Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 17:31:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmj_3532/04_2023/5mmj_3532.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmj_3532/04_2023/5mmj_3532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmj_3532/04_2023/5mmj_3532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmj_3532/04_2023/5mmj_3532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmj_3532/04_2023/5mmj_3532.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mmj_3532/04_2023/5mmj_3532.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.010 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: 6 Type Number sf(0) Gaussians P 1484 5.49 5 Mg 185 5.21 5 S 80 5.16 5 C 28819 2.51 5 N 10362 2.21 5 O 14385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c GLU 172": "OE1" <-> "OE2" Residue "d GLU 62": "OE1" <-> "OE2" Residue "d GLU 195": "OE1" <-> "OE2" Residue "e GLU 196": "OE1" <-> "OE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "h GLU 128": "OE1" <-> "OE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "m GLU 95": "OE1" <-> "OE2" Residue "p TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 42": "OE1" <-> "OE2" Residue "s PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 168": "OE1" <-> "OE2" Residue "u GLU 94": "OE1" <-> "OE2" Residue "v PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 55315 Number of models: 1 Model: "" Number of chains: 31 Chain: "0" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 98 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "8" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 870 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'TRANS': 173} Chain breaks: 2 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 522 Unresolved non-hydrogen dihedrals: 174 Planarities with less than four sites: {'UNK:plan-1': 174} Unresolved non-hydrogen planarities: 174 Chain: "a" Number of atoms: 31868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1484, 31868 Classifications: {'RNA': 1484} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 80, 'rna3p_pur': 734, 'rna3p_pyr': 552} Link IDs: {'rna2p': 198, 'rna3p': 1285} Chain: "b" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1844 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain: "c" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1736 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "d" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1633 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain: "e" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1331 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 181} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "f" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 911 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "g" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1210 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain: "h" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1079 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "i" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1119 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "j" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 805 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "k" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 882 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 959 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 113} Chain: "m" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "n" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 820 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "o" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 635 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "p" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 664 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "q" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 7, 'TRANS': 78} Chain: "r" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 490 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "s" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 853 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 2, 'TRANS': 104} Chain: "u" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 568 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "v" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 613 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 686 Classifications: {'peptide': 82} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 74} Chain: "x" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 309 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 5, 'TRANS': 34} Chain: "y" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 919 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "a" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 182 Unusual residues: {' MG': 182} Classifications: {'undetermined': 182} Link IDs: {None: 181} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.23, per 1000 atoms: 0.38 Number of scatterers: 55315 At special positions: 0 Unit cell: (186.26, 180.7, 243.