 GLN cc_start: 0.9259 (tp-100) cc_final: 0.8991 (tp-100) REVERT: b 31 ARG cc_start: 0.8891 (mmm160) cc_final: 0.8498 (mmp80) REVERT: b 59 MET cc_start: 0.6793 (tpp) cc_final: 0.6510 (ppp) REVERT: b 126 LEU cc_start: 0.8676 (mm) cc_final: 0.8354 (pt) REVERT: W 28 LYS cc_start: 0.9223 (mmmm) cc_final: 0.8896 (mmmm) REVERT: W 111 GLN cc_start: 0.9166 (pm20) cc_final: 0.8910 (pm20) REVERT: X 88 MET cc_start: 0.8618 (mtt) cc_final: 0.8412 (mtt) REVERT: X 89 ASP cc_start: 0.8553 (m-30) cc_final: 0.8127 (m-30) REVERT: X 140 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.6749 (p-80) REVERT: X 201 THR cc_start: 0.9510 (m) cc_final: 0.9073 (p) REVERT: Y 7 TYR cc_start: 0.9097 (m-10) cc_final: 0.8829 (m-80) REVERT: Y 128 ASP cc_start: 0.9158 (p0) cc_final: 0.8888 (p0) REVERT: Y 132 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7576 (p0) REVERT: Z 38 MET cc_start: 0.9028 (tpp) cc_final: 0.8650 (tpp) REVERT: Z 83 MET cc_start: 0.9108 (mpp) cc_final: 0.8664 (mpp) REVERT: Z 96 MET cc_start: 0.9206 (tmm) cc_final: 0.8847 (ptm) REVERT: Z 122 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.6213 (m-10) REVERT: Z 128 TYR cc_start: 0.8759 (t80) cc_final: 0.8410 (t80) REVERT: a 39 HIS cc_start: 0.9243 (t-90) cc_final: 0.8814 (t70) REVERT: a 48 ASP cc_start: 0.8815 (p0) cc_final: 0.8606 (p0) REVERT: a 59 GLN cc_start: 0.9272 (mm-40) cc_final: 0.8892 (mm-40) REVERT: a 107 ASN cc_start: 0.8987 (m-40) cc_final: 0.8748 (m-40) REVERT: a 110 TYR cc_start: 0.9203 (m-10) cc_final: 0.8869 (m-10) REVERT: a 148 ASN cc_start: 0.9297 (m-40) cc_final: 0.8860 (m110) REVERT: c 118 GLN cc_start: 0.9571 (tm-30) cc_final: 0.9339 (tm-30) REVERT: d 53 LYS cc_start: 0.9327 (mmmm) cc_final: 0.9009 (mmmt) REVERT: d 66 LYS cc_start: 0.9253 (mtpp) cc_final: 0.8794 (ttpp) REVERT: d 81 GLU cc_start: 0.8110 (pm20) cc_final: 0.7810 (pm20) REVERT: d 105 GLU cc_start: 0.9186 (mp0) cc_final: 0.8895 (mp0) REVERT: e 17 ASN cc_start: 0.9232 (t0) cc_final: 0.8986 (t0) REVERT: e 71 ARG cc_start: 0.9357 (tpt-90) cc_final: 0.9129 (tpp80) REVERT: e 106 ASN cc_start: 0.9193 (m-40) cc_final: 0.8305 (p0) REVERT: f 9 TYR cc_start: 0.9156 (m-80) cc_final: 0.8591 (m-80) REVERT: f 37 LEU cc_start: 0.9503 (mt) cc_final: 0.9280 (mt) REVERT: f 43 THR cc_start: 0.9446 (OUTLIER) cc_final: 0.9094 (p) REVERT: g 45 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8232 (mm-30) REVERT: g 72 ASN cc_start: 0.8772 (t0) cc_final: 0.8235 (t0) REVERT: g 92 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.7868 (pp20) REVERT: g 93 GLU cc_start: 0.8904 (pm20) cc_final: 0.8019 (pm20) REVERT: g 118 GLU cc_start: 0.8791 (pm20) cc_final: 0.8328 (pm20) REVERT: h 60 ASP cc_start: 0.8080 (t70) cc_final: 0.7072 (t70) REVERT: h 62 ASP cc_start: 0.9108 (t0) cc_final: 0.8747 (p0) REVERT: h 63 LEU cc_start: 0.8683 (mp) cc_final: 0.7717 (pp) REVERT: i 9 GLU cc_start: 0.9113 (tp30) cc_final: 0.8659 (tm-30) REVERT: i 47 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7809 (tp30) REVERT: i 114 LYS cc_start: 0.8882 (ptpp) cc_final: 0.8633 (ptpp) REVERT: j 108 GLN cc_start: 0.9256 (tp40) cc_final: 0.8556 (tp40) REVERT: k 39 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8293 (pp) REVERT: l 48 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8139 (tm-30) REVERT: l 52 LYS cc_start: 0.9539 (mtpp) cc_final: 0.9008 (mmtp) REVERT: m 5 ARG cc_start: 0.9570 (OUTLIER) cc_final: 0.8992 (mtt90) REVERT: m 31 ASP cc_start: 0.9166 (t70) cc_final: 0.8759 (t70) REVERT: m 33 ARG cc_start: 0.8865 (mtm180) cc_final: 0.8653 (mtm-85) REVERT: m 41 ASP cc_start: 0.8698 (p0) cc_final: 