Starting phenix.real_space_refine on Mon Sep 30 03:29:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flx_3221/09_2024/5flx_3221.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flx_3221/09_2024/5flx_3221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flx_3221/09_2024/5flx_3221.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flx_3221/09_2024/5flx_3221.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flx_3221/09_2024/5flx_3221.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flx_3221/09_2024/5flx_3221.cif" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= -0.008 sd= 0.997 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 2 6.06 5 P 1972 5.49 5 Mg 74 5.21 5 S 177 5.16 5 C 43075 2.51 5 N 14784 2.21 5 O 20508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 80592 Number of models: 1 Model: "" Number of chains: 40 Chain: "1" Number of atoms: 36456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1708, 36456 Classifications: {'RNA': 1708} Modifications used: {'p5*END': 1, 'rna2p_pur': 156, 'rna2p_pyr': 118, 'rna3p_pur': 746, 'rna3p_pyr': 688} Link IDs: {'rna2p': 274, 'rna3p': 1433} Chain breaks: 7 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1704 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "B" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1722 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 5, 'TRANS': 206} Chain: "C" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1724 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "D" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1709 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 10, 'TRANS': 209} Chain: "E" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2031 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain: "F" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1502 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "G" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1884 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain: "H" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1479 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "I" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1696 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "J" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1495 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain: "K" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 827 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "L" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1258 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 146} Chain: "M" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "P" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 999 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "Q" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1109 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "R" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "S" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1154 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "T" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "U" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 769 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "V" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 617 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "X" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1080 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "Y" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1015 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "Z" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 585 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "a" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 774 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "b" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 625 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 5, 'TRANS': 74} Chain: "c" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "d" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 427 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "e" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "f" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 601 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "g" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "z" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 5637 Classifications: {'RNA': 264} Modifications used: {'rna2p_pur': 21, 'rna2p_pyr': 19, 'rna3p_pur': 115, 'rna3p_pyr': 109} Link IDs: {'rna2p': 40, 'rna3p': 223} Chain breaks: 1 Chain: "1" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Unusual residues: {' MG': 72} Classifications: {'undetermined': 72} Link IDs: {None: 71} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 71141 SG CYS d 24 55.290 95.502 73.049 1.00 20.00 S ATOM 71262 SG CYS d 39 54.338 94.084 75.953 1.00 20.00 S Time building chain proxies: 33.48, per 1000 atoms: 0.42 Number of scatterers: 80592 At special positions: 0 Unit cell: (228.98, 252.52, 220.42, 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 2 29.99 S 177 16.00 P 1972 15.00 Mg 74 11.99 O 20508 8.00 N 14784 7.00 C 43075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS a 26 " - pdb=" SG CYS a 77 " distance=2.23 Simple disulfide: pdb=" SG CYS f 126 " - pdb=" SG CYS f 144 " distance=2.03 Simple disulfide: pdb=" SG CYS f 141 " - pdb=" SG CYS f 144 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 14.51 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d 101 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 24 " 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB ILE a 44 " pdb=" CB ALA a 48 " Number of C-beta restraints generated: 8918 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 55 sheets defined 34.0% alpha, 16.0% beta 543 base pairs and 910 stacking pairs defined. Time for finding SS restraints: 26.06 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.748A pdb=" N GLY A 45 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 46 " --> pdb=" O SER A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 46' Processing helix chain 'A' and resid 51 through 67 removed outlier: 3.639A pdb=" N TRP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.538A pdb=" N GLN A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 137 Processing helix chain 'A' and resid 167 through 186 removed outlier: 3.714A pdb=" N VAL A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 218 removed outlier: 3.939A pdb=" N GLU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 64 removed outlier: 3.739A pdb=" N GLY B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.705A pdb=" N MET B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 removed outlier: 3.629A pdb=" N ARG B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.973A pdb=" N LEU C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 85 removed outlier: 4.161A pdb=" N ILE C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.713A pdb=" N ASP C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 207 through 217 Processing helix chain 'C' and resid 232 through 246 removed outlier: 3.663A pdb=" N PHE C 236 " --> pdb=" O THR C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 269 through 278 removed outlier: 3.513A pdb=" N LEU C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 29 removed outlier: 3.852A pdb=" N PHE D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 63 through 76 removed outlier: 3.771A pdb=" N ARG D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG D 76 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 110 removed outlier: 3.657A pdb=" N GLN D 101 " --> pdb=" O CYS D 97 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TYR D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS D 108 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 129 removed outlier: 3.528A pdb=" N ALA D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 43 through 50 Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.943A pdb=" N VAL E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET E 66 " --> pdb=" O LYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 120 removed outlier: 3.652A pdb=" N ALA E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 115 through 120' Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 246 through 258 removed outlier: 3.574A pdb=" N THR E 258 " --> pdb=" O LYS E 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 77 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 85 through 103 removed outlier: 3.759A pdb=" N THR F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU F 103 " --> pdb=" O ILE F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 removed outlier: 4.024A pdb=" N VAL F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY F 120 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 162 removed outlier: 3.593A pdb=" N VAL F 147 " --> pdb=" O PRO F 143 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA F 162 " --> pdb=" O ALA F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 180 removed outlier: 3.658A pdb=" N CYS F 172 " --> pdb=" O THR F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 203 removed outlier: 3.871A pdb=" N ASN F 203 " --> pdb=" O VAL F 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 25 removed outlier: 3.960A pdb=" N LEU G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 28 No H-bonds generated for 'chain 'G' and resid 26 through 28' Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.574A pdb=" N ILE G 141 " --> pdb=" O ARG G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 232 Processing helix chain 'H' and resid 17 through 33 removed outlier: 3.519A pdb=" N GLU H 31 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET H 32 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN H 33 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 75 removed outlier: 4.165A pdb=" N ILE H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 87 removed outlier: 4.357A pdb=" N LEU H 79 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 120 Processing helix chain 'H' and resid 121 through 132 removed outlier: 3.591A pdb=" N ASP H 127 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA H 128 " --> pdb=" O ALA H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'I' and resid 25 through 28 removed outlier: 3.595A pdb=" N GLU I 28 " --> pdb=" O ARG I 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 25 through 28' Processing helix chain 'I' and resid 87 through 94 removed outlier: 3.983A pdb=" N VAL I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 removed outlier: 4.192A pdb=" N GLN I 111 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TRP I 112 " --> pdb=" O PRO I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 152 Processing helix chain 'I' and resid 158 through 167 removed outlier: 4.018A pdb=" N LEU I 162 " --> pdb=" O ILE I 158 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 192 through 208 Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 39 through 63 removed outlier: 3.856A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU J 63 " --> pdb=" O GLU J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 85 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 109 through 117 removed outlier: 3.813A pdb=" N LEU J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 132 Processing helix chain 'J' and resid 171 through 180 removed outlier: 4.297A pdb=" N ARG J 175 " --> pdb=" O GLY J 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 18 removed outlier: 3.926A pdb=" N ARG K 8 " --> pdb=" O PRO K 4 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE K 9 " --> pdb=" O LYS K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 55 removed outlier: 3.896A pdb=" N MET K 46 " --> pdb=" O ASN K 42 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER K 51 " --> pdb=" O LYS K 47 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG K 55 " --> pdb=" O SER K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 78 Processing helix chain 'K' and resid 78 through 84 removed outlier: 3.896A pdb=" N TYR K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 51 Processing helix chain 'L' and resid 114 through 118 removed outlier: 3.612A pdb=" N ARG L 118 " --> pdb=" O PRO L 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 28 removed outlier: 3.939A pdb=" N ASN M 15 " --> pdb=" O VAL M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 44 Processing helix chain 'M' and resid 61 through 72 removed outlier: 3.790A pdb=" N VAL M 65 " --> pdb=" O TYR M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 90 removed outlier: 3.887A pdb=" N LEU M 85 " --> pdb=" O ASP M 81 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 129 Processing helix chain 'N' and resid 30 through 43 removed outlier: 4.086A pdb=" N LYS N 34 " --> pdb=" O SER N 30 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS N 43 " --> pdb=" O LYS N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 59 removed outlier: 3.592A pdb=" N VAL N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 removed outlier: 3.740A pdb=" N VAL N 66 " --> pdb=" O GLN