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 1484 15.00 Mg 185 11.99 O 14385 8.00 N 10362 7.00 C 28819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.64 Conformation dependent library (CDL) restraints added in 2.6 seconds 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5566 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 27 sheets defined 47.7% alpha, 21.2% beta 452 base pairs and 809 stacking pairs defined. Time for finding SS restraints: 15.62 Creating SS restraints... Processing helix chain '0' and resid 93 through 101 removed outlier: 3.625A pdb=" N LYS 0 100 " --> pdb=" O LYS 0 96 " (cutoff:3.500A) Processing helix chain '8' and resid 1039 through 1043 removed outlier: 3.533A pdb=" N UNK 81042 " --> pdb=" O UNK 81039 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N UNK 81043 " --> pdb=" O UNK 81040 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 1039 through 1043' Processing helix chain '8' and resid 1102 through 1126 Processing helix chain '8' and resid 1134 through 1141 removed outlier: 3.892A pdb=" N UNK 81138 " --> pdb=" O UNK 81134 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N UNK 81141 " --> pdb=" O UNK 81137 " (cutoff:3.500A) Processing helix chain '8' and resid 1221 through 1230 Processing helix chain '8' and resid 1237 through 1245 Processing helix chain '8' and resid 1246 through 1258 Processing helix chain 'b' and resid 9 through 17 removed outlier: 3.505A pdb=" N GLY b 17 " --> pdb=" O MET b 13 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 32 Processing helix chain 'b' and resid 46 through 68 removed outlier: 3.777A pdb=" N ARG b 52 " --> pdb=" O THR b 48 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 92 removed outlier: 3.819A pdb=" N ASP b 82 " --> pdb=" O ASN b 78 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG b 86 " --> pdb=" O ASP b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 128 removed outlier: 3.904A pdb=" N THR b 111 " --> pdb=" O ASN b 107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR b 126 " --> pdb=" O ARG b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 134 through 153 Processing helix chain 'b' and resid 173 through 184 Processing helix chain 'b' and resid 210 through 235 Processing helix chain 'c' and resid 6 through 11 removed outlier: 3.645A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 52 removed outlier: 4.343A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL c 47 " --> pdb=" O ILE c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 103 removed outlier: 3.940A pdb=" N ASN c 98 " --> pdb=" O ASP c 94 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 Processing helix chain 'c' and resid 140 through 155 Processing helix chain 'c' and resid 168 through 171 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.049A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 42 through 59 Processing helix chain 'd' and resid 61 through 75 removed outlier: 3.548A pdb=" N LYS d 67 " --> pdb=" O ARG d 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 78 through 89 Processing helix chain 'd' and resid 90 through 98 Processing helix chain 'd' and resid 103 through 113 Processing helix chain 'd' and resid 141 through 154 Processing helix chain 'd' and resid 180 through 184 removed outlier: 3.753A pdb=" N VAL d 184 " --> pdb=" O SER d 181 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 197 removed outlier: 3.738A pdb=" N VAL d 193 " --> pdb=" O ASN d 189 " (cutoff:3.500A) Processing helix chain 'd' and resid 198 through 200 No H-bonds generated for 'chain 'd' and resid 198 through 200' Processing helix chain 'e' and resid 124 through 136 removed outlier: 3.586A pdb=" N ALA e 128 " --> pdb=" O ASN e 124 " (cutoff:3.500A) Processing helix chain 'e' and resid 146 through 150 Processing helix chain 'e' and resid 196 through 212 Processing helix chain 'e' and resid 250 through 261 Processing helix chain 'e' and resid 274 through 288 Processing helix chain 'e' and resid 291 through 300 Processing helix chain 'e' and resid 302 through 308 removed outlier: 3.634A pdb=" N LEU e 306 " --> pdb=" O PRO e 302 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS e 308 " --> pdb=" O GLU e 304 " (cutoff:3.500A) Processing helix chain 'f' and resid 119 through 137 Processing helix chain 'f' and resid 184 through 195 removed outlier: 4.374A pdb=" N LEU f 188 " --> pdb=" O SER f 184 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU f 189 " --> pdb=" O ILE f 185 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA f 190 " --> pdb=" O SER f 186 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP f 195 " --> pdb=" O ALA f 191 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 30 removed outlier: 3.858A pdb=" N ASN g 24 " --> pdb=" O ASN g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.800A pdb=" N GLN g 41 " --> pdb=" O SER g 37 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.889A pdb=" N ARG g 63 " --> pdb=" O LEU g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 110 Processing helix chain 'g' and resid 115 through 129 Processing helix chain 'g' and resid 132 through 147 removed outlier: 3.611A pdb=" N LYS g 138 " --> pdb=" O ALA g 134 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 152 Processing helix chain 'h' and resid 4 through 19 removed outlier: 3.700A pdb=" N ASP h 8 " --> pdb=" O ASP h 4 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 92 through 96 removed outlier: 3.586A pdb=" N ILE h 96 " --> pdb=" O TYR h 93 " (cutoff:3.500A) Processing helix chain 'h' and resid 99 through 103 Processing helix chain 'h' and resid 116 through 124 Processing helix chain 'i' and resid 66 through 74 Processing helix chain 'i' and resid 112 through 116 Processing helix chain 'i' and resid 119 through 132 Proline residue: i 129 - end of helix removed outlier: 3.656A pdb=" N THR i 132 " --> pdb=" O THR i 128 " (cutoff:3.500A) Processing helix chain 'i' and resid 149 through 169 Processing helix chain 'i' and resid 172 through 180 Processing helix chain 'j' and resid 107 through 125 removed outlier: 3.685A pdb=" N ILE j 111 " --> pdb=" O TRP j 107 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR j 125 " --> pdb=" O ALA j 121 " (cutoff:3.500A) Processing helix chain 'j' and resid 173 through 182 Processing helix chain 'k' and resid 64 through 67 Processing helix chain 'k' and resid 68 through 86 removed outlier: 3.951A pdb=" N THR k 82 " --> pdb=" O ASN k 78 " (cutoff:3.500A) Processing helix chain 'k' and resid 100 through 112 removed outlier: 3.805A pdb=" N ALA k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU k 106 " --> pdb=" O ARG k 102 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG k 107 " --> pdb=" O ASP k 103 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA k 108 " --> pdb=" O ALA k 104 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 8 Processing helix chain 'l' and resid 21 through 25 Processing helix chain 'l' and resid 113 through 118 removed outlier: 3.911A pdb=" N TYR l 117 " --> pdb=" O GLY l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 54 removed outlier: 3.532A pdb=" N VAL m 53 " --> pdb=" O VAL m 50 " (cutoff:3.500A) Processing helix chain 'm' and resid 60 through 66 Processing helix chain 'm' and resid 73 through 83 Processing helix chain 'm' and resid 94 through 106 Processing helix chain 'm' and resid 110 through 129 Processing helix chain 'm' and resid 130 through 139 Processing helix chain 'm' and resid 151 through 156 Processing helix chain 'n' and resid 3 through 34 removed outlier: 3.680A pdb=" N ILE n 7 " --> pdb=" O ARG n 3 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU n 22 " --> pdb=" O GLN n 18 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ILE n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 36 through 48 removed outlier: 4.423A pdb=" N GLU n 42 " --> pdb=" O SER n 38 " (cutoff:3.500A) Processing helix chain 'n' and resid 51 through 59 Proline residue: n 56 - end of helix Processing helix chain 'n' and resid 79 through 89 Processing helix chain 'o' and resid 21 through 43 removed outlier: 4.069A pdb=" N LEU o 38 " --> pdb=" O ARG o 34 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N HIS o 39 " --> pdb=" O ARG o 35 " (cutoff:3.500A) Processing helix chain 'o' and resid 46 through 71 removed outlier: 3.561A pdb=" N GLN o 50 " --> pdb=" O ASP o 46 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY o 52 " --> pdb=" O SER o 48 " (cutoff:3.500A) Processing helix chain 'o' and resid 71 through 82 Processing helix chain 'p' and resid 49 through 59 removed outlier: 3.529A pdb=" N ILE p 53 " --> pdb=" O ASN p 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS p 59 " --> pdb=" O ASP p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 64 through 74 Processing helix chain 'p' and resid 75 through 80 removed outlier: 4.191A pdb=" N GLU p 79 " --> pdb=" O GLU p 75 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE p 80 " --> pdb=" O VAL p 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 75 through 80' Processing helix chain 'q' and resid 102 through 105 removed outlier: 4.527A pdb=" N GLN q 105 " --> pdb=" O PRO q 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 102 through 105' Processing helix chain 'r' and resid 32 through 39 removed outlier: 3.632A pdb=" N PHE r 39 " --> pdb=" O LEU r 35 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 53 Processing helix chain 'r' and resid 55 through 72 Processing helix chain 's' and resid 12 through 25 Processing helix chain 's' and resid 63 through 67 removed outlier: 3.777A pdb=" N VAL s 67 " --> pdb=" O ASP s 64 " (cutoff:3.500A) Processing helix chain 's' and resid 71 through 75 removed outlier: 3.634A pdb=" N ALA s 75 " --> pdb=" O GLY s 72 " (cutoff:3.500A) Processing helix chain 't' and resid 76 through 117 removed outlier: 3.552A pdb=" N ALA t 80 " --> pdb=" O ALA t 76 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL t 100 " --> pdb=" O ARG t 96 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS t 117 " --> pdb=" O ALA t 113 " (cutoff:3.500A) Processing helix chain 't' and resid 120 through 145 removed outlier: 4.730A pdb=" N VAL t 126 " --> pdb=" O THR t 122 " (cutoff:3.500A) Proline residue: t 127 - end of helix Processing helix chain 't' and resid 149 through 172 