0.8465 (p0) REVERT: m 72 MET cc_start: 0.8889 (mtp) cc_final: 0.8640 (mmm) REVERT: n 7 ASP cc_start: 0.8243 (m-30) cc_final: 0.7892 (m-30) REVERT: n 77 GLU cc_start: 0.8826 (tp30) cc_final: 0.8344 (mm-30) REVERT: o 19 LYS cc_start: 0.9253 (mtmm) cc_final: 0.9011 (mmtm) REVERT: o 46 TYR cc_start: 0.9094 (t80) cc_final: 0.8872 (t80) REVERT: o 52 LYS cc_start: 0.9511 (mttt) cc_final: 0.9047 (mttp) REVERT: o 78 GLU cc_start: 0.8506 (pm20) cc_final: 0.8222 (mp0) REVERT: o 82 ARG cc_start: 0.8797 (mtp85) cc_final: 0.7534 (mmm-85) REVERT: o 85 LYS cc_start: 0.9226 (mttp) cc_final: 0.8960 (mttm) REVERT: o 86 LYS cc_start: 0.9165 (ttpp) cc_final: 0.8609 (ttmm) REVERT: p 53 ASP cc_start: 0.8918 (t0) cc_final: 0.8665 (t0) REVERT: q 14 GLU cc_start: 0.9003 (pt0) cc_final: 0.8422 (pm20) REVERT: q 31 GLU cc_start: 0.8993 (pm20) cc_final: 0.8768 (pm20) REVERT: q 38 ARG cc_start: 0.8968 (ptm160) cc_final: 0.8342 (ptm160) REVERT: s 38 GLN cc_start: 0.9198 (tp40) cc_final: 0.8959 (tp-100) REVERT: s 56 LYS cc_start: 0.9490 (ttpt) cc_final: 0.9272 (ttpt) REVERT: u 17 ASN cc_start: 0.9134 (t0) cc_final: 0.8759 (t0) REVERT: u 43 LYS cc_start: 0.9054 (mttt) cc_final: 0.8707 (mmmt) REVERT: u 46 LYS cc_start: 0.9527 (ptmt) cc_final: 0.9310 (mtmm) REVERT: v 5 GLU cc_start: 0.9226 (mp0) cc_final: 0.8490 (mp0) REVERT: v 8 ASP cc_start: 0.9563 (OUTLIER) cc_final: 0.9126 (t0) REVERT: v 15 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9194 (tm-30) REVERT: v 16 GLN cc_start: 0.9481 (mm110) cc_final: 0.8726 (mm-40) REVERT: v 23 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8291 (tm-30) REVERT: w 57 LYS cc_start: 0.9124 (tmmt) cc_final: 0.8853 (tmtt) outliers start: 144 outliers final: 121 residues processed: 859 average time/residue: 0.8830 time to fit residues: 1289.3094 Evaluate side-chains 902 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 773 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 25 THR Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 55 TYR Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 203 ILE Chi-restraints excluded: chain W residue 229 ASP Chi-restraints excluded: chain W residue 254 THR Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 21 ASP Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain X residue 192 VAL Chi-restraints excluded: chain Y residue 35 ASP Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 120 ASP Chi-restraints excluded: chain Y residue 130 THR Chi-restraints excluded: chain Y residue 132 ASP Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 183 VAL Chi-restraints excluded: chain Z residue 17 MET Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 122 PHE Chi-restraints excluded: chain Z residue 141 ILE Chi-restraints excluded: chain Z residue 144 ASP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 173 VAL Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 95 TYR Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain c residue 6 MET Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 53 ASP Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 130 GLU Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 80 ASP Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain g residue 75 ASN Chi-restraints excluded: chain g residue 92 GLU Chi-restraints excluded: chain g residue 99 THR Chi-restraints excluded: chain h residue 3 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 THR Chi-restraints excluded: chain h residue 106 VAL Chi-restraints excluded: chain i residue 13 LYS Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 