N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 79 removed outlier: 3.725A pdb=" N SER N 77 " --> pdb=" O ARG N 73 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS N 78 " --> pdb=" O ILE N 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 105 removed outlier: 3.739A pdb=" N LEU N 91 " --> pdb=" O ASP N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 132 Processing helix chain 'N' and resid 143 through 149 removed outlier: 3.560A pdb=" N LEU N 149 " --> pdb=" O THR N 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 89 removed outlier: 3.608A pdb=" N ALA O 74 " --> pdb=" O SER O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 122 removed outlier: 4.172A pdb=" N GLN O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA O 115 " --> pdb=" O GLY O 111 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU O 116 " --> pdb=" O ALA O 112 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER O 122 " --> pdb=" O ALA O 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 28 removed outlier: 3.714A pdb=" N ASP P 27 " --> pdb=" O ASP P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 35 removed outlier: 4.208A pdb=" N GLN P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 47 Processing helix chain 'P' and resid 49 through 66 removed outlier: 3.923A pdb=" N GLN P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU P 57 " --> pdb=" O GLN P 53 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS P 58 " --> pdb=" O HIS P 54 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU P 66 " --> pdb=" O LYS P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.667A pdb=" N ILE P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'Q' and resid 52 through 59 removed outlier: 3.761A pdb=" N LEU Q 57 " --> pdb=" O GLU Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 64 Processing helix chain 'Q' and resid 76 through 99 removed outlier: 3.675A pdb=" N ILE Q 81 " --> pdb=" O HIS Q 77 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL Q 93 " --> pdb=" O SER Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 116 removed outlier: 3.748A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU Q 107 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 20 removed outlier: 3.571A pdb=" N LYS R 10 " --> pdb=" O THR R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 24 Processing helix chain 'R' and resid 27 through 38 removed outlier: 4.006A pdb=" N ARG R 33 " --> pdb=" O HIS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 64 removed outlier: 3.660A pdb=" N ARG R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY R 64 " --> pdb=" O ARG R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 82 removed outlier: 3.969A pdb=" N ARG R 80 " --> pdb=" O GLU R 76 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG R 81 " --> pdb=" O GLU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 110 removed outlier: 4.033A pdb=" N MET R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU R 108 " --> pdb=" O GLU R 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 31 Processing helix chain 'S' and resid 37 through 49 removed outlier: 4.018A pdb=" N ALA S 41 " --> pdb=" O GLY S 37 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS S 42 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 59 removed outlier: 3.674A pdb=" N LEU S 59 " --> pdb=" O ALA S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 73 removed outlier: 3.876A pdb=" N ASN S 73 " --> pdb=" O THR S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 84 Processing helix chain 'S' and resid 99 through 116 removed outlier: 4.264A pdb=" N ASP S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN S 105 " --> pdb=" O ASN S 101 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS S 116 " --> pdb=" O GLU S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 127 Processing helix chain 'T' and resid 10 through 25 removed outlier: 4.028A pdb=" N ARG T 16 " --> pdb=" O GLN T 12 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA T 17 " --> pdb=" O GLU T 13 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA T 20 " --> pdb=" O ARG T 16 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS T 23 " --> pdb=" O ALA T 19 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 36 Processing helix chain 'T' and resid 51 through 67 Processing helix chain 'T' and resid 71 through 79 Processing helix chain 'T' and resid 96 through 109 removed outlier: 3.646A pdb=" N ALA T 100 " --> pdb=" O SER T 96 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY T 109 " --> pdb=" O GLN T 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 143 Processing helix chain 'U' and resid 28 through 45 removed outlier: 3.596A pdb=" N LEU U 32 " --> pdb=" O ASN U 28 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU U 45 " --> pdb=" O ARG U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 103 removed outlier: 3.661A pdb=" N VAL U 98 " --> pdb=" O PRO U 94 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS U 99 " --> pdb=" O SER U 95 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER U 103 " --> pdb=" O LYS U 99 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 62 Processing helix chain 'V' and resid 64 through 77 removed outlier: 3.704A pdb=" N ALA V 75 " --> pdb=" O ARG V 71 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP V 76 " --> pdb=" O LEU V 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 21 removed outlier: 3.683A pdb=" N SER W 13 " --> pdb=" O ASP W 9 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 45 Processing helix chain 'W' and resid 85 through 94 removed outlier: 4.285A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 120 removed outlier: 4.347A pdb=" N ARG W 117 " --> pdb=" O HIS W 113 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG W 118 " --> pdb=" O GLU W 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 21 Processing helix chain 'X' and resid 24 through 32 removed outlier: 3.500A pdb=" N LEU X 32 " --> pdb=" O LYS X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 39 removed outlier: 3.594A pdb=" N ASN X 39 " --> pdb=" O ALA X 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 44 removed outlier: 4.168A pdb=" N GLY X 43 " --> pdb=" O PRO X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 135 removed outlier: 3.525A pdb=" N LYS X 135 " --> pdb=" O LEU X 131 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 49 removed outlier: 3.595A pdb=" N ILE Y 40 " --> pdb=" O PRO Y 36 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG Y 41 " --> pdb=" O LYS Y 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 78 through 86 removed outlier: 3.905A pdb=" N GLU Y 86 " --> pdb=" O ALA Y 82 " (cutoff:3.500A) Processing helix chain 'Y' and resid 87 through 92 Processing helix chain 'Y' and resid 105 through 117 removed outlier: 3.663A pdb=" N VAL Y 117 " --> pdb=" O ARG Y 113 " (cutoff:3.500A) Processing helix chain 'Y' and resid 119 through 128 Processing helix chain 'Z' and resid 52 through 62 removed outlier: 3.967A pdb=" N LYS Z 57 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 65 No H-bonds generated for 'chain 'Z' and resid 63 through 65' Processing helix chain 'Z' and resid 69 through 77 Processing helix chain 'Z' and resid 80 through 94 removed outlier: 3.601A pdb=" N ALA Z 86 " --> pdb=" O SER Z 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 49 through 54 Processing helix chain 'a' and resid 76 through 82 removed outlier: 4.067A pdb=" N HIS a 80 " --> pdb=" O SER a 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 18 Processing helix chain 'd' and resid 42 through 51 removed outlier: 4.821A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 16 Processing helix chain 'e' and resid 30 through 42 removed outlier: 3.551A pdb=" N ARG e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG e 41 " --> pdb=" O GLN e 37 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.891A pdb=" N LYS A 40 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.969A pdb=" N SER A 78 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 43 through 49 removed outlier: 3.713A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 23.255A pdb=" N TRP B 30 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 20.375A pdb=" N PHE B 100 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 12.789A pdb=" N ASP B 32 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS B 96 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 13.349A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.152A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 215 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N PHE B 138 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N MET B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG B 136 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 134 " --> pdb=" O LYS B 219 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'B' and resid 43 through 49 removed outlier: 3.713A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 23.255A pdb=" N TRP B 30 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 20.375A pdb=" N PHE B 100 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 12.789A pdb=" N ASP B 32 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS B 96 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS B 96 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 91 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR B 98 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLU B 89 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE B 100 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 104 through 115 removed outlier: 5.505A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS C 108 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C 142 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 128 " --> pdb=" O GLY C 140 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 184 through 188 removed outlier: 3.671A pdb=" N LEU C 192 " --> pdb=" O ARG C 227 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 205 " --> pdb=" O CYS C 222 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR C 224 " --> pdb=" O VAL C 205 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.714A pdb=" N ALA D 52 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing sheet with id=DB, first strand: chain 'D' and resid 150 through 155 removed outlier: 5.002A pdb=" N GLY D 133 " --> pdb=" O MET D 189 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET D 189 " --> pdb=" O GLY D 133 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL D 186 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA D 171 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 188 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing sheet with id=DC, first strand: chain 'D' and resid 209 through 210 removed outlier: 3.820A pdb=" N SER D 209 " --> pdb=" O ILE R 40 " (cutoff:3.500A) Processing sheet with id=EA, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.840A pdb=" N LYS E 71 " --> pdb=" O SER E 91 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER E 91 " --> pdb=" O LYS E 71 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.788A pdb=" N VAL E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=EC, first strand: chain 'E' and resid 147 through 148 removed outlier: 3.643A pdb=" N ILE E 147 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS E 138 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE E 129 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N THR E 159 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE E 172 " --> pdb=" O THR E 159 " (cutoff:3.500A) Processing sheet with id=ED, first strand: chain 'E' and resid 217 through 221 removed outlier: 7.296A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG E 191 " --> pdb=" O VAL E 183 " (cutoff:3.500A) Processing sheet with id=EE, first strand: chain 'E' and resid 229 through 230 Processing sheet with id=FA, first strand: chain 'F' and resid 123 through 124 removed outlier: 4.085A pdb=" N ASP F 124 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL F 139 " --> pdb=" O ASP F 124 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE c 42 " --> pdb=" O VAL c 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL c 30 " --> pdb=" O ARG c 44 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLN c 29 " --> pdb=" O LEU c 18 " (cutoff:3.500A) Processing sheet with id=GA, first strand: chain 'G' and resid 13 through 17 removed outlier: 3.803A pdb=" N ILE G 113 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL G 108 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLY G 55 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN G 110 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL G 36 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=GB, first strand: chain 'G' and resid 73 through 77 removed outlier: 3.556A pdb=" N LEU G 75 " --> pdb=" O LYS G 95 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS G 93 " --> pdb=" O LEU G 77 " (cutoff:3.500A) Processing sheet with id=GC, first strand: chain 'G' and resid 160 through 163 removed outlier: 3.580A pdb=" N LYS G 160 " --> pdb=" O LYS G 172 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS G 172 " --> pdb=" O LYS G 160 " (cutoff:3.500A) Processing sheet with id=HA, first strand: chain 'H' and resid 48 through 52 removed outlier: 3.867A pdb=" N ILE H 51 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA H 59 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id=HB, first strand: chain 'H' and resid 184 through 188 removed outlier: 3.649A pdb=" N VAL H 156 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU H 153 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE H 144 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS H 155 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS H 142 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N HIS H 157 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS H 142 " --> pdb=" O ASP W 54 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL H 146 " --> pdb=" O PHE W 50 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU W 49 " --> pdb=" O ASN W 64 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN W 64 " --> pdb=" O GLU W 49 " (cutoff:3.500A) Processing sheet with id=IA, first strand: chain 'I' and resid 42 through 46 removed outlier: 6.859A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS I 54 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id=IB, first strand: chain 'I' and resid 101 through 104 removed outlier: 7.478A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU I 103 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE I 79 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG I 74 " --> pdb=" O PHE I 65 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE I 65 " --> pdb=" O ARG I 74 " (cutoff:3.500A) Processing sheet with id=JA, first strand: chain 'J' and resid 136 through 137 Processing sheet with id=KA, first strand: chain 'K' and resid 59 through 63 Processing sheet with id=LA, first strand: chain 'L' and resid 68 through 79 removed outlier: 5.945A pdb=" N ARG L 71 " --> pdb=" O GLU L 130 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN L 141 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ARG L 139 " --> pdb=" O CYS L 131 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N VAL L 138 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N SER L 110 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE L 140 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS L 107 " --> pdb=" O ARG L 90 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG L 90 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL L 87 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL L 76 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASP L 91 " --> pdb=" O SER L 74 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N SER L 74 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 14.738A pdb=" N LEU L 93 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 17.345A pdb=" N ILE L 72 " --> pdb=" O LEU L 93 " (cutoff:3.500A) Processing sheet with id=MA, first strand: chain 'M' and resid 31 through 33 removed outlier: 3.756A pdb=" N VAL M 110 " --> pdb=" O ALA M 32 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU M 49 " --> pdb=" O VAL M 111 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS M 50 " --> pdb=" O ASN M 75 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE M 77 " --> pdb=" O CYS M 50 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU M 52 " --> pdb=" O ILE M 77 " (cutoff:3.500A) Processing sheet with id=MB, first strand: chain 'M' and resid 93 through 94 removed outlier: 3.979A pdb=" N LYS M 93 " --> pdb=" O ARG M 101 " (cutoff:3.500A) Processing sheet with id=OA, first strand: chain 'O' and resid 52 through 57 removed outlier: 3.756A pdb=" N VAL O 42 " --> pdb=" O VAL O 56 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU O 97 " --> pdb=" O GLU O 130 " (cutoff:3.500A) Processing sheet with id=PA, first strand: chain 'P' and resid 93 through 96 removed outlier: 3.729A pdb=" N VAL P 94 " --> pdb=" O VAL P 105 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL P 105 " --> pdb=" O VAL P 94 " (cutoff:3.500A) Processing sheet with id=QA, first strand: chain 'Q' and resid 10 through 13 removed outlier: 3.525A pdb=" N VAL Q 10 " --> pdb=" O CYS Q 25 " (cutoff:3.500A) Processing sheet with id=TA, first strand: chain 'T' and resid 81 through 85 removed outlier: 7.248A pdb=" N GLY T 81 " --> pdb=" O PHE T 92 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE T 92 " --> pdb=" O GLY T 81 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN T 83 " --> pdb=" O SER T 90 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER T 90 " --> pdb=" O GLN T 83 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN T 85 " --> pdb=" O MET T 88 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET T 88 " --> pdb=" O ASN T 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=TA Processing sheet with id=TB, first strand: chain 'T' and resid 113 through 114 Processing sheet with id=UA, first strand: chain 'U' and resid 54 through 55 Processing sheet with id=UB, first strand: chain 'U' and resid 59 through 60 removed outlier: 8.420A pdb=" N LYS U 86 " --> pdb=" O LYS U 59 " (cutoff:3.500A) Processing sheet with id=UC, first strand: chain 'U' and resid 110 through 115 removed outlier: 3.595A pdb=" N THR U 25 " --> pdb=" O GLU U 111 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE U 89 " --> pdb=" O ILE U 22 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS U 85 " --> pdb=" O SER U 26 " (cutoff:3.500A) Processing sheet with id=UD, first strand: chain 'U' and resid 110 through 115 removed outlier: 3.595A pdb=" N THR U 25 " --> pdb=" O GLU U 111 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE U 89 " --> pdb=" O ILE U 22 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS U 85 " --> pdb=" O SER U 26 " (cutoff:3.500A) Processing sheet with id=UE, first strand: chain 'U' and resid 63 through 65 removed outlier: 3.504A pdb=" N THR U 65 " --> pdb=" O ASP U 78 " (cutoff:3.500A) Processing sheet with id=VA, first strand: chain 'V' and resid 32 through 39 removed outlier: 6.972A pdb=" N ILE V 32 " --> pdb=" O TYR V 53 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR V 53 " --> pdb=" O ILE V 32 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET V 34 " --> pdb=" O LYS V 51 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS V 51 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL V 36 " --> pdb=" O GLN V 49 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLN V 49 " --> pdb=" O VAL V 36 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLU V 38 " --> pdb=" O ASN V 47 " (cutoff:3.500A) Processing sheet with id=WA, first strand: chain 'W' and resid 71 through 74 removed outlier: 7.093A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) Processing sheet with id=XA, first strand: chain 'X' and resid 47 through 58 removed outlier: 3.813A pdb=" N ALA X 47 " --> pdb=" O VAL X 102 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG X 67 " --> pdb=" O GLY X 56 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY X 56 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N CYS X 69 " --> pdb=" O LYS X 54 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS X 54 " --> pdb=" O CYS X 69 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARG X 71 " --> pdb=" O LEU X 52 " (cutoff:3.500A) Processing sheet with id=YA, first strand: chain 'Y' and resid 6 through 12 removed outlier: 3.720A pdb=" N THR Y 6 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL Y 24 " --> pdb=" O ARG Y 10 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLN Y 22 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE Y 75 " --> pdb=" O LYS Y 21 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET Y 23 " --> pdb=" O GLY Y 73 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS Y 29 " --> pdb=" O GLY Y 67 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY Y 67 " --> pdb=" O HIS Y 29 " (cutoff:3.500A) Processing sheet with id=ZA, first strand: chain 'Z' and resid 67 through 68 removed outlier: 4.263A pdb=" N ILE Z 68 " --> pdb=" O TYR Z 109 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR Z 109 " --> pdb=" O ILE Z 68 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS Z 98 " --> pdb=" O THR Z 110 " (cutoff:3.500A) Processing sheet with id=aA, first strand: chain 'a' and resid 20 through 21 No H-bonds generated for sheet with id=aA Processing sheet with id=aB, first strand: chain 'a' and resid 36 through 43 No H-bonds generated for sheet with id=aB Processing sheet with id=bA, first strand: chain 'b' and resid 44 through 47 No H-bonds generated for sheet with id=bA Processing sheet with id=cA, first strand: chain 'c' and resid 10 through 13 No H-bonds generated for sheet with id=cA Processing sheet with id=fA, first strand: chain 'f' and resid 106 through 109 No H-bonds generated for sheet with id=fA Processing sheet with id=fB, first strand: chain 'f' and resid 138 through 140 removed outlier: 3.902A pdb=" N TYR f 148 " --> pdb=" O HIS f 139 " (cutoff:3.500A) Processing sheet with id=gA, first strand: chain 'g' and resid 3 through 11 No H-bonds generated for sheet with id=gA Processing sheet with id=gB, first strand: chain 'g' and resid 18 through 23 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 18 through 23 current: chain 'g' and resid 40 through 44 removed outlier: 5.983A pdb=" N ILE g 40 " --> pdb=" O ALA g 58 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA g 58 " --> pdb=" O ILE g 40 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET g 42 " --> pdb=" O GLN g 56 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS g 44 " --> pdb=" O ILE g 54 " (cutoff:3.500A) Processing sheet with id=gC, first strand: chain 'g' and resid 69 through 71 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 69 through 71 current: chain 'g' and resid 87 through 91 Processing sheet with id=gD, first strand: chain 'g' and resid 112 through 113 removed outlier: 3.915A pdb=" N LYS g 130 " --> pdb=" O SER g 122 " (cutoff:3.500A) Processing sheet with id=gE, first strand: chain 'g' and resid 151 through 156 removed outlier: 5.043A pdb=" N CYS g 153 " --> pdb=" O CYS g 168 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS g 175 " --> pdb=" O SER g 167 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL g 174 " --> pdb=" O ASN g 187 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASN g 187 " --> pdb=" O VAL g 174 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL g 176 " --> pdb=" O LYS g 185 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS g 183 " --> pdb=" O ASN g 178 " (cutoff:3.500A) Processing sheet with id=gF, first strand: chain 'g' and resid 195 through 200 removed outlier: 4.075A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA g 216 " --> pdb=" O THR g 229 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N THR g 229 " --> pdb=" O ALA g 216 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU g 218 " --> pdb=" O LEU g 227 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU g 227 " --> pdb=" O LEU g 218 " (cutoff:3.500A) Processing sheet with id=gG, first strand: chain 'g' and resid 236 through 241 removed outlier: 4.452A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS g 240 " --> pdb=" O CYS g 249 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE g 256 " --> pdb=" O GLU g 269 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU g 269 " --> pdb=" O ILE g 256 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE g 258 " --> pdb=" O VAL g 267 " (cutoff:3.500A) 1271 hydrogen bonds defined for protein. 3618 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1364 hydrogen bonds 2204 hydrogen bond angles 0 basepair planarities 543 basepair parallelities 910 stacking parallelities Total time for adding SS restraints: 66.92 Time building geometry restraints manager: 17.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 9135 1.32 - 1.45: 34352 1.45 - 1.58: 38451 1.58 - 1.71: 3934 1.71 - 1.83: 269 Bond restraints: 86141 Sorted by residual: bond pdb=" CA SER c 39 " pdb=" CB SER c 39 " ideal model delta sigma weight residual 1.530 1.213 0.317 1.69e-02 3.50e+03 3.53e+02 bond pdb=" CA ALA a 48 " pdb=" C ALA a 48 " ideal model delta sigma weight residual 1.523 1.289 0.234 1.34e-02 5.57e+03 3.06e+02 bond pdb=" CA ILE a 44 " pdb=" CB ILE a 44 " ideal model delta sigma weight residual 1.540 1.323 0.217 1.36e-02 5.41e+03 2.54e+02 bond pdb=" CA ALA a 48 " pdb=" CB ALA a 48 " ideal model delta sigma weight residual 1.530 1.280 0.250 1.69e-02 3.50e+03 2.19e+02 bond pdb=" N ILE a 44 " pdb=" CA ILE a 44 " ideal model delta sigma weight residual 1.459 1.331 0.128 1.25e-02 6.40e+03 1.05e+02 ... (remaining 86136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.71: 125737 8.71 - 17.41: 35 17.41 - 26.12: 7 26.12 - 34.83: 3 34.83 - 43.54: 2 Bond angle restraints: 125784 Sorted by residual: angle pdb=" C ALA a 48 " pdb=" CA ALA a 48 " pdb=" CB ALA a 48 " ideal model delta sigma weight residual 110.42 153.96 -43.54 1.99e+00 2.53e-01 4.79e+02 angle pdb=" C SER c 39 " pdb=" CA SER c 39 " pdb=" CB SER c 39 " ideal model delta sigma weight residual 110.42 145.36 -34.94 1.99e+00 2.53e-01 3.08e+02 angle pdb=" N ILE a 44 " pdb=" CA ILE a 44 " pdb=" CB ILE a 44 " ideal model delta sigma weight residual 111.23 138.22 -26.99 1.65e+00 3.67e-01 2.68e+02 angle pdb=" P U z 234 " pdb=" O5' U z 234 " pdb=" C5' U z 234 " ideal model delta sigma weight residual 120.90 145.42 -24.52 1.50e+00 4.44e-01 2.67e+02 angle pdb=" CA ALA a 48 " pdb=" C ALA a 48 " pdb=" O ALA a 48 " ideal model delta sigma weight residual 120.51 99.03 21.48 1.43e+00 4.89e-01 2.26e+02 ... (remaining 125779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 49776 36.00 - 72.00: 4633 72.00 - 108.00: 586 108.00 - 144.00: 7 144.00 - 180.00: 29 Dihedral angle restraints: 55031 sinusoidal: 41202 harmonic: 13829 Sorted by residual: dihedral pdb=" C SER c 39 " pdb=" N SER c 39 " pdb=" CA SER c 39 " pdb=" CB SER c 39 " ideal model delta harmonic sigma weight residual -122.60 -178.59 55.99 0 2.50e+00 1.60e-01 5.02e+02 dihedral pdb=" N SER c 39 " pdb=" C SER c 39 " pdb=" CA SER c 39 " pdb=" CB SER c 39 " ideal model delta harmonic sigma weight residual 122.80 177.65 -54.85 0 2.50e+00 1.60e-01 4.81e+02 dihedral pdb=" CA ARG D 76 " pdb=" C ARG D 76 " pdb=" N PHE D 77 " pdb=" CA PHE D 77 " ideal model delta harmonic sigma weight residual 180.00 129.04 50.96 0 5.00e+00 4.00e-02 1.04e+02 ... (remaining 55028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.588: 15665 0.588 - 1.177: 1 1.177 - 1.765: 2 1.765 - 2.353: 0 2.353 - 2.941: 3 Chirality restraints: 15671 Sorted by residual: chirality pdb=" CA ALA a 48 " pdb=" N ALA a 48 " pdb=" C ALA a 48 " pdb=" CB ALA a 48 " both_signs ideal model delta sigma weight residual False 2.48 -0.46 2.94 2.00e-01 2.50e+01 2.16e+02 chirality pdb=" CA ILE a 44 " pdb=" N ILE a 44 " pdb=" C ILE a 44 " pdb=" CB ILE a 44 " both_signs ideal model delta sigma weight residual False 2.43 -0.13 2.56 2.00e-01 2.50e+01 1.64e+02 chirality pdb=" CA SER c 39 " pdb=" N SER c 39 " pdb=" C SER c 39 " pdb=" CB SER c 39 " both_signs ideal model delta sigma weight residual False 2.51 0.06 2.45 2.00e-01 2.50e+01 1.51e+02 ... (remaining 15668 not shown) Planarity restraints: 8637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G z 233 " 0.031 2.00e-02 2.50e+03 2.84e-02 2.42e+01 pdb=" N9 G z 233 " -0.085 2.00e-02 2.50e+03 pdb=" C8 G z 233 " 0.024 2.00e-02 2.50e+03 pdb=" N7 G z 233 " 0.020 2.00e-02 2.50e+03 pdb=" C5 G z 233 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G z 233 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G z 233 " 0.002 2.00e-02 2.50e+03 pdb=" N1 G z 233 " -0.012 2.00e-02 2.50e+03 pdb=" C2 G z 233 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G z 233 " 0.009 2.00e-02 2.50e+03 pdb=" N3 G z 233 " 0.011 2.00e-02 2.50e+03 pdb=" C4 G z 233 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U z 353 " -0.012 2.00e-02 2.50e+03 3.07e-02 2.12e+01 pdb=" N1 U z 353 " 0.053 2.00e-02 2.50e+03 pdb=" C2 U z 353 " -0.025 2.00e-02 2.50e+03 pdb=" O2 U z 353 " -0.015 2.00e-02 2.50e+03 pdb=" N3 U z 353 " 0.049 2.00e-02 2.50e+03 pdb=" C4 U z 353 " -0.044 2.00e-02 2.50e+03 pdb=" O4 U z 353 " 0.007 2.00e-02 2.50e+03 pdb=" C5 U z 353 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U z 353 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U z 234 " 0.028 2.00e-02 2.50e+03 2.81e-02 1.77e+01 pdb=" N1 U z 234 " -0.074 2.00e-02 2.50e+03 pdb=" C2 U z 234 " -0.005 2.00e-02 2.50e+03 pdb=" O2 U z 234 " 0.018 2.00e-02 2.50e+03 pdb=" N3 U z 234 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U z 234 " 0.006 2.00e-02 2.50e+03 pdb=" O4 U z 234 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U z 234 " 0.014 2.00e-02 2.50e+03 pdb=" C6 U z 234 " 0.016 2.00e-02 2.50e+03 ... (remaining 8634 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.70: 9 1.70 - 2.50: 595 2.50 - 3.30: 88104 3.30 - 4.10: 236059 4.10 - 4.90: 359582 Warning: very small nonbonded interaction distances. Nonbonded interactions: 684349 Sorted by model distance: nonbonded pdb=" CB SER F 125 " pdb=" NZ LYS c 47 " model vdw 0.894 3.520 nonbonded pdb=" O3' G 1 991 " pdb=" NZ LYS a 13 " model vdw 1.221 3.120 nonbonded pdb=" P A 1 992 " pdb=" NZ LYS a 13 " model vdw 1.329 3.480 nonbonded pdb=" NE2 GLN B 149 " pdb=" O ARG B 151 " model vdw 1.443 3.120 nonbonded pdb=" OP2 A 1 992 " pdb=" NZ LYS a 13 " model vdw 1.509 3.120 ... (remaining 684344 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 2.490 Check model and map are aligned: 0.480 Set scattering table: 0.590 Process input model: 199.940 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 211.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5678 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 : 0.003 0.317 86141 Z= 0.186 Angle : 0.711 43.535 125784 Z= 0.411 Chirality : 0.053 2.941 15671 Planarity : 0.004 0.068 8637 Dihedral : 21.367 179.998 46104 Min Nonbonded Distance : 0.894 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.77 % Favored : 92.64 % Rotamer: Outliers : 0.19 % Allowed : 0.48 % Favored : 99.33 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.10), residues: 4744 helix: -2.65 (0.10), residues: 1348 sheet: -1.09 (0.16), residues: 735 loop : -1.85 (0.10), residues: 2661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP T 52 HIS 0.010 0.001 HIS K 44 PHE 0.016 0.001 PHE G 7 TYR 0.024 0.001 TYR A 204 ARG 0.010 0.000 ARG a 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2359 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2351 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 SER cc_start: 0.8112 (p) cc_final: 0.7432 (p) REVERT: B 139 CYS cc_start: 0.6343 (t) cc_final: 0.4201 (t) REVERT: B 144 LYS cc_start: 0.8357 (tptm) cc_final: 0.8065 (tptm) REVERT: B 212 VAL cc_start: 0.8235 (m) cc_final: 0.8029 (m) REVERT: E 61 VAL cc_start: 0.6968 (t) cc_final: 0.6563 (t) REVERT: E 171 ASN cc_start: 0.6726 (t0) cc_final: 0.6487 (t0) REVERT: F 16 ASP cc_start: 0.6842 (m-30) cc_final: 0.6561 (m-30) REVERT: F 71 ARG cc_start: 0.6108 (mmm160) cc_final: 0.5902 (mtp180) REVERT: F 73 THR cc_start: 0.7312 (p) cc_final: 0.7008 (p) REVERT: F 142 SER cc_start: 0.7240 (t) cc_final: 0.7032 (t) REVERT: F 165 ASN cc_start: 0.3949 (p0) cc_final: 0.2177 (p0) REVERT: G 111 LEU cc_start: 0.7614 (mt) cc_final: 0.7158 (mt) REVERT: J 124 HIS cc_start: 0.6787 (m-70) cc_final: 0.6257 (m170) REVERT: N 125 LEU cc_start: 0.6993 (mt) cc_final: 0.6711 (mt) REVERT: O 30 VAL cc_start: 0.7214 (t) cc_final: 0.6855 (t) REVERT: O 44 VAL cc_start: 0.6574 (t) cc_final: 0.6149 (t) REVERT: U 58 THR cc_start: 0.5653 (m) cc_final: 0.5256 (p) REVERT: W 34 ILE cc_start: 0.7677 (mt) cc_final: 0.7476 (mt) REVERT: Y 7 ILE cc_start: 0.7385 (mt) cc_final: 0.6673 (mp) REVERT: a 15 ARG cc_start: 0.5033 (OUTLIER) cc_final: 0.4652 (mtt180) REVERT: b 19 HIS cc_start: 0.5625 (t70) cc_final: 0.5234 (t70) REVERT: g 90 TRP cc_start: 0.5688 (m100) cc_final: 0.5317 (m100) REVERT: g 150 TRP cc_start: 0.7511 (m-10) cc_final: 0.6909 (m-10) REVERT: g 289 LEU cc_start: 0.5123 (pp) cc_final: 0.4790 (tp) outliers start: 8 outliers final: 3 residues processed: 2356 average time/residue: 0.9054 time to fit residues: 3399.5584 Evaluate side-chains 1463 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1459 time to evaluate : 4.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain F residue 182 LYS Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain a residue 15 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 559 optimal weight: 10.0000 chunk 502 optimal weight: 20.0000 chunk 278 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 chunk 338 optimal weight: 9.9990 chunk 268 optimal weight: 7.9990 chunk 519 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 315 optimal weight: 5.9990 chunk 386 optimal weight: 40.0000 chunk 602 optimal weight: 50.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 165 ASN A 193 HIS B 148 ASN B 208 HIS C 113 GLN D 57 ASN D 159 HIS E 8 HIS ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN F 186 ASN F 203 ASN G 13 GLN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN G 186 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 HIS H 186 ASN H 193 GLN I 84 ASN ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 GLN ** J 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 HIS L 11 GLN ** L 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 ASN P 32 GLN P 54 HIS P 128 HIS ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 HIS Q 86 GLN ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 GLN T 128 GLN T 137 GLN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 HIS ** V 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN W 16 ASN ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS W 98 GLN W 113 HIS ** X 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 61 GLN ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 77 ASN X 127 ASN Y 85 ASN ** e 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 56 ASN f 139 HIS g 20 GLN ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 86141 Z= 0.339 Angle : 0.801 38.211 125784 Z= 0.403 Chirality : 0.043 1.562 15671 Planarity : 0.007 0.096 8637 Dihedral : 23.367 179.892 36187 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.28 % Favored : 93.23 % Rotamer: Outliers : 6.65 % Allowed : 19.21 % Favored : 74.14 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.11 % 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: -2.05 (0.11), residues: 4744 helix: -1.01 (0.12), residues: 1422 sheet: -0.78 (0.16), residues: 820 loop : -1.76 (0.11), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 55 HIS 0.015 0.002 HIS J 124 PHE 0.035 0.003 PHE Y 64 TYR 0.032 0.003 TYR A 47 ARG 0.016 0.001 ARG O 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1895 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1619 time to evaluate : 4.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.4855 (OUTLIER) cc_final: 0.3867 (t0) REVERT: A 36 GLN cc_start: 0.7615 (pm20) cc_final: 0.7166 (pp30) REVERT: A 70 ASN cc_start: 0.6595 (t0) cc_final: 0.6344 (t0) REVERT: A 120 ARG cc_start: 0.6387 (OUTLIER) cc_final: 0.6153 (mtp-110) REVERT: A 149 ASN cc_start: 0.6743 (p0) cc_final: 0.6312 (p0) REVERT: B 26 SER cc_start: 0.7909 (p) cc_final: 0.7586 (p) REVERT: B 115 LYS cc_start: 0.5243 (tttp) cc_final: 0.4910 (mtpp) REVERT: B 126 ASP cc_start: 0.7612 (m-30) cc_final: 0.7369 (m-30) REVERT: B 152 LYS cc_start: 0.6319 (OUTLIER) cc_final: 0.5912 (pttm) REVERT: B 155 TYR cc_start: 0.7714 (m-10) cc_final: 0.7132 (m-80) REVERT: C 68 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.6369 (ptm160) REVERT: C 93 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7932 (tt) REVERT: E 62 LYS cc_start: 0.6491 (tptt) cc_final: 0.6160 (tptt) REVERT: E 182 MET cc_start: 0.8239 (tmm) cc_final: 0.7942 (tmm) REVERT: F 190 ILE cc_start: 0.6736 (mt) cc_final: 0.6399 (tp) REVERT: F 202 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7295 (m) REVERT: G 12 CYS cc_start: 0.7635 (p) cc_final: 0.7230 (p) REVERT: H 43 LEU cc_start: 0.5713 (OUTLIER) cc_final: 0.5323 (mm) REVERT: H 97 GLN cc_start: 0.4419 (pt0) cc_final: 0.3739 (tt0) REVERT: H 122 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.5298 (mt) REVERT: H 133 LEU cc_start: 0.7180 (mt) cc_final: 0.6742 (mt) REVERT: I 92 ARG cc_start: 0.5518 (mmm-85) cc_final: 0.4506 (tpt-90) REVERT: I 152 ARG cc_start: 0.4904 (mpt180) cc_final: 0.4697 (mmt90) REVERT: J 52 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7544 (mtpp) REVERT: J 107 GLU cc_start: 0.6787 (tp30) cc_final: 0.6522 (tp30) REVERT: J 129 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8166 (tp) REVERT: J 152 ASP cc_start: 0.6568 (p0) cc_final: 0.6298 (p0) REVERT: M 26 LEU cc_start: 0.4826 (OUTLIER) cc_final: 0.3960 (tp) REVERT: N 32 ASP cc_start: 0.5197 (m-30) cc_final: 0.4646 (m-30) REVERT: N 127 ARG cc_start: 0.5960 (ttt180) cc_final: 0.5743 (tpp80) REVERT: O 60 MET cc_start: 0.5156 (OUTLIER) cc_final: 0.4897 (mtp) REVERT: P 86 LEU cc_start: 0.1994 (OUTLIER) cc_final: 0.1613 (tt) REVERT: R 79 GLU cc_start: 0.5253 (pt0) cc_final: 0.4769 (pt0) REVERT: S 90 VAL cc_start: 0.3099 (OUTLIER) cc_final: 0.2699 (t) REVERT: T 54 TYR cc_start: 0.4825 (m-80) cc_final: 0.4518 (m-80) REVERT: T 64 LEU cc_start: 0.8015 (pp) cc_final: 0.7672 (tt) REVERT: V 11 LEU cc_start: 0.7627 (mt) cc_final: 0.7013 (mt) REVERT: V 47 ASN cc_start: 0.7425 (m110) cc_final: 0.7073 (m110) REVERT: W 11 LEU cc_start: 0.7645 (mt) cc_final: 0.7444 (mt) REVERT: W 98 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7211 (mm-40) REVERT: X 96 GLU cc_start: 0.7927 (tp30) cc_final: 0.7647 (tp30) REVERT: X 97 ASN cc_start: 0.7684 (m110) cc_final: 0.6948 (m110) REVERT: Y 74 MET cc_start: 0.5649 (mmm) cc_final: 0.5440 (mmm) REVERT: d 52 PHE cc_start: 0.3719 (m-80) cc_final: 0.3400 (m-10) REVERT: g 197 THR cc_start: 0.5914 (t) cc_final: 0.5509 (m) outliers start: 276 outliers final: 167 residues processed: 1747 average time/residue: 0.8261 time to fit residues: 2396.4396 Evaluate side-chains 1513 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1332 time to evaluate : 4.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 TRP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 181 CYS Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 182 LYS Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 149 TYR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 100 ASN Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 82 TYR Chi-restraints excluded: chain Q residue 89 SER Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 116 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain S residue 11 HIS Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 77 TYR Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 111 LYS Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 66 ARG Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain V residue 56 CYS Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 28 ARG Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 113 HIS Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 107 ARG Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 34 THR Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 93 SER Chi-restraints excluded: chain Z residue 110 THR Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 51 ARG Chi-restraints excluded: chain a residue 54 SER Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 85 ARG Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain c residue 34 PHE Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain e residue 16 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 56 ASN Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 170 TRP Chi-restraints excluded: chain g residue 239 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 334 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 501 optimal weight: 9.9990 chunk 409 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 603 optimal weight: 9.9990 chunk 651 optimal weight: 20.0000 chunk 537 optimal weight: 3.9990 chunk 598 optimal weight: 20.0000 chunk 205 optimal weight: 5.9990 chunk 483 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 157 GLN C 115 GLN C 267 GLN ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN G 65 GLN G 81 HIS G 186 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 HIS I 84 ASN J 111 GLN ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS L 19 ASN L 83 GLN ** L 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 ASN N 13 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 ASN Q 11 GLN ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 81 GLN U 85 HIS ** V 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN V 33 GLN W 16 ASN ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 90 GLN W 92 ASN W 98 GLN W 113 HIS X 20 GLN X 31 HIS ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 ASN ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 GLN ** d 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 86141 Z= 0.252 Angle : 0.718 37.233 125784 Z= 0.361 Chirality : 0.040 1.583 15671 Planarity : 0.006 0.083 8637 Dihedral : 23.374 179.974 36181 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.96 % Favored : 92.62 % Rotamer: Outliers : 7.04 % Allowed : 22.56 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.80 (0.11), residues: 4744 helix: -0.60 (0.13), residues: 1430 sheet: -0.71 (0.17), residues: 843 loop : -1.73 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP g 17 HIS 0.018 0.002 HIS W 113 PHE 0.029 0.003 PHE A 103 TYR 0.035 0.002 TYR K 12 ARG 0.015 0.001 ARG Z 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1773 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1481 time to evaluate : 4.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.4972 (OUTLIER) cc_final: 0.4202 (t0) REVERT: A 149 ASN cc_start: 0.6676 (p0) cc_final: 0.6242 (p0) REVERT: B 152 LYS cc_start: 0.6255 (OUTLIER) cc_final: 0.5938 (pttm) REVERT: B 155 TYR cc_start: 0.7523 (m-10) cc_final: 0.7108 (m-80) REVERT: E 20 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7371 (mm) REVERT: E 62 LYS cc_start: 0.6619 (tptt) cc_final: 0.6344 (tptt) REVERT: F 145 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6981 (ttt-90) REVERT: G 12 CYS cc_start: 0.7562 (p) cc_final: 0.7149 (p) REVERT: G 13 GLN cc_start: 0.7702 (mp10) cc_final: 0.7409 (mp10) REVERT: H 43 LEU cc_start: 0.5468 (OUTLIER) cc_final: 0.5184 (mm) REVERT: I 53 LYS cc_start: 0.6693 (mmmt) cc_final: 0.6469 (mmmt) REVERT: I 92 ARG cc_start: 0.5408 (mmm-85) cc_final: 0.4866 (mmt180) REVERT: I 198 TYR cc_start: 0.7722 (m-80) cc_final: 0.7504 (m-80) REVERT: J 129 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8001 (tp) REVERT: J 152 ASP cc_start: 0.6579 (p0) cc_final: 0.6296 (p0) REVERT: K 3 MET cc_start: 0.2298 (mpp) cc_final: 0.2086 (mpp) REVERT: K 69 TRP cc_start: 0.3771 (m-90) cc_final: 0.3565 (m-90) REVERT: M 26 LEU cc_start: 0.4866 (OUTLIER) cc_final: 0.4010 (tp) REVERT: M 44 LYS cc_start: 0.6072 (mttt) cc_final: 0.5479 (mmtt) REVERT: N 109 LYS cc_start: 0.7141 (ptpp) cc_final: 0.6935 (ptpt) REVERT: O 52 THR cc_start: 0.7795 (p) cc_final: 0.7538 (p) REVERT: R 79 GLU cc_start: 0.5413 (pt0) cc_final: 0.5032 (pt0) REVERT: V 46 PHE cc_start: 0.6682 (t80) cc_final: 0.6459 (t80) REVERT: W 11 LEU cc_start: 0.7446 (mt) cc_final: 0.7114 (mt) REVERT: W 118 ARG cc_start: 0.6502 (mtm110) cc_final: 0.6288 (mtm110) REVERT: X 96 GLU cc_start: 0.8001 (tp30) cc_final: 0.7601 (tp30) REVERT: X 97 ASN cc_start: 0.7649 (m110) cc_final: 0.6791 (m110) REVERT: b 31 TYR cc_start: 0.7322 (p90) cc_final: 0.7041 (p90) REVERT: c 59 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7202 (pt) REVERT: d 52 PHE cc_start: 0.4057 (m-80) cc_final: 0.3507 (m-10) REVERT: g 79 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7871 (tp) REVERT: g 220 ASP cc_start: 0.3231 (t0) cc_final: 0.2045 (t0) outliers start: 292 outliers final: 173 residues processed: 1602 average time/residue: 0.8613 time to fit residues: 2322.1286 Evaluate side-chains 1493 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1311 time to evaluate : 4.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 181 CYS Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 182 LYS Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 168 HIS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 149 TYR Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 100 ASN Chi-restraints excluded: chain L residue 101 ARG Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 116 ASP Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 105 MET Chi-restraints excluded: chain S residue 11 HIS Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 77 TYR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 79 TYR Chi-restraints excluded: chain T residue 105 GLN Chi-restraints excluded: chain T residue 111 LYS Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain U residue 66 ARG Chi-restraints excluded: chain V residue 56 CYS Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 28 ARG Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 61 ILE Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 96 SER Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 113 HIS Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 19 ASP Chi-restraints excluded: chain X residue 34 THR Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 110 THR Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 71 LEU Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 34 PHE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 59 LEU Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 170 TRP Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 239 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 595 optimal weight: 8.9990 chunk 453 optimal weight: 30.0000 chunk 313 optimal weight: 10.0000 chunk 66 optimal weight: 30.0000 chunk 287 optimal weight: 8.9990 chunk 405 optimal weight: 20.0000 chunk 605 optimal weight: 30.0000 chunk 640 optimal weight: 20.0000 chunk 316 optimal weight: 3.9990 chunk 573 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 193 HIS B 208 HIS ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN F 186 ASN G 56 ASN G 186 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN N 36 GLN N 62 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 HIS O 79 GLN ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN T 137 GLN ** V 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 33 GLN ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 GLN ** W 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 61 GLN ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 64 ASN b 26 GLN ** d 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 GLN e 56 ASN g 56 GLN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 86141 Z= 0.305 Angle : 0.782 39.172 125784 Z= 0.393 Chirality : 0.043 1.610 15671 Planarity : 0.006 0.081 8637 Dihedral : 23.479 179.297 36177 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.76 % Favored : 91.74 % Rotamer: Outliers : 7.95 % Allowed : 23.36 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.79 (0.11), residues: 4744 helix: -0.49 (0.13), residues: 1431 sheet: -0.71 (0.17), residues: 849 loop : -1.80 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP S 82 HIS 0.029 0.002 HIS H 168 PHE 0.027 0.003 PHE J 48 TYR 0.041 0.003 TYR X 27 ARG 0.018 0.001 ARG Z 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1738 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 1408 time to evaluate : 4.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.5219 (OUTLIER) cc_final: 0.4344 (t0) REVERT: A 39 TYR cc_start: 0.6320 (t80) cc_final: 0.6039 (t80) REVERT: B 120 MET cc_start: 0.7633 (ttp) cc_final: 0.7423 (ttm) REVERT: B 155 TYR cc_start: 0.7673 (m-10) cc_final: 0.7447 (m-80) REVERT: B 180 ASP cc_start: 0.5871 (t70) cc_final: 0.5410 (t0) REVERT: B 220 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7959 (mmtt) REVERT: E 9 LEU cc_start: 0.8042 (tp) cc_final: 0.7740 (tp) REVERT: E 20 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7460 (mm) REVERT: E 72 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7919 (pt) REVERT: E 182 MET cc_start: 0.8401 (tmm) cc_final: 0.8127 (tmm) REVERT: F 191 LYS cc_start: 0.5932 (mptt) cc_final: 0.4976 (mptt) REVERT: F 202 SER cc_start: 0.8113 (OUTLIER) cc_final: 0.7725 (p) REVERT: G 12 CYS cc_start: 0.7648 (p) cc_final: 0.7389 (p) REVERT: H 77 VAL cc_start: 0.7655 (t) cc_final: 0.7319 (t) REVERT: H 97 GLN cc_start: 0.4296 (OUTLIER) cc_final: 0.3692 (tt0) REVERT: I 93 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7999 (m) REVERT: I 152 ARG cc_start: 0.5091 (mpt180) cc_final: 0.4852 (mmt90) REVERT: J 3 VAL cc_start: 0.6971 (m) cc_final: 0.6740 (m) REVERT: J 42 GLU cc_start: 0.6161 (mp0) cc_final: 0.5887 (pm20) REVERT: J 107 GLU cc_start: 0.6851 (tp30) cc_final: 0.6364 (tp30) REVERT: J 129 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8194 (tp) REVERT: J 152 ASP cc_start: 0.6761 (p0) cc_final: 0.6478 (p0) REVERT: M 26 LEU cc_start: 0.5057 (OUTLIER) cc_final: 0.4053 (tp) REVERT: O 52 THR cc_start: 0.7662 (p) cc_final: 0.7396 (p) REVERT: P 62 LYS cc_start: 0.5316 (OUTLIER) cc_final: 0.4798 (pttt) REVERT: Q 82 TYR cc_start: 0.4824 (OUTLIER) cc_final: 0.4179 (t80) REVERT: Q 105 LYS cc_start: 0.3563 (tppt) cc_final: 0.3253 (tppt) REVERT: Q 141 TYR cc_start: 0.6293 (m-80) cc_final: 0.5838 (m-10) REVERT: R 79 GLU cc_start: 0.5175 (pt0) cc_final: 0.4811 (pt0) REVERT: S 90 VAL cc_start: 0.3188 (OUTLIER) cc_final: 0.2573 (t) REVERT: T 94 ARG cc_start: 0.4773 (mmp80) cc_final: 0.3642 (mmm160) REVERT: V 3 ASN cc_start: 0.4819 (p0) cc_final: 0.4492 (p0) REVERT: W 39 THR cc_start: 0.7872 (p) cc_final: 0.7475 (t) REVERT: b 31 TYR cc_start: 0.7185 (p90) cc_final: 0.6796 (p90) REVERT: c 59 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7220 (pt) REVERT: d 52 PHE cc_start: 0.4194 (m-80) cc_final: 0.3873 (m-10) REVERT: g 79 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8124 (tp) REVERT: g 223 GLU cc_start: 0.5948 (pt0) cc_final: 0.5497 (pt0) outliers start: 330 outliers final: 212 residues processed: 1563 average time/residue: 0.8720 time to fit residues: 2309.6185 Evaluate side-chains 1499 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1273 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 181 CYS Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 182 LYS Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 100 ASN Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 53 GLU Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain Q residue 82 TYR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 116 ASP Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain S residue 11 HIS Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 77 TYR Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 79 TYR Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 111 LYS Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 56 CYS Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 28 ARG Chi-restraints excluded: chain W residue 34 ILE Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 61 ILE Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 96 SER Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 113 HIS Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 19 ASP Chi-restraints excluded: chain X residue 34 THR Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 61 GLN Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 93 SER Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Z residue 110 THR Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 71 LEU Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 34 PHE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 59 LEU Chi-restraints excluded: chain c residue 62 GLU Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain e residue 16 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain g residue 48 ASP Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 170 TRP Chi-restraints excluded: chain g residue 189 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 533 optimal weight: 5.9990 chunk 363 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 477 optimal weight: 8.9990 chunk 264 optimal weight: 9.9990 chunk 546 optimal weight: 5.9990 chunk 442 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 327 optimal weight: 3.9990 chunk 575 optimal weight: 2.9990 chunk 161 optimal weight: 30.