Starting phenix.real_space_refine on Thu Dec 14 02:02:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flx_3221/12_2023/5flx_3221.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flx_3221/12_2023/5flx_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_3221/12_2023/5flx_3221.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flx_3221/12_2023/5flx_3221.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flx_3221/12_2023/5flx_3221.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5flx_3221/12_2023/5flx_3221.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 31.80, per 1000 atoms: 0.39 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.21 Conformation dependent library (CDL) restraints added in 5.8 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: 24.66 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: 64.92 Time building geometry restraints manager: 34.92 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: 77.58 - 92.86: 4 92.86 - 108.13: 21080 108.13 - 123.41: 94365 123.41 - 138.68: 10330 138.68 - 153.96: 5 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: 48814 36.00 - 72.00: 3847 72.00 - 108.00: 586 108.00 - 144.00: 7 144.00 - 180.00: 29 Dihedral angle restraints: 53283 sinusoidal: 39454 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 53280 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 2.520 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 2.520 nonbonded pdb=" OP2 A 1 992 " pdb=" NZ LYS a 13 " model vdw 1.509 2.520 ... (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 ========== 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 13.890 Check model and map are aligned: 0.890 Set scattering table: 0.560 Process input model: 228.000 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 251.030 ------------------------------------------------------------------------------- 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 : 20.432 179.998 44356 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 : 4.299 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 outliers start: 8 outliers final: 3 residues processed: 2356 average time/residue: 0.9653 time to fit residues: 3656.3931 Evaluate side-chains 1455 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1452 time to evaluate : 4.320 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.1058 time to fit residues: 10.2709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 559 optimal weight: 8.9990 chunk 502 optimal weight: 20.0000 chunk 278 optimal weight: 20.0000 chunk 171 optimal weight: 8.9990 chunk 338 optimal weight: 20.0000 chunk 268 optimal weight: 7.9990 chunk 519 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 chunk 386 optimal weight: 0.0270 chunk 602 optimal weight: 50.0000 overall best weight: 6.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 138 HIS ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 65 GLN G 81 HIS G 163 ASN G 186 GLN H 39 GLN H 168 HIS H 186 ASN H 193 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** L 11 GLN ** L 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 ASN P 32 GLN P 54 HIS P 128 HIS Q 11 GLN Q 77 HIS Q 86 GLN S 87 GLN T 128 GLN T 137 GLN ** V 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 16 ASN ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 GLN ** W 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 56 ASN f 139 HIS g 20 GLN ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 86141 Z= 0.306 Angle : 0.757 35.029 125784 Z= 0.382 Chirality : 0.042 1.713 15671 Planarity : 0.007 0.086 8637 Dihedral : 22.395 178.977 34425 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.34 % Favored : 93.15 % Rotamer: Outliers : 7.04 % Allowed : 19.04 % Favored : 73.92 % Cbeta Deviations : 0.02 % 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: -2.06 (0.11), residues: 4744 helix: -1.04 (0.12), residues: 1427 sheet: -0.79 (0.16), residues: 828 loop : -1.75 (0.11), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 176 HIS 0.013 0.002 HIS g 14 PHE 0.035 0.003 PHE g 27 TYR 0.032 0.003 TYR N 38 ARG 0.018 0.001 ARG Z 104 *********************** 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 1884 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1592 time to evaluate : 4.406 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 outliers start: 292 outliers final: 183 residues processed: 1722 average time/residue: 0.8152 time to fit residues: 2324.2800 Evaluate side-chains 1515 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1332 time to evaluate : 4.381 Switching outliers to nearest non-outliers outliers start: 183 outliers final: 0 residues processed: 183 average time/residue: 0.6187 time to fit residues: 215.0526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 334 optimal weight: 0.8980 chunk 186 optimal weight: 20.0000 chunk 501 optimal weight: 4.9990 chunk 409 optimal weight: 0.1980 chunk 166 optimal weight: 20.0000 chunk 603 optimal weight: 9.9990 chunk 651 optimal weight: 20.0000 chunk 537 optimal weight: 8.9990 chunk 598 optimal weight: 30.0000 chunk 205 optimal weight: 10.0000 chunk 483 optimal weight: 0.9980 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 GLN C 115 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN D 159 HIS ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN H 97 GLN H 168 HIS ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** J 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 HIS ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 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** N 138 ASN ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 16 ASN ** 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 31 HIS X 61 GLN c 45 ASN ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 272 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.4220 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= 0.188 Angle : 0.655 33.815 125784 Z= 0.327 Chirality : 0.038 1.724 15671 Planarity : 0.005 0.090 8637 Dihedral : 22.367 179.712 34425 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.75 % Favored : 92.85 % Rotamer: Outliers : 3.81 % Allowed : 22.78 % Favored : 73.42 % 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: -1.67 (0.11), residues: 4744 helix: -0.49 (0.13), residues: 1423 sheet: -0.57 (0.16), residues: 839 loop : -1.68 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP g 17 HIS 0.009 0.001 HIS S 135 PHE 0.034 0.003 PHE B 142 TYR 0.037 0.002 TYR K 12 ARG 0.020 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 1671 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1513 time to evaluate : 4.418 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 outliers start: 158 outliers final: 67 residues processed: 1579 average time/residue: 0.8078 time to fit residues: 2117.2218 Evaluate side-chains 1384 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1317 time to evaluate : 4.311 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.6255 time to fit residues: 81.9314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 595 optimal weight: 10.0000 chunk 453 optimal weight: 0.9990 chunk 313 optimal weight: 7.9990 chunk 66 optimal weight: 30.0000 chunk 287 optimal weight: 20.0000 chunk 405 optimal weight: 0.6980 chunk 605 optimal weight: 40.0000 chunk 640 optimal weight: 20.0000 chunk 316 optimal weight: 1.9990 chunk 573 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN A 193 HIS B 208 HIS ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN G 186 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN ** 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** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 GLN ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 16 ASN ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 113 HIS X 61 GLN ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 GLN ** c 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 44 ASN g 56 GLN g 64 HIS ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 86141 Z= 0.204 Angle : 0.667 34.154 125784 Z= 0.332 Chirality : 0.038 1.738 15671 Planarity : 0.005 0.072 8637 Dihedral : 22.358 179.476 34425 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.08 % Favored : 92.43 % Rotamer: Outliers : 4.29 % Allowed : 24.87 % Favored : 70.84 % 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: -1.56 (0.11), residues: 4744 helix: -0.26 (0.13), residues: 1425 sheet: -0.64 (0.17), residues: 815 loop : -1.64 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP S 82 HIS 0.012 0.001 HIS K 66 PHE 0.035 0.002 PHE A 103 TYR 0.039 0.002 TYR K 12 ARG 0.021 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 1569 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1391 time to evaluate : 4.336 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 outliers start: 178 outliers final: 103 residues processed: 1470 average time/residue: 0.8382 time to fit residues: 2084.2510 Evaluate side-chains 1387 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1284 time to evaluate : 4.335 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 0 residues processed: 103 average time/residue: 0.6213 time to fit residues: 127.2185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 533 optimal weight: 6.9990 chunk 363 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 477 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 546 optimal weight: 6.9990 chunk 442 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 327 optimal weight: 10.0000 chunk 575 optimal weight: 0.0020 chunk 161 optimal weight: 30.0000 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS D 57 ASN ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN G 186 GLN H 68 GLN H 168 HIS ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 GLN R 62 GLN T 126 GLN ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 ASN Z 64 ASN a 25 ASN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 44 ASN f 91 ASN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 86141 Z= 0.204 Angle : 0.665 34.528 125784 Z= 0.331 Chirality : 0.039 1.755 15671 Planarity : 0.005 0.068 8637 Dihedral : 22.381 179.528 34425 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.80 % Favored : 91.72 % Rotamer: Outliers : 3.06 % Allowed : 26.03 % Favored : 70.91 % 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: -1.48 (0.12), residues: 4744 helix: -0.06 (0.13), residues: 1419 sheet: -0.62 (0.17), residues: 827 loop : -1.68 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 23 HIS 0.010 0.001 HIS Y 89 PHE 0.031 0.002 PHE J 48 TYR 0.035 0.002 TYR I 149 ARG 0.022 0.001 ARG Z 104 *********************** 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 1494 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1367 time to evaluate : 4.361 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 outliers start: 127 outliers final: 70 residues processed: 1421 average time/residue: 0.8299 time to fit residues: 1978.4924 Evaluate side-chains 1334 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1264 time to evaluate : 4.327 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 0.6019 time to fit residues: 84.6929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 215 optimal weight: 10.0000 chunk 577 optimal weight: 6.9990 chunk 126 optimal weight: 30.0000 chunk 376 optimal weight: 0.6980 chunk 158 optimal weight: 20.0000 chunk 641 optimal weight: 20.0000 chunk 532 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 212 optimal weight: 2.9990 chunk 336 optimal weight: 20.0000 overall best weight: 6.