116 ILE Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain j residue 92 ARG Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 50 ASN Chi-restraints excluded: chain k residue 53 VAL Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain l residue 65 ASP Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 6 ASP Chi-restraints excluded: chain m residue 35 ASN Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 80 PHE Chi-restraints excluded: chain o residue 92 VAL Chi-restraints excluded: chain p residue 11 MET Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 23 LYS Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 64 ASN Chi-restraints excluded: chain t residue 25 VAL Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain v residue 4 ASN Chi-restraints excluded: chain v residue 8 ASP Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 6.9990 chunk 576 optimal weight: 2.9990 chunk 525 optimal weight: 8.9990 chunk 560 optimal weight: 5.9990 chunk 337 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 440 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 506 optimal weight: 8.9990 chunk 530 optimal weight: 8.9990 chunk 558 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 GLN ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 38 GLN ** i 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 99690 Z= 0.369 Angle : 0.653 13.791 149672 Z= 0.332 Chirality : 0.038 0.308 19191 Planarity : 0.005 0.117 7613 Dihedral : 23.861 179.615 51131 Min Nonbonded Distance : 1.110 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.91 % Favored : 92.03 % Rotamer: Outliers : 5.39 % Allowed : 28.71 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.14), residues: 3288 helix: 0.38 (0.18), residues: 929 sheet: -1.23 (0.20), residues: 625 loop : -2.20 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP W 213 HIS 0.010 0.001 HIS e 4 PHE 0.024 0.002 PHE Z 59 TYR 0.032 0.002 TYR Z 97 ARG 0.010 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 757 time to evaluate : 4.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 PHE cc_start: 0.8893 (t80) cc_final: 0.8658 (t80) REVERT: B 172 PHE cc_start: 0.9305 (m-80) cc_final: 0.9076 (m-80) REVERT: A 125 GLU cc_start: 0.9640 (mm-30) cc_final: 0.9299 (mp0) REVERT: A 140 ARG cc_start: 0.9076 (mtp85) cc_final: 0.8475 (ptm160) REVERT: A 172 PHE cc_start: 0.9454 (t80) cc_final: 0.9030 (t80) REVERT: A 173 TYR cc_start: 0.9241 (m-80) cc_final: 0.8730 (m-80) REVERT: A 178 GLN cc_start: 0.9256 (tp-100) cc_final: 0.8987 (tp-100) REVERT: b 59 MET cc_start: 0.6889 (tpp) cc_final: 0.6609 (ppp) REVERT: b 126 LEU cc_start: 0.8710 (mm) cc_final: 0.8456 (pt) REVERT: W 28 LYS cc_start: 0.9245 (mmmm) cc_final: 0.8920 (mmmm) REVERT: W 111 GLN cc_start: 0.9193 (pm20) cc_final: 0.8939 (pm20) REVERT: X 140 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.6454 (p-80) REVERT: X 201 THR cc_start: 0.9513 (m) cc_final: 0.9064 (p) REVERT: Y 7 TYR cc_start: 0.9124 (m-10) cc_final: 0.8888 (m-80) REVERT: Y 128 ASP cc_start: 0.9180 (p0) cc_final: 0.8901 (p0) REVERT: Y 132 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7516 (p0) REVERT: Z 38 MET cc_start: 0.8978 (tpp) cc_final: 0.8607 (tpp) REVERT: Z 83 MET cc_start: 0.9058 (mpp) cc_final: 0.8567 (mpp) REVERT: Z 96 MET cc_start: 0.9182 (tmm) cc_final: 0.8673 (ptm) REVERT: Z 122 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.6286 (m-10) REVERT: Z 128 TYR cc_start: 0.8703 (t80) cc_final: 0.8460 (t80) REVERT: a 59 GLN cc_start: 0.9278 (mm-40) cc_final: 0.8890 (mm-40) REVERT: a 107 ASN cc_start: 0.8997 (m-40) cc_final: 0.8732 (m-40) REVERT: a 148 ASN cc_start: 0.9305 (m-40) cc_final: 0.8873 (m110) REVERT: c 92 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8402 (pt0) REVERT: c 118 GLN cc_start: 0.9576 (tm-30) cc_final: 0.9349 (tm-30) REVERT: c 142 GLU cc_start: 0.8745 (pm20) cc_final: 0.8355 (pm20) REVERT: c 144 ARG cc_start: 0.8480 (tpp80) cc_final: 0.8071 (tpp80) REVERT: d 1 MET cc_start: 0.8810 (tpp) cc_final: 0.8551 (mtt) REVERT: d 66 LYS cc_start: 0.9264 (mtpp) cc_final: 0.8798 (ttpp) REVERT: d 81 GLU cc_start: 0.8030 (pm20) cc_final: 0.7757 (pm20) REVERT: d 105 GLU cc_start: 0.9191 (mp0) cc_final: 0.8889 (mp0) REVERT: e 17 ASN cc_start: 0.9262 (t0) cc_final: 0.9008 (t0) REVERT: e 71 ARG cc_start: 0.9388 (tpt-90) cc_final: 0.9166 (tpp80) REVERT: e 73 GLU cc_start: 0.8280 (pm20) cc_final: 0.8072 (pm20) REVERT: e 106 ASN cc_start: 0.9214 (m-40) cc_final: 0.8330 (p0) REVERT: f 9 TYR cc_start: 0.9161 (m-80) cc_final: 0.8566 (m-80) REVERT: f 37 LEU cc_start: 0.9486 (mt) cc_final: 0.9234 (mt) REVERT: f 43 THR cc_start: 0.9472 (OUTLIER) cc_final: 0.9127 (p) REVERT: g 45 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8278 (mm-30) REVERT: g 72 ASN cc_start: 0.8878 (t0) cc_final: 0.8626 (t0) REVERT: g 118 GLU cc_start: 0.8843 (pm20) cc_final: 0.8369 (pm20) REVERT: h 60 ASP cc_start: 0.8103 (t70) cc_final: 0.6911 (t70) REVERT: h 62 ASP cc_start: 0.9117 (t0) cc_final: 0.8807 (p0) REVERT: i 9 GLU cc_start: 0.9117 (tp30) cc_final: 0.8661 (tm-30) REVERT: i 114 LYS cc_start: 0.8913 (ptpp) cc_final: 0.8661 (ptpp) REVERT: j 19 LYS cc_start: 0.9023 (mmmt) cc_final: 0.8795 (mtpp) REVERT: k 39 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8341 (pp) REVERT: l 48 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8108 (tm-30) REVERT: l 52 LYS cc_start: 0.9536 (mtpp) cc_final: 0.9035 (mmtp) REVERT: m 5 ARG cc_start: 0.9577 (OUTLIER) cc_final: 0.9023 (mtt90) REVERT: m 31 ASP cc_start: 0.9177 (t70) cc_final: 0.8766 (t70) REVERT: m 33 ARG cc_start: 0.8877 (mtm180) cc_final: 0.8659 (mtm-85) REVERT: n 7 ASP cc_start: 0.8244 (m-30) cc_final: 0.7883 (m-30) REVERT: n 77 GLU cc_start: 0.8868 (tp30) cc_final: 0.8335 (mm-30) REVERT: o 46 TYR cc_start: 0.9188 (t80) cc_final: 0.8955 (t80) REVERT: o 52 LYS cc_start: 0.9509 (mttt) cc_final: 0.9051 (mttp) REVERT: o 78 GLU cc_start: 0.8537 (pm20) cc_final: 0.8223 (mp0) REVERT: o 82 ARG cc_start: 0.8775 (mtp85) cc_final: 0.7512 (mmm-85) REVERT: o 85 LYS cc_start: 0.9238 (mttp) cc_final: 0.8960 (mttm) REVERT: o 86 LYS cc_start: 0.9178 (ttpp) cc_final: 0.8574 (ttmm) REVERT: p 53 ASP cc_start: 0.8897 (t0) cc_final: 0.8651 (t0) REVERT: q 14 GLU cc_start: 0.9009 (pt0) cc_final: 0.8782 (pm20) REVERT: q 31 GLU cc_start: 0.9020 (pm20) cc_final: 0.8795 (pm20) REVERT: r 25 LYS cc_start: 0.8282 (tppt) cc_final: 0.8057 (ttpt) REVERT: s 38 GLN cc_start: 0.9249 (tp40) cc_final: 0.9005 (tp-100) REVERT: s 56 LYS cc_start: 0.9483 (ttpt) cc_final: 0.9269 (ttpt) REVERT: u 17 ASN cc_start: 0.9142 (t0) cc_final: 0.8813 (t0) REVERT: u 46 LYS cc_start: 0.9531 (ptmt) cc_final: 0.9302 (mtmm) REVERT: v 5 GLU cc_start: 0.8861 (mp0) cc_final: 0.8562 (mp0) REVERT: v 15 GLU cc_start: 0.9484 (mm-30) cc_final: 0.9204 (tm-30) REVERT: v 16 GLN cc_start: 0.9481 (mm110) cc_final: 0.8746 (mm-40) REVERT: v 23 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8315 (tm-30) REVERT: w 57 LYS cc_start: 0.9122 (tmmt) cc_final: 0.8851 (tmtt) outliers start: 149 outliers final: 131 residues processed: 832 average time/residue: 0.8916 time to fit residues: 1257.1456 Evaluate side-chains 884 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 747 time to evaluate : 4.