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN D 159 HIS ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 HIS I 84 ASN J 113 GLN ** J 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 HIS ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 HIS L 83 GLN N 49 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 HIS Q 11 GLN ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 GLN ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN Z 106 GLN ** d 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 86141 Z= 0.189 Angle : 0.695 36.316 125784 Z= 0.347 Chirality : 0.040 1.697 15671 Planarity : 0.005 0.067 8637 Dihedral : 23.431 179.671 36177 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.65 % Favored : 91.88 % Rotamer: Outliers : 6.10 % Allowed : 26.80 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.63 (0.12), residues: 4744 helix: -0.28 (0.13), residues: 1433 sheet: -0.66 (0.17), residues: 836 loop : -1.73 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 45 HIS 0.012 0.001 HIS O 43 PHE 0.039 0.002 PHE A 203 TYR 0.044 0.002 TYR X 27 ARG 0.023 0.001 ARG U 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1658 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1405 time to evaluate : 4.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.5488 (OUTLIER) cc_final: 0.4884 (t0) REVERT: A 198 MET cc_start: 0.6029 (tpp) cc_final: 0.4066 (ttt) REVERT: B 155 TYR cc_start: 0.7700 (m-10) cc_final: 0.7298 (m-80) REVERT: D 167 TYR cc_start: 0.6102 (OUTLIER) cc_final: 0.5433 (t80) REVERT: E 19 MET cc_start: 0.8205 (mtt) cc_final: 0.7757 (ttm) REVERT: F 187 SER cc_start: 0.5660 (p) cc_final: 0.5207 (p) REVERT: F 191 LYS cc_start: 0.6024 (mptt) cc_final: 0.5792 (mptt) REVERT: G 26 THR cc_start: 0.7503 (p) cc_final: 0.7031 (m) REVERT: H 97 GLN cc_start: 0.4017 (OUTLIER) cc_final: 0.3746 (tt0) REVERT: H 120 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7065 (mmp80) REVERT: H 130 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7101 (tm) REVERT: I 95 THR cc_start: 0.8165 (p) cc_final: 0.7860 (t) REVERT: J 152 ASP cc_start: 0.6662 (p0) cc_final: 0.6316 (p0) REVERT: L 13 GLN cc_start: 0.6322 (pp30) cc_final: 0.5991 (pt0) REVERT: L 39 ASN cc_start: 0.8460 (t0) cc_final: 0.8169 (t0) REVERT: M 26 LEU cc_start: 0.5125 (OUTLIER) cc_final: 0.4333 (tp) REVERT: N 74 ILE cc_start: 0.7728 (mt) cc_final: 0.7502 (tt) REVERT: O 52 THR cc_start: 0.7786 (p) cc_final: 0.7475 (p) REVERT: Q 96 TYR cc_start: 0.2524 (OUTLIER) cc_final: 0.2079 (m-10) REVERT: Q 129 SER cc_start: 0.6809 (t) cc_final: 0.6406 (p) REVERT: R 63 ARG cc_start: 0.6207 (tpp80) cc_final: 0.5944 (tpp80) REVERT: R 79 GLU cc_start: 0.4939 (pt0) cc_final: 0.4703 (pt0) REVERT: S 16 LEU cc_start: 0.7245 (mm) cc_final: 0.6915 (mt) REVERT: T 94 ARG cc_start: 0.4557 (mmp80) cc_final: 0.3780 (mmm160) REVERT: W 4 MET cc_start: 0.8278 (pmm) cc_final: 0.8029 (mpp) REVERT: W 114 GLU cc_start: 0.5929 (tm-30) cc_final: 0.5698 (tm-30) REVERT: b 31 TYR cc_start: 0.7076 (p90) cc_final: 0.6844 (p90) REVERT: d 52 PHE cc_start: 0.4255 (m-80) cc_final: 0.3888 (m-10) outliers start: 253 outliers final: 168 residues processed: 1520 average time/residue: 0.8167 time to fit residues: 2097.9304 Evaluate side-chains 1452 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1277 time to evaluate : 4.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 181 CYS Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 182 LYS Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 120 ARG Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 105 PHE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 121 GLN Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 5 HIS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 53 GLU Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 96 TYR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 77 TYR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 79 TYR Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 111 LYS Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain V residue 21 ASN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 56 CYS Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 28 ARG Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 113 HIS Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 67 ARG Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 93 SER Chi-restraints excluded: chain Z residue 98 LYS Chi-restraints excluded: chain a residue 8 ASN Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 71 LEU Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 34 PHE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain e residue 16 THR Chi-restraints excluded: chain e residue 56 ASN Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain g residue 48 ASP Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 170 TRP Chi-restraints excluded: chain g residue 195 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 215 optimal weight: 4.9990 chunk 577 optimal weight: 8.9990 chunk 126 optimal weight: 30.0000 chunk 376 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 641 optimal weight: 20.0000 chunk 532 optimal weight: 8.9990 chunk 297 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 212 optimal weight: 7.9990 chunk 336 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN H 126 HIS ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 HIS O 43 HIS O 94 HIS P 46 ASN Q 11 GLN ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 GLN ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 61 GLN Z 106 GLN ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 ASN ** d 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 44 ASN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 296 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 86141 Z= 0.307 Angle : 0.784 39.879 125784 Z= 0.394 Chirality : 0.043 1.693 15671 Planarity : 0.006 0.084 8637 Dihedral : 23.542 179.650 36177 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.66 % Favored : 90.81 % Rotamer: Outliers : 6.80 % Allowed : 27.50 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.12), residues: 4744 helix: -0.39 (0.13), residues: 1417 sheet: -0.78 (0.17), residues: 867 loop : -1.79 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP G 45 HIS 0.011 0.002 HIS g 14 PHE 0.036 0.003 PHE J 48 TYR 0.026 0.003 TYR K 12 ARG 0.023 0.001 ARG Z 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1617 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1335 time to evaluate : 4.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.5466 (OUTLIER) cc_final: 0.4778 (t0) REVERT: A 149 ASN cc_start: 0.7264 (p0) cc_final: 0.6730 (p0) REVERT: A 156 TYR cc_start: 0.7728 (m-80) cc_final: 0.7219 (m-80) REVERT: A 198 MET cc_start: 0.6113 (tpp) cc_final: 0.3856 (ttt) REVERT: B 39 PHE cc_start: 0.5861 (OUTLIER) cc_final: 0.5110 (m-80) REVERT: B 155 TYR cc_start: 0.7844 (m-10) cc_final: 0.7492 (m-80) REVERT: B 163 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6733 (mp10) REVERT: C 122 THR cc_start: 0.6911 (m) cc_final: 0.6640 (p) REVERT: C 266 TYR cc_start: 0.4922 (m-80) cc_final: 0.4565 (m-10) REVERT: E 9 LEU cc_start: 0.8180 (tp) cc_final: 0.7907 (tp) REVERT: E 19 MET cc_start: 0.8193 (mtt) cc_final: 0.7739 (ttm) REVERT: E 182 MET cc_start: 0.8430 (tmm) cc_final: 0.8167 (tmm) REVERT: F 97 PHE cc_start: 0.5421 (t80) cc_final: 0.5137 (t80) REVERT: F 142 SER cc_start: 0.8507 (t) cc_final: 0.7750 (p) REVERT: F 187 SER cc_start: 0.6169 (p) cc_final: 0.5728 (p) REVERT: F 191 LYS cc_start: 0.6080 (mptt) cc_final: 0.5336 (mptt) REVERT: F 202 SER cc_start: 0.8013 (OUTLIER) cc_final: 0.7763 (p) REVERT: G 26 THR cc_start: 0.7661 (p) cc_final: 0.7236 (m) REVERT: H 52 GLU cc_start: 0.5615 (OUTLIER) cc_final: 0.5403 (tt0) REVERT: H 97 GLN cc_start: 0.4531 (OUTLIER) cc_final: 0.4239 (tt0) REVERT: H 120 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7312 (mmp-170) REVERT: H 154 ILE cc_start: 0.7761 (mp) cc_final: 0.7482 (mp) REVERT: I 137 LEU cc_start: 0.5377 (pt) cc_final: 0.5033 (pt) REVERT: J 152 ASP cc_start: 0.6665 (p0) cc_final: 0.6389 (p0) REVERT: K 3 MET cc_start: 0.2237 (mpp) cc_final: 0.2011 (mpp) REVERT: L 13 GLN cc_start: 0.6457 (pp30) cc_final: 0.6182 (pt0) REVERT: L 37 TYR cc_start: 0.5333 (t80) cc_final: 0.5122 (t80) REVERT: L 39 ASN cc_start: 0.8397 (t0) cc_final: 0.8126 (t0) REVERT: M 26 LEU cc_start: 0.4959 (OUTLIER) cc_final: 0.4224 (tp) REVERT: O 43 HIS cc_start: 0.6310 (OUTLIER) cc_final: 0.6085 (t70) REVERT: O 52 THR cc_start: 0.7816 (p) cc_final: 0.7513 (p) REVERT: P 62 LYS cc_start: 0.5529 (OUTLIER) cc_final: 0.5171 (pttt) REVERT: Q 96 TYR cc_start: 0.2996 (OUTLIER) cc_final: 0.2713 (m-10) REVERT: Q 141 TYR cc_start: 0.6185 (m-80) cc_final: 0.5972 (m-10) REVERT: R 79 GLU cc_start: 0.5385 (pt0) cc_final: 0.4950 (pt0) REVERT: T 94 ARG cc_start: 0.4676 (mmp80) cc_final: 0.3699 (mmm160) REVERT: U 77 TRP cc_start: 0.6126 (m100) cc_final: 0.5669 (m100) REVERT: V 3 ASN cc_start: 0.5417 (p0) cc_final: 0.5182 (p0) REVERT: X 96 GLU cc_start: 0.8167 (tp30) cc_final: 0.7815 (tp30) REVERT: a 73 TYR cc_start: 0.6700 (m-10) cc_final: 0.6262 (m-10) REVERT: b 31 TYR cc_start: 0.7289 (p90) cc_final: 0.6995 (p90) REVERT: d 23 VAL cc_start: 0.6638 (t) cc_final: 0.6428 (t) REVERT: d 52 PHE cc_start: 0.4533 (OUTLIER) cc_final: 0.4197 (m-10) outliers start: 282 outliers final: 198 residues processed: 1468 average time/residue: 0.7947 time to fit residues: 1971.5691 Evaluate side-chains 1458 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1248 time to evaluate : 4.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 181 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 182 LYS Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 120 ARG Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 168 HIS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 121 GLN Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 5 HIS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 43 HIS Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 HIS Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 96 TYR Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 21 TYR Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 45 LYS Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 77 TYR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 135 HIS Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 79 TYR Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 111 LYS Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 56 CYS Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 28 ARG Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 113 HIS Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 67 ARG Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 93 SER Chi-restraints excluded: chain Z residue 98 LYS Chi-restraints excluded: chain Z residue 110 THR Chi-restraints excluded: chain a residue 8 ASN Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 71 LEU Chi-restraints excluded: chain a residue 88 SER Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain c residue 34 PHE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain d residue 52 PHE Chi-restraints excluded: chain e residue 16 THR Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 56 ASN Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 48 ASP Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 170 TRP Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 268 ASP Chi-restraints excluded: chain g residue 309 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 618 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 365 optimal weight: 2.9990 chunk 468 optimal weight: 4.9990 chunk 362 optimal weight: 10.0000 chunk 539 optimal weight: 9.9990 chunk 358 optimal weight: 0.0270 chunk 639 optimal weight: 30.0000 chunk 399 optimal weight: 5.9990 chunk 389 optimal weight: 6.9990 chunk 295 optimal weight: 3.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS E 17 HIS E 216 ASN ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 181 GLN ** J 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 62 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 HIS O 94 HIS Q 97 GLN ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 GLN ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 61 GLN Z 106 GLN ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 24 GLN ** d 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 GLN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 86141 Z= 0.210 Angle : 0.721 37.511 125784 Z= 0.360 Chirality : 0.041 1.749 15671 Planarity : 0.006 0.098 8637 Dihedral : 23.506 179.498 36177 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.18 % Favored : 91.32 % Rotamer: Outliers : 6.12 % Allowed : 29.77 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.12), residues: 4744 helix: -0.26 (0.13), residues: 1420 sheet: -0.75 (0.17), residues: 857 loop : -1.77 (0.12), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP G 45 HIS 0.023 0.002 HIS O 94 PHE 0.042 0.003 PHE A 32 TYR 0.029 0.002 TYR S 95 ARG 0.022 0.001 ARG Z 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1567 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1313 time to evaluate : 4.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.5557 (OUTLIER) cc_final: 0.5056 (t0) REVERT: A 148 CYS cc_start: 0.6929 (p) cc_final: 0.6465 (p) REVERT: A 156 TYR cc_start: 0.7728 (m-80) cc_final: 0.7294 (m-80) REVERT: A 198 MET cc_start: 0.6009 (tpp) cc_final: 0.4155 (ttt) REVERT: B 155 TYR cc_start: 0.7751 (m-10) cc_final: 0.7429 (m-80) REVERT: B 163 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6621 (mp10) REVERT: B 179 ASN cc_start: 0.5502 (m110) cc_final: 0.4831 (m110) REVERT: B 205 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.6443 (m-80) REVERT: B 220 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7994 (mmtt) REVERT: E 19 MET cc_start: 0.8156 (mtt) cc_final: 0.7839 (ttm) REVERT: F 191 LYS cc_start: 0.6061 (OUTLIER) cc_final: 0.5510 (mptt) REVERT: G 26 THR cc_start: 0.7651 (p) cc_final: 0.7315 (m) REVERT: G 65 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7620 (tp-100) REVERT: H 52 GLU cc_start: 0.5842 (OUTLIER) cc_final: 0.5639 (tt0) REVERT: H 120 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7185 (mmp80) REVERT: I 95 THR cc_start: 0.8150 (p) cc_final: 0.7826 (t) REVERT: I 137 LEU cc_start: 0.5338 (pt) cc_final: 0.5137 (pt) REVERT: J 152 ASP cc_start: 0.6573 (p0) cc_final: 0.6315 (p0) REVERT: L 13 GLN cc_start: 0.6337 (pp30) cc_final: 0.6097 (pt0) REVERT: L 39 ASN cc_start: 0.8371 (t0) cc_final: 0.8128 (t0) REVERT: L 90 ARG cc_start: 0.7708 (mmm-85) cc_final: 0.7485 (mtp85) REVERT: M 26 LEU cc_start: 0.4881 (OUTLIER) cc_final: 0.4119 (tp) REVERT: O 52 THR cc_start: 0.7677 (p) cc_final: 0.7406 (p) REVERT: O 124 MET cc_start: 0.6801 (mmm) cc_final: 0.6544 (mmm) REVERT: P 62 LYS cc_start: 0.5385 (OUTLIER) cc_final: 0.4850 (pttt) REVERT: S 59 LEU cc_start: 0.4973 (mp) cc_final: 0.4771 (mp) REVERT: T 94 ARG cc_start: 0.4625 (mmp80) cc_final: 0.3833 (mmm160) REVERT: U 77 TRP cc_start: 0.6084 (m100) cc_final: 0.5710 (m100) REVERT: V 3 ASN cc_start: 0.5322 (p0) cc_final: 0.5068 (p0) REVERT: W 87 GLU cc_start: 0.5997 (mm-30) cc_final: 0.5676 (mm-30) REVERT: W 90 GLN cc_start: 0.7883 (mp10) cc_final: 0.7398 (mp10) REVERT: X 96 GLU cc_start: 0.8236 (tp30) cc_final: 0.7993 (tp30) REVERT: Y 51 THR cc_start: 0.7803 (t) cc_final: 0.7563 (m) REVERT: Y 53 ASP cc_start: 0.7429 (p0) cc_final: 0.6593 (t70) REVERT: a 73 TYR cc_start: 0.6501 (m-10) cc_final: 0.6242 (m-10) REVERT: b 31 TYR cc_start: 0.7129 (p90) cc_final: 0.6913 (p90) REVERT: b 36 LYS cc_start: 0.6879 (mptt) cc_final: 0.6668 (mtpp) REVERT: d 52 PHE cc_start: 0.4722 (m-80) cc_final: 0.4321 (m-10) REVERT: g 302 TYR cc_start: 0.5459 (m-80) cc_final: 0.5055 (m-10) outliers start: 254 outliers final: 192 residues processed: 1437 average time/residue: 0.7901 time to fit residues: 1927.2396 Evaluate side-chains 1453 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1251 time to evaluate : 4.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 181 CYS Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 218 PHE Chi-restraints excluded: chain E residue 221 ARG Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 182 LYS Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 120 ARG Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 168 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 174 CYS Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 121 GLN Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 5 HIS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 54 CYS Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 94 HIS Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 77 TYR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain S residue 135 HIS Chi-restraints excluded: chain T residue 79 TYR Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 111 LYS Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 56 CYS Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 28 ARG Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 113 HIS Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 61 GLN Chi-restraints excluded: chain X residue 67 ARG Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 75 ILE Chi-restraints excluded: chain Y residue 89 HIS Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 93 SER Chi-restraints excluded: chain Z residue 98 LYS Chi-restraints excluded: chain a residue 8 ASN Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 71 LEU Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain c residue 34 PHE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain e residue 16 THR Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 56 ASN Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 115 SER Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain g residue 14 HIS Chi-restraints excluded: chain g residue 48 ASP Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 170 TRP Chi-restraints excluded: chain g residue 195 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 395 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 381 optimal weight: 10.0000 chunk 192 optimal weight: 0.9980 chunk 125 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 406 optimal weight: 7.9990 chunk 435 optimal weight: 0.9990 chunk 315 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 502 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 181 GLN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 HIS O 43 HIS O 94 HIS ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 GLN ** V 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 61 GLN ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 24 GLN ** d 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.6890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 86141 Z= 0.237 Angle : 0.733 37.532 125784 Z= 0.367 Chirality : 0.041 1.756 15671 Planarity : 0.006 0.079 8637 Dihedral : 23.502 179.663 36177 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.06 % Favored : 90.41 % Rotamer: Outliers : 6.00 % Allowed : 30.44 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.71 (0.12), residues: 4744 helix: -0.24 (0.13), residues: 1408 sheet: -0.78 (0.17), residues: 865 loop : -1.82 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP F 23 HIS 0.035 0.002 HIS O 94 PHE 0.039 0.003 PHE A 203 TYR 0.033 0.002 TYR S 95 ARG 0.024 0.001 ARG Z 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1547 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1298 time to evaluate : 4.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.5526 (OUTLIER) cc_final: 0.5190 (t0) REVERT: A 118 GLU cc_start: 0.7547 (pp20) cc_final: 0.7218 (pp20) REVERT: A 156 TYR cc_start: 0.7738 (m-80) cc_final: 0.7263 (m-80) REVERT: A 198 MET cc_start: 0.6088 (tpp) cc_final: 0.4406 (ttt) REVERT: A 200 ASP cc_start: 0.5914 (m-30) cc_final: 0.5690 (m-30) REVERT: B 155 TYR cc_start: 0.7734 (m-10) cc_final: 0.7452 (m-80) REVERT: B 163 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6653 (mp10) REVERT: B 205 TYR cc_start: 0.6946 (OUTLIER) cc_final: 0.6414 (m-10) REVERT: B 220 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8081 (mmtt) REVERT: D 135 GLU cc_start: 0.5067 (mp0) cc_final: 0.4679 (mp0) REVERT: E 19 MET cc_start: 0.8249 (mtt) cc_final: 0.7891 (ttm) REVERT: F 142 SER cc_start: 0.8447 (t) cc_final: 0.7610 (p) REVERT: F 187 SER cc_start: 0.6115 (p) cc_final: 0.5802 (p) REVERT: F 202 SER cc_start: 0.7880 (p) cc_final: 0.7620 (p) REVERT: H 52 GLU cc_start: 0.5759 (OUTLIER) cc_final: 0.5548 (tt0) REVERT: H 120 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7213 (mmp80) REVERT: J 107 GLU cc_start: 0.6945 (tp30) cc_final: 0.6711 (tp30) REVERT: J 152 ASP cc_start: 0.6615 (p0) cc_final: 0.6369 (p0) REVERT: L 39 ASN cc_start: 0.8324 (t0) cc_final: 0.8096 (t0) REVERT: L 90 ARG cc_start: 0.7765 (mmm-85) cc_final: 0.7427 (mtp85) REVERT: M 26 LEU cc_start: 0.5045 (OUTLIER) cc_final: 0.4356 (tp) REVERT: O 52 THR cc_start: 0.7775 (p) cc_final: 0.7517 (p) REVERT: O 69 SER cc_start: 0.7310 (t) cc_final: 0.6973 (t) REVERT: O 142 ARG cc_start: 0.7064 (tpt90) cc_final: 0.6859 (tpt90) REVERT: S 59 LEU cc_start: 0.4962 (mp) cc_final: 0.4740 (mp) REVERT: T 94 ARG cc_start: 0.4666 (mmp80) cc_final: 0.3872 (mmm160) REVERT: U 77 TRP cc_start: 0.5974 (m100) cc_final: 0.5731 (m100) REVERT: V 3 ASN cc_start: 0.5311 (p0) cc_final: 0.5063 (p0) REVERT: W 61 ILE cc_start: 0.8569 (mp) cc_final: 0.8368 (mp) REVERT: W 90 GLN cc_start: 0.7972 (mp10) cc_final: 0.7595 (mp10) REVERT: X 96 GLU cc_start: 0.8128 (tp30) cc_final: 0.7923 (tp30) REVERT: a 89 ARG cc_start: 0.7855 (tmm-80) cc_final: 0.7539 (ttp80) REVERT: b 31 TYR cc_start: 0.7198 (p90) cc_final: 0.6824 (p90) REVERT: d 52 PHE cc_start: 0.4520 (m-80) cc_final: 0.4019 (m-10) REVERT: d 54 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7211 (mmtm) REVERT: g 302 TYR cc_start: 0.5616 (m-80) cc_final: 0.5156 (m-10) outliers start: 249 outliers final: 202 residues processed: 1419 average time/residue: 0.7997 time to fit residues: 1925.6808 Evaluate side-chains 1469 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1259 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 181 CYS Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 182 LYS Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 120 ARG Chi-restraints excluded: chain H residue 168 HIS Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 121 GLN Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 5 HIS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 43 HIS Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 94 HIS Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 53 GLU Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 45 LYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 77 TYR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 135 HIS Chi-restraints excluded: chain T residue 79 TYR Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 111 LYS Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 21 ASN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 56 CYS Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain W residue 28 ARG Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 19 ASP Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 67 ARG Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 75 ILE Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 93 SER Chi-restraints excluded: chain Z residue 98 LYS Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Z residue 110 THR Chi-restraints excluded: chain a residue 8 ASN Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 71 LEU Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain c residue 34 PHE Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 62 GLU Chi-restraints excluded: chain d residue 54 LYS Chi-restraints excluded: chain e residue 16 THR Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 56 ASN Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 114 ILE Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain g residue 14 HIS Chi-restraints excluded: chain g residue 48 ASP Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 170 TRP Chi-restraints excluded: chain g residue 195 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 581 optimal weight: 0.7980 chunk 612 optimal weight: 6.9990 chunk 558 optimal weight: 6.9990 chunk 595 optimal weight: 7.9990 chunk 358 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 467 optimal weight: 5.9990 chunk 182 optimal weight: 0.0060 chunk 538 optimal weight: 0.9980 chunk 563 optimal weight: 9.9990 chunk 593 optimal weight: 9.9990 overall best weight: 2.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN E 216 ASN F 95 HIS ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 HIS ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN ** N 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 HIS ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 HIS Q 35 ASN ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN T 83 GLN T 126 GLN W 24 GLN W 64 ASN W 113 HIS X 61 GLN c 24 GLN e 37 GLN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.6986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 86141 Z= 0.195 Angle : 0.720 35.978 125784 Z= 0.358 Chirality : 0.040 1.781 15671 Planarity : 0.005 0.105 8637 Dihedral : 23.461 179.099 36177 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.62 % Favored : 90.87 % Rotamer: Outliers : 5.28 % Allowed : 31.57 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.12), residues: 4744 helix: -0.22 (0.13), residues: 1414 sheet: -0.81 (0.17), residues: 848 loop : -1.80 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.003 TRP J 44 HIS 0.026 0.001 HIS O 94 PHE 0.037 0.002 PHE A 32 TYR 0.029 0.002 TYR Y 76 ARG 0.024 0.001 ARG Z 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1530 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1311 time to evaluate : 4.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7573 (pp20) cc_final: 0.7185 (pp20) REVERT: A 156 TYR cc_start: 0.7725 (m-80) cc_final: 0.7202 (m-80) REVERT: A 198 MET cc_start: 0.6131 (tpp) cc_final: 0.4479 (ttt) REVERT: A 200 ASP cc_start: 0.5804 (m-30) cc_final: 0.5583 (m-30) REVERT: B 155 TYR cc_start: 0.7656 (m-10) cc_final: 0.7392 (m-80) REVERT: B 163 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6682 (mp10) REVERT: B 205 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.6122 (m-10) REVERT: B 220 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8015 (mmtt) REVERT: C 248 TYR cc_start: 0.7877 (m-80) cc_final: 0.7558 (m-80) REVERT: E 19 MET cc_start: 0.8182 (mtt) cc_final: 0.7878 (ttm) REVERT: F 70 GLU cc_start: 0.5832 (mm-30) cc_final: 0.5168 (mm-30) REVERT: H 30 LEU cc_start: 0.7164 (mt) cc_final: 0.6794 (mt) REVERT: H 52 GLU cc_start: 0.5620 (OUTLIER) cc_final: 0.5328 (tt0) REVERT: H 77 VAL cc_start: 0.7831 (t) cc_final: 0.7621 (m) REVERT: H 120 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.7037 (mmp80) REVERT: H 162 GLN cc_start: 0.6526 (mp10) cc_final: 0.6259 (mp-120) REVERT: J 152 ASP cc_start: 0.6503 (p0) cc_final: 0.6293 (p0) REVERT: L 39 ASN cc_start: 0.8306 (t0) cc_final: 0.8064 (t0) REVERT: L 44 PHE cc_start: 0.6918 (m-80) cc_final: 0.6623 (m-80) REVERT: L 90 ARG cc_start: 0.7692 (mmm-85) cc_final: 0.7366 (mtp85) REVERT: M 26 LEU cc_start: 0.5076 (OUTLIER) cc_final: 0.4381 (tp) REVERT: N 74 ILE cc_start: 0.7971 (mt) cc_final: 0.7770 (tt) REVERT: O 52 THR cc_start: 0.7720 (p) cc_final: 0.7433 (p) REVERT: O 69 SER cc_start: 0.7138 (t) cc_final: 0.6887 (t) REVERT: O 142 ARG cc_start: 0.7079 (tpt90) cc_final: 0.6831 (tpt90) REVERT: R 79 GLU cc_start: 0.5055 (pt0) cc_final: 0.4591 (pt0) REVERT: S 59 LEU cc_start: 0.4916 (mp) cc_final: 0.4680 (mp) REVERT: T 94 ARG cc_start: 0.4351 (mmp80) cc_final: 0.3704 (mmm160) REVERT: U 77 TRP cc_start: 0.5869 (m100) cc_final: 0.5622 (m100) REVERT: V 3 ASN cc_start: 0.5179 (p0) cc_final: 0.4953 (p0) REVERT: W 34 ILE cc_start: 0.7353 (pt) cc_final: 0.6675 (mt) REVERT: X 96 GLU cc_start: 0.8016 (tp30) cc_final: 0.7427 (tp30) REVERT: X 97 ASN cc_start: 0.7666 (m110) cc_final: 0.7052 (m110) REVERT: Y 51 THR cc_start: 0.7863 (t) cc_final: 0.7534 (m) REVERT: Y 53 ASP cc_start: 0.7403 (p0) cc_final: 0.6567 (t70) REVERT: a 89 ARG cc_start: 0.7814 (tmm-80) cc_final: 0.7512 (ttp80) REVERT: b 31 TYR cc_start: 0.7121 (p90) cc_final: 0.6881 (p90) REVERT: d 52 PHE cc_start: 0.4411 (OUTLIER) cc_final: 0.4070 (m-10) REVERT: g 302 TYR cc_start: 0.5617 (m-80) cc_final: 0.5280 (m-10) outliers start: 219 outliers final: 182 residues processed: 1418 average time/residue: 0.8152 time to fit residues: 1966.5646 Evaluate side-chains 1436 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1247 time to evaluate : 4.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 181 CYS Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 182 LYS Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 120 ARG Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 168 HIS Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 121 GLN Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 5 HIS Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 94 HIS Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 77 TYR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 135 HIS Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 79 TYR Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 111 LYS Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 56 CYS Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 28 ARG Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 113 HIS Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 67 ARG Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 89 HIS Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 98 LYS Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 71 LEU Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain c residue 34 PHE Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 62 GLU Chi-restraints excluded: chain d residue 52 PHE Chi-restraints excluded: chain e residue 16 THR Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 56 ASN Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 114 ILE Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain g residue 14 HIS Chi-restraints excluded: chain g residue 48 ASP Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 170 TRP Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 391 optimal weight: 5.9990 chunk 629 optimal weight: 7.9990 chunk 384 optimal weight: 7.9990 chunk 298 optimal weight: 1.9990 chunk 437 optimal weight: 9.9990 chunk 660 optimal weight: 20.0000 chunk 607 optimal weight: 30.0000 chunk 525 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 406 optimal weight: 8.9990 chunk 322 optimal weight: 0.0470 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 HIS ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 GLN I 181 GLN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 HIS ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 GLN W 24 GLN W 64 ASN W 113 HIS X 61 GLN ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 ASN d 10 HIS ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.7199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 86141 Z= 0.235 Angle : 0.749 37.487 125784 Z= 0.374 Chirality : 0.042 1.830 15671 Planarity : 0.006 0.107 8637 Dihedral : 23.465 179.942 36177 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.94 % Favored : 90.56 % Rotamer: Outliers : 5.13 % Allowed : 32.20 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.12), residues: 4744 helix: -0.27 (0.13), residues: 1411 sheet: -0.84 (0.17), residues: 849 loop : -1.82 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP F 23 HIS 0.031 0.002 HIS O 94 PHE 0.049 0.003 PHE D 17 TYR 0.029 0.002 TYR S 95 ARG 0.025 0.001 ARG Z 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1497 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1284 time to evaluate : 4.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7549 (pp20) cc_final: 0.7173 (pp20) REVERT: A 156 TYR cc_start: 0.7789 (m-80) cc_final: 0.7390 (m-80) REVERT: A 198 MET cc_start: 0.6336 (tpp) cc_final: 0.4811 (ttt) REVERT: B 155 TYR cc_start: 0.7704 (m-10) cc_final: 0.7430 (m-80) REVERT: B 163 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6655 (mp10) REVERT: B 205 TYR cc_start: 0.6678 (OUTLIER) cc_final: 0.6001 (m-10) REVERT: E 19 MET cc_start: 0.8188 (mtt) cc_final: 0.7897 (ttm) REVERT: F 70 GLU cc_start: 0.5883 (mm-30) cc_final: 0.5337 (mm-30) REVERT: F 202 SER cc_start: 0.8038 (p) cc_final: 0.7749 (p) REVERT: H 30 LEU cc_start: 0.7242 (mt) cc_final: 0.6590 (mt) REVERT: H 52 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.5397 (tt0) REVERT: H 77 VAL cc_start: 0.7871 (t) cc_final: 0.7657 (m) REVERT: H 120 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7118 (mmp80) REVERT: J 97 ILE cc_start: 0.8157 (tt) cc_final: 0.7932 (tt) REVERT: J 152 ASP cc_start: 0.6571 (p0) cc_final: 0.6363 (p0) REVERT: L 39 ASN cc_start: 0.8368 (t0) cc_final: 0.8039 (t0) REVERT: M 12 MET cc_start: 0.1070 (OUTLIER) cc_final: 0.0624 (tpp) REVERT: M 26 LEU cc_start: 0.5338 (OUTLIER) cc_final: 0.4690 (tp) REVERT: O 52 THR cc_start: 0.7775 (p) cc_final: 0.7441 (p) REVERT: O 69 SER cc_start: 0.7144 (t) cc_final: 0.6935 (t) REVERT: O 142 ARG cc_start: 0.7050 (tpt90) cc_final: 0.6836 (tpt90) REVERT: S 141 ARG cc_start: 0.4823 (tpt170) cc_final: 0.4301 (tpp-160) REVERT: T 51 ASN cc_start: 0.5659 (OUTLIER) cc_final: 0.5357 (p0) REVERT: T 94 ARG cc_start: 0.4477 (mmp80) cc_final: 0.3782 (mmm160) REVERT: U 77 TRP cc_start: 0.5904 (m100) cc_final: 0.5509 (m100) REVERT: V 3 ASN cc_start: 0.5167 (p0) cc_final: 0.4960 (p0) REVERT: V 7 GLU cc_start: 0.5609 (pt0) cc_final: 0.5208 (pt0) REVERT: X 96 GLU cc_start: 0.8080 (tp30) cc_final: 0.7433 (tp30) REVERT: X 97 ASN cc_start: 0.7660 (m110) cc_final: 0.6921 (m110) REVERT: X 134 TYR cc_start: 0.7026 (t80) cc_final: 0.6492 (t80) REVERT: Y 53 ASP cc_start: 0.7403 (p0) cc_final: 0.6518 (t70) REVERT: Y 56 PHE cc_start: 0.7060 (m-10) cc_final: 0.6833 (m-10) REVERT: a 89 ARG cc_start: 0.7822 (tmm-80) cc_final: 0.7555 (ttp80) REVERT: b 31 TYR cc_start: 0.7164 (p90) cc_final: 0.6826 (p90) REVERT: d 52 PHE cc_start: 0.4661 (OUTLIER) cc_final: 0.3945 (m-10) REVERT: g 302 TYR cc_start: 0.5771 (m-80) cc_final: 0.5255 (m-10) outliers start: 213 outliers final: 186 residues processed: 1390 average time/residue: 0.7992 time to fit residues: 1887.2316 Evaluate side-chains 1438 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1244 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 181 CYS Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 182 LYS Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 120 ARG Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 168 HIS Chi-restraints excluded: chain H residue 189 PHE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 121 GLN Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 5 HIS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 141 TYR Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 94 HIS Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 77 TYR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 135 HIS Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 79 TYR Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 111 LYS Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 21 ASN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 56 CYS Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain W residue 28 ARG Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 113 HIS Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 61 GLN Chi-restraints excluded: chain X residue 67 ARG Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 75 ILE Chi-restraints excluded: chain Y residue 89 HIS Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 98 LYS Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain a residue 25 ASN Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 71 LEU Chi-restraints excluded: chain a residue 96 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain c residue 34 PHE Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 62 GLU Chi-restraints excluded: chain d residue 52 PHE Chi-restraints excluded: chain e residue 16 THR Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 56 ASN Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 114 ILE Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain g residue 14 HIS Chi-restraints excluded: chain g residue 48 ASP Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 170 TRP Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 417 optimal weight: 5.9990 chunk 560 optimal weight: 5.9990 chunk 161 optimal weight: 30.0000 chunk 484 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 chunk 146 optimal weight: 40.0000 chunk 526 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 540 optimal weight: 50.0000 chunk 66 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 GLN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN X 61 GLN ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN a 25 ASN ** a 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 24 GLN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 285 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.119480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.094217 restraints weight = 280617.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.097047 restraints weight = 102857.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.098684 restraints weight = 54751.588| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.7212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.350 86141 Z= 0.346 Angle : 0.870 59.198 125784 Z= 0.480 Chirality : 0.044 1.835 15671 Planarity : 0.007 0.188 8637 Dihedral : 23.464 179.943 36177 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.92 % Favored : 90.60 % Rotamer: Outliers : 5.09 % Allowed : 32.71 % Favored : 62.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.12), residues: 4744 helix: -0.27 (0.13), residues: 1411 sheet: -0.84 (0.17), residues: 847 loop : -1.81 (0.12), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP F 23 HIS 0.206 0.004 HIS H 126 PHE 0.050 0.003 PHE F 97 TYR 0.028 0.002 TYR S 95 ARG 0.061 0.001 ARG B 42 =============================================================================== Job complete usr+sys time: 28872.51 seconds wall clock time: 495 minutes 28.61 seconds (29728.61 seconds total)