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS F 79 HIS ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN H 68 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 GLN W 113 HIS ** X 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 296 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.6023 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= 0.282 Angle : 0.739 38.021 125784 Z= 0.370 Chirality : 0.041 1.737 15671 Planarity : 0.006 0.091 8637 Dihedral : 22.537 179.925 34425 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.49 % Favored : 90.98 % Rotamer: Outliers : 4.05 % Allowed : 27.04 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.57 (0.12), residues: 4744 helix: -0.12 (0.13), residues: 1424 sheet: -0.72 (0.17), residues: 845 loop : -1.73 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP F 23 HIS 0.010 0.002 HIS S 135 PHE 0.037 0.003 PHE J 48 TYR 0.033 0.003 TYR Y 76 ARG 0.032 0.001 ARG B 162 *********************** 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 1543 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1375 time to evaluate : 5.097 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 outliers start: 168 outliers final: 106 residues processed: 1439 average time/residue: 0.8161 time to fit residues: 1974.1019 Evaluate side-chains 1352 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1246 time to evaluate : 4.394 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 0 residues processed: 106 average time/residue: 0.6030 time to fit residues: 126.7783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 618 optimal weight: 50.0000 chunk 72 optimal weight: 20.0000 chunk 365 optimal weight: 0.9990 chunk 468 optimal weight: 0.9980 chunk 362 optimal weight: 6.9990 chunk 539 optimal weight: 6.9990 chunk 358 optimal weight: 0.9990 chunk 639 optimal weight: 30.0000 chunk 399 optimal weight: 5.9990 chunk 389 optimal weight: 20.0000 chunk 295 optimal weight: 30.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN F 179 ASN ** 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** ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 GLN ** S 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 GLN T 51 ASN T 128 GLN U 81 GLN ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 61 GLN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 24 GLN ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 44 ASN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 272 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 86141 Z= 0.195 Angle : 0.689 35.859 125784 Z= 0.343 Chirality : 0.040 1.766 15671 Planarity : 0.005 0.068 8637 Dihedral : 22.505 179.811 34425 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.07 % Favored : 91.42 % Rotamer: Outliers : 2.36 % Allowed : 29.69 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.50 (0.12), residues: 4744 helix: -0.08 (0.13), residues: 1428 sheet: -0.66 (0.17), residues: 842 loop : -1.67 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP F 23 HIS 0.015 0.001 HIS O 43 PHE 0.049 0.002 PHE g 27 TYR 0.043 0.002 TYR Y 76 ARG 0.023 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 1446 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1348 time to evaluate : 4.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 47 residues processed: 1382 average time/residue: 0.7998 time to fit residues: 1862.3766 Evaluate side-chains 1302 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1255 time to evaluate : 4.409 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.6113 time to fit residues: 59.0293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 395 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 381 optimal weight: 0.8980 chunk 192 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 406 optimal weight: 40.0000 chunk 435 optimal weight: 2.9990 chunk 315 optimal weight: 0.0470 chunk 59 optimal weight: 10.0000 chunk 502 optimal weight: 9.9990 overall best weight: 3.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN H 68 GLN H 73 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 GLN ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 113 HIS X 61 GLN ** X 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 GLN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 86141 Z= 0.200 Angle : 0.688 35.383 125784 Z= 0.343 Chirality : 0.039 1.788 15671 Planarity : 0.005 0.097 8637 Dihedral : 22.478 179.539 34425 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.47 % Favored : 91.00 % Rotamer: Outliers : 2.15 % Allowed : 30.66 % Favored : 67.20 % 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: -1.41 (0.12), residues: 4744 helix: 0.09 (0.14), residues: 1401 sheet: -0.70 (0.17), residues: 849 loop : -1.64 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP F 23 HIS 0.010 0.001 HIS O 43 PHE 0.037 0.002 PHE A 203 TYR 0.036 0.002 TYR I 149 ARG 0.025 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 1413 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1324 time to evaluate : 4.350 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 outliers start: 89 outliers final: 52 residues processed: 1358 average time/residue: 0.7990 time to fit residues: 1825.9680 Evaluate side-chains 1321 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1269 time to evaluate : 4.611 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.6220 time to fit residues: 66.7872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 581 optimal weight: 0.0070 chunk 612 optimal weight: 20.0000 chunk 558 optimal weight: 6.9990 chunk 595 optimal weight: 0.0050 chunk 358 optimal weight: 10.0000 chunk 259 optimal weight: 0.9980 chunk 467 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 538 optimal weight: 10.0000 chunk 563 optimal weight: 8.9990 chunk 593 optimal weight: 9.9990 overall best weight: 1.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS E 98 HIS G 186 GLN ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN ** I 84 ASN ** 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** ** L 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN N 49 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 ASN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 7 GLN e 44 ASN g 56 GLN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.6507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 86141 Z= 0.173 Angle : 0.689 33.802 125784 Z= 0.339 Chirality : 0.039 1.809 15671 Planarity : 0.005 0.099 8637 Dihedral : 22.436 179.988 34425 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.14 % Favored : 91.36 % Rotamer: Outliers : 1.08 % Allowed : 32.32 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.40 (0.12), residues: 4744 helix: 0.03 (0.14), residues: 1411 sheet: -0.62 (0.17), residues: 841 loop : -1.62 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP J 44 HIS 0.009 0.001 HIS O 43 PHE 0.054 0.002 PHE A 32 TYR 0.036 0.002 TYR I 149 ARG 0.023 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 1383 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1338 time to evaluate : 4.329 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 outliers start: 45 outliers final: 31 residues processed: 1347 average time/residue: 0.8122 time to fit residues: 1844.0276 Evaluate side-chains 1304 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1273 time to evaluate : 5.955 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.6059 time to fit residues: 41.0922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 391 optimal weight: 9.9990 chunk 629 optimal weight: 2.9990 chunk 384 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 chunk 437 optimal weight: 0.0970 chunk 660 optimal weight: 20.0000 chunk 607 optimal weight: 8.9990 chunk 525 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 406 optimal weight: 0.7980 chunk 322 optimal weight: 5.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 GLN ** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 113 HIS ** X 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 8 ASN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.6679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 86141 Z= 0.186 Angle : 0.697 33.788 125784 Z= 0.345 Chirality : 0.039 1.813 15671 Planarity : 0.005 0.112 8637 Dihedral : 22.409 179.667 34425 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.68 % Favored : 90.77 % Rotamer: Outliers : 0.72 % Allowed : 33.12 % Favored : 66.16 % 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: -1.43 (0.12), residues: 4744 helix: 0.03 (0.14), residues: 1400 sheet: -0.61 (0.17), residues: 862 loop : -1.67 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP F 23 HIS 0.008 0.001 HIS S 135 PHE 0.037 0.002 PHE A 32 TYR 0.032 0.002 TYR I 149 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 1322 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1292 time to evaluate : 4.528 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 outliers start: 30 outliers final: 14 residues processed: 1301 average time/residue: 0.7953 time to fit residues: 1744.7477 Evaluate side-chains 1272 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1258 time to evaluate : 4.244 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.6005 time to fit residues: 21.1309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 417 optimal weight: 0.8980 chunk 560 optimal weight: 4.9990 chunk 161 optimal weight: 30.0000 chunk 484 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 146 optimal weight: 40.0000 chunk 526 optimal weight: 0.9980 chunk 220 optimal weight: 20.0000 chunk 540 optimal weight: 7.9990 chunk 66 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 GLN ** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 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 49 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 HIS ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN T 137 GLN ** W 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 GLN X 61 GLN ** X 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 64 ASN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 44 ASN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 311 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.121196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.095922 restraints weight = 280176.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.098776 restraints weight = 102937.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.100450 restraints weight = 55136.102| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 86141 Z= 0.224 Angle : 0.720 35.547 125784 Z= 0.357 Chirality : 0.040 1.795 15671 Planarity : 0.005 0.071 8637 Dihedral : 22.479 179.761 34425 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.77 % Favored : 90.70 % Rotamer: Outliers : 1.08 % Allowed : 33.53 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.12), residues: 4744 helix: -0.03 (0.13), residues: 1415 sheet: -0.63 (0.17), residues: 869 loop : -1.70 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP J 44 HIS 0.011 0.001 HIS N 5 PHE 0.035 0.003 PHE A 203 TYR 0.043 0.002 TYR T 54 ARG 0.026 0.001 ARG Z 104 =============================================================================== Job complete usr+sys time: 27985.15 seconds wall clock time: 488 minutes 3.04 seconds (29283.04 seconds total)