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 25 THR Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 55 TYR Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 203 ILE Chi-restraints excluded: chain W residue 229 ASP Chi-restraints excluded: chain W residue 254 THR Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 21 ASP Chi-restraints excluded: chain X residue 74 THR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain X residue 192 VAL Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 120 ASP Chi-restraints excluded: chain Y residue 130 THR Chi-restraints excluded: chain Y residue 132 ASP Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 183 VAL Chi-restraints excluded: chain Z residue 17 MET Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 90 THR Chi-restraints excluded: chain Z residue 122 PHE Chi-restraints excluded: chain Z residue 141 ILE Chi-restraints excluded: chain Z residue 144 ASP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 173 VAL Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 95 TYR Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 53 ASP Chi-restraints excluded: chain c residue 130 GLU Chi-restraints excluded: chain d residue 18 GLU Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 34 ASN Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 80 ASP Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 108 GLU Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 54 MET Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain g residue 99 THR Chi-restraints excluded: chain h residue 3 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 THR Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 106 VAL Chi-restraints excluded: chain i residue 13 LYS Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 60 GLU Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 71 VAL Chi-restraints excluded: chain i residue 116 ILE Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 8 THR Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 42 SER Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain k residue 38 VAL Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 50 ASN Chi-restraints excluded: chain k residue 53 VAL Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain l residue 24 ILE Chi-restraints excluded: chain l residue 65 ASP Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 6 ASP Chi-restraints excluded: chain m residue 35 ASN Chi-restraints excluded: chain m residue 68 ARG Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 16 ASP Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain o residue 80 PHE Chi-restraints excluded: chain o residue 92 VAL Chi-restraints excluded: chain p residue 11 MET Chi-restraints excluded: chain p residue 23 ASN Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 23 LYS Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 30 SER Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 64 ASN Chi-restraints excluded: chain t residue 25 VAL Chi-restraints excluded: chain u residue 13 THR Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain v residue 4 ASN Chi-restraints excluded: chain v residue 8 ASP Chi-restraints excluded: chain v residue 34 THR Chi-restraints excluded: chain v residue 57 ILE Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 29 LYS Chi-restraints excluded: chain w residue 30 LYS Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 1.9990 chunk 592 optimal weight: 7.9990 chunk 361 optimal weight: 0.0980 chunk 281 optimal weight: 30.0000 chunk 411 optimal weight: 5.9990 chunk 621 optimal weight: 2.9990 chunk 572 optimal weight: 9.9990 chunk 495 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 382 optimal weight: 0.8980 chunk 303 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN A 157 GLN W 54 GLN ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 99690 Z= 0.166 Angle : 0.582 13.519 149672 Z= 0.297 Chirality : 0.034 0.306 19191 Planarity : 0.004 0.052 7613 Dihedral : 23.828 179.659 51131 Min Nonbonded Distance : 1.164 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.65 % Allowed : 30.51 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.14), residues: 3288 helix: 0.48 (0.18), residues: 925 sheet: -1.02 (0.20), residues: 620 loop : -2.08 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP W 213 HIS 0.008 0.001 HIS w 52 PHE 0.021 0.001 PHE Z 138 TYR 0.023 0.001 TYR f 74 ARG 0.014 0.000 ARG Y 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 813 time to evaluate : 4.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 PHE cc_start: 0.8897 (t80) cc_final: 0.8632 (t80) REVERT: A 125 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9270 (mp0) REVERT: A 140 ARG cc_start: 0.9052 (mtp85) cc_final: 0.8753 (ptp90) REVERT: A 156 ARG cc_start: 0.8967 (mmp80) cc_final: 0.8489 (mmp-170) REVERT: A 162 LEU cc_start: 0.9478 (mm) cc_final: 0.9257 (mm) REVERT: A 172 PHE cc_start: 0.9444 (t80) cc_final: 0.8922 (t80) REVERT: A 173 TYR cc_start: 0.9262 (m-80) cc_final: 0.9002 (m-80) REVERT: A 178 GLN cc_start: 0.9270 (tp-100) cc_final: 0.9012 (tp-100) REVERT: b 59 MET cc_start: 0.6658 (tpp) cc_final: 0.6427 (ppp) REVERT: b 126 LEU cc_start: 0.8650 (mm) cc_final: 0.8366 (pt) REVERT: W 28 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8890 (mmmm) REVERT: W 98 ASP cc_start: 0.8984 (p0) cc_final: 0.8079 (t0) REVERT: W 111 GLN cc_start: 0.9110 (pm20) cc_final: 0.8597 (pm20) REVERT: X 140 HIS cc_start: 0.8474 (OUTLIER) cc_final: 0.6765 (p-80) REVERT: X 201 THR cc_start: 0.9519 (m) cc_final: 0.9124 (p) REVERT: Y 7 TYR cc_start: 0.9084 (m-10) cc_final: 0.8848 (m-80) REVERT: Y 128 ASP cc_start: 0.9144 (p0) cc_final: 0.8871 (p0) REVERT: Y 132 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7536 (p0) REVERT: Z 38 MET cc_start: 0.9025 (tpp) cc_final: 0.8662 (tpp) REVERT: Z 83 MET cc_start: 0.9119 (mpp) cc_final: 0.8655 (mpp) REVERT: Z 96 MET cc_start: 0.9156 (tmm) cc_final: 0.8604 (ptm) REVERT: a 42 MET cc_start: 0.8138 (tpp) cc_final: 0.7661 (tpp) REVERT: a 58 ASP cc_start: 0.9277 (t0) cc_final: 0.9006 (t0) REVERT: a 59 GLN cc_start: 0.9261 (mm-40) cc_final: 0.8881 (mp10) REVERT: a 107 ASN cc_start: 0.8971 (m-40) cc_final: 0.8697 (p0) REVERT: a 148 ASN cc_start: 0.9291 (m-40) cc_final: 0.8852 (m110) REVERT: c 92 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8427 (pt0) REVERT: c 118 GLN cc_start: 0.9575 (tm-30) cc_final: 0.9348 (tm-30) REVERT: c 142 GLU cc_start: 0.8653 (pm20) cc_final: 0.8254 (pm20) REVERT: c 144 ARG cc_start: 0.8493 (tpp80) cc_final: 0.8116 (tpp80) REVERT: d 23 LYS cc_start: 0.9647 (tppp) cc_final: 0.9193 (tppt) REVERT: d 53 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8796 (mmmt) REVERT: d 54 LYS cc_start: 0.9685 (tttp) cc_final: 0.9388 (tttm) REVERT: d 66 LYS cc_start: 0.9270 (mtpp) cc_final: 0.8847 (ttpp) REVERT: d 81 GLU cc_start: 0.8024 (pm20) cc_final: 0.7791 (pm20) REVERT: d 91 LYS cc_start: 0.9084 (mmtp) cc_final: 0.8251 (mmmm) REVERT: d 105 GLU cc_start: 0.9165 (mp0) cc_final: 0.8863 (mp0) REVERT: d 120 GLU cc_start: 0.8535 (pm20) cc_final: 0.8325 (pm20) REVERT: e 17 ASN cc_start: 0.9219 (t0) cc_final: 0.8980 (t0) REVERT: e 106 ASN cc_start: 0.9148 (m-40) cc_final: 0.8273 (p0) REVERT: f 9 TYR cc_start: 0.9086 (m-80) cc_final: 0.8516 (m-80) REVERT: f 37 LEU cc_start: 0.9489 (mt) cc_final: 0.9285 (mt) REVERT: f 43 THR cc_start: 0.9428 (OUTLIER) cc_final: 0.9063 (p) REVERT: g 27 ASN cc_start: 0.9316 (m-40) cc_final: 0.8997 (m-40) REVERT: g 45 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8212 (mm-30) REVERT: g 118 GLU cc_start: 0.8731 (pm20) cc_final: 0.8274 (pm20) REVERT: h 60 ASP cc_start: 0.8070 (t70) cc_final: 0.7019 (t70) REVERT: h 62 ASP cc_start: 0.9136 (t0) cc_final: 0.8799 (p0) REVERT: h 63 LEU cc_start: 0.8603 (mp) cc_final: 0.7664 (pp) REVERT: i 9 GLU cc_start: 0.9076 (tp30) cc_final: 0.8614 (tm-30) REVERT: i 114 LYS cc_start: 0.8820 (ptpp) cc_final: 0.8573 (ptpp) REVERT: j 98 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9314 (tt) REVERT: k 39 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8087 (pp) REVERT: k 63 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8824 (mm-30) REVERT: l 48 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8095 (tm-30) REVERT: l 52 LYS cc_start: 0.9554 (mtpp) cc_final: 0.9012 (mmtp) REVERT: m 5 ARG cc_start: 0.9528 (OUTLIER) cc_final: 0.8914 (mtt90) REVERT: m 31 ASP cc_start: 0.9120 (t70) cc_final: 0.8785 (t0) REVERT: m 76 ARG cc_start: 0.9029 (mtm180) cc_final: 0.8461 (mtm-85) REVERT: n 7 ASP cc_start: 0.8153 (m-30) cc_final: 0.7817 (m-30) REVERT: n 77 GLU cc_start: 0.8809 (tp30) cc_final: 0.8321 (mm-30) REVERT: o 19 LYS cc_start: 0.9255 (mtmm) cc_final: 0.9009 (mmtm) REVERT: o 52 LYS cc_start: 0.9488 (mttt) cc_final: 0.8981 (mttp) REVERT: o 76 LYS cc_start: 0.9191 (mmtp) cc_final: 0.8857 (mmmm) REVERT: o 78 GLU cc_start: 0.8468 (pm20) cc_final: 0.8185 (mp0) REVERT: o 82 ARG cc_start: 0.8845 (mtp85) cc_final: 0.7570 (mmm-85) REVERT: o 85 LYS cc_start: 0.9208 (mttp) cc_final: 0.8814 (mttm) REVERT: o 86 LYS cc_start: 0.9150 (ttpp) cc_final: 0.8563 (ttmm) REVERT: p 21 LYS cc_start: 0.9427 (pttm) cc_final: 0.9200 (pttm) REVERT: p 53 ASP cc_start: 0.8887 (t0) cc_final: 0.8597 (t0) REVERT: q 14 GLU cc_start: 0.8891 (pt0) cc_final: 0.8575 (pm20) REVERT: q 31 GLU cc_start: 0.8971 (pm20) cc_final: 0.8767 (pm20) REVERT: s 38 GLN cc_start: 0.9128 (tp40) cc_final: 0.8896 (tp-100) REVERT: s 56 LYS cc_start: 0.9493 (ttpt) cc_final: 0.9246 (ttpt) REVERT: t 24 MET cc_start: 0.8485 (mtp) cc_final: 0.8189 (mmt) REVERT: t 35 LYS cc_start: 0.9321 (ttmt) cc_final: 0.8958 (ttpp) REVERT: u 17 ASN cc_start: 0.9079 (t0) cc_final: 0.8763 (t0) REVERT: u 46 LYS cc_start: 0.9518 (ptmt) cc_final: 0.9314 (mtmm) REVERT: v 5 GLU cc_start: 0.8800 (mp0) cc_final: 0.8487 (mp0) REVERT: v 8 ASP cc_start: 0.9593 (OUTLIER) cc_final: 0.9245 (t0) REVERT: v 15 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9201 (tm-30) REVERT: v 16 GLN cc_start: 0.9451 (mm110) cc_final: 0.8726 (mm-40) REVERT: v 23 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8229 (tm-30) REVERT: w 19 GLN cc_start: 0.9271 (mt0) cc_final: 0.9062 (mt0) REVERT: w 57 LYS cc_start: 0.9134 (tmmt) cc_final: 0.8851 (tmtt) outliers start: 101 outliers final: 83 residues processed: 860 average time/residue: 0.9001 time to fit residues: 1309.5599 Evaluate side-chains 881 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 791 time to evaluate : 3.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 25 THR Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 55 TYR Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 64 VAL Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain W residue 54 GLN Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 203 ILE Chi-restraints excluded: chain W residue 229 ASP Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 21 ASP Chi-restraints excluded: chain X residue 140 HIS Chi-restraints excluded: chain Y residue 130 THR Chi-restraints excluded: chain Y residue 132 ASP Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 183 VAL Chi-restraints excluded: chain Z residue 17 MET Chi-restraints excluded: chain Z residue 141 ILE Chi-restraints excluded: chain Z residue 144 ASP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 173 VAL Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 THR Chi-restraints excluded: chain a residue 95 TYR Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 53 ASP Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain e residue 9 SER Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain g residue 2 SER Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain g residue 89 THR Chi-restraints excluded: chain g residue 99 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 65 VAL Chi-restraints excluded: chain h residue 68 THR Chi-restraints excluded: chain i residue 13 LYS Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 116 ILE Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 42 SER Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain j residue 97 ASP Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 50 ASN Chi-restraints excluded: chain k residue 53 VAL Chi-restraints excluded: chain k residue 81 ASN Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain l residue 65 ASP Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 6 ASP Chi-restraints excluded: chain m residue 35 ASN Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain p residue 23 ASN Chi-restraints excluded: chain p residue 24 VAL Chi-restraints excluded: chain q residue 23 LYS Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 64 ASN Chi-restraints excluded: chain t residue 25 VAL Chi-restraints excluded: chain v residue 4 ASN Chi-restraints excluded: chain v residue 8 ASP Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 29 LYS Chi-restraints excluded: chain w residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 6.9990 chunk 527 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 456 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 495 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 509 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 GLN ** X 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.042577 restraints weight = 395015.208| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 1.75 r_work: 0.2499 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2402 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.370 99690 Z= 0.337 Angle : 0.648 59.149 149672 Z= 0.337 Chirality : 0.039 1.252 19191 Planarity : 0.004 0.061 7613 Dihedral : 23.825 179.683 51131 Min Nonbonded Distance : 1.163 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.42 % Favored : 93.55 % Rotamer: Outliers : 3.54 % Allowed : 30.84 % Favored : 65.62 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3288 helix: 0.39 (0.18), residues: 931 sheet: -0.97 (0.21), residues: 615 loop : -2.08 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP W 213 HIS 0.018 0.001 HIS X 140 PHE 0.117 0.002 PHE B 172 TYR 0.056 0.002 TYR Z 128 ARG 0.011 0.000 ARG f 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22337.60 seconds wall clock time: 393 minutes 31.20 seconds (23611.20 seconds total)