removed outlier: 3.778A pdb=" N ARG t 155 " --> pdb=" O ASN t 151 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU t 168 " --> pdb=" O LYS t 164 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE t 169 " --> pdb=" O LYS t 165 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS t 170 " --> pdb=" O VAL t 166 " (cutoff:3.500A) Processing helix chain 'u' and resid 95 through 111 removed outlier: 3.564A pdb=" N LEU u 99 " --> pdb=" O ASN u 95 " (cutoff:3.500A) Processing helix chain 'u' and resid 111 through 119 Processing helix chain 'u' and resid 124 through 146 removed outlier: 3.626A pdb=" N GLY u 146 " --> pdb=" O ARG u 142 " (cutoff:3.500A) Processing helix chain 'v' and resid 196 through 204 Processing helix chain 'v' and resid 234 through 245 removed outlier: 3.709A pdb=" N ALA v 244 " --> pdb=" O ALA v 240 " (cutoff:3.500A) Processing helix chain 'w' and resid 136 through 148 removed outlier: 3.560A pdb=" N LYS w 148 " --> pdb=" O LEU w 144 " (cutoff:3.500A) Processing helix chain 'w' and resid 152 through 173 removed outlier: 3.578A pdb=" N LEU w 159 " --> pdb=" O GLN w 155 " (cutoff:3.500A) Processing helix chain 'x' and resid 61 through 69 Processing helix chain 'y' and resid 87 through 106 removed outlier: 3.605A pdb=" N SER y 101 " --> pdb=" O LYS y 97 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS y 104 " --> pdb=" O LYS y 100 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N HIS y 105 " --> pdb=" O SER y 101 " (cutoff:3.500A) Processing helix chain 'y' and resid 152 through 177 removed outlier: 3.579A pdb=" N ARG y 166 " --> pdb=" O SER y 162 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP y 177 " --> pdb=" O ASP y 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '8' and resid 1002 through 1010 removed outlier: 6.898A pdb=" N UNK 81016 " --> pdb=" O UNK 81008 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N UNK 81010 " --> pdb=" O UNK 81014 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N UNK 81014 " --> pdb=" O UNK 81010 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N UNK 81064 " --> pdb=" O UNK 81024 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N UNK 81066 " --> pdb=" O UNK 81026 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N UNK 81028 " --> pdb=" O UNK 81066 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N UNK 81063 " --> pdb=" O UNK 81057 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N UNK 81057 " --> pdb=" O UNK 81063 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N UNK 81065 " --> pdb=" O UNK 81055 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '8' and resid 1205 through 1207 Processing sheet with id=AA3, first strand: chain 'b' and resid 94 through 96 removed outlier: 6.314A pdb=" N PHE b 71 " --> pdb=" O HIS b 94 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL b 96 " --> pdb=" O PHE b 71 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE b 73 " --> pdb=" O VAL b 96 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU b 72 " --> pdb=" O ILE b 166 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR b 187 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE b 204 " --> pdb=" O THR b 187 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS b 189 " --> pdb=" O ILE b 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 60 through 67 removed outlier: 6.343A pdb=" N ILE c 72 " --> pdb=" O ASN c 111 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ALA c 113 " --> pdb=" O ILE c 72 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL c 74 " --> pdb=" O ALA c 113 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR c 115 " --> pdb=" O VAL c 74 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE c 76 " --> pdb=" O THR c 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 175 through 182 Processing sheet with id=AA6, first strand: chain 'd' and resid 116 through 118 Processing sheet with id=AA7, first strand: chain 'e' and resid 153 through 165 removed outlier: 5.338A pdb=" N GLU e 154 " --> pdb=" O GLY e 181 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLY e 181 " --> pdb=" O GLU e 154 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL e 156 " --> pdb=" O VAL e 179 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL e 179 " --> pdb=" O VAL e 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 227 through 231 Processing sheet with id=AA9, first strand: chain 'f' and resid 140 through 147 removed outlier: 5.625A pdb=" N TYR f 141 " --> pdb=" O PHE f 179 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE f 179 " --> pdb=" O TYR f 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 156 through 159 removed outlier: 3.692A pdb=" N ILE f 156 " --> pdb=" O TYR f 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'g' and resid 76 through 80 Processing sheet with id=AB3, first strand: chain 'h' and resid 23 through 27 removed outlier: 3.623A pdb=" N ASN h 47 " --> pdb=" O THR h 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 79 through 81 Processing sheet with id=AB5, first strand: chain 'h' and resid 79 through 81 removed outlier: 6.943A pdb=" N ILE h 107 " --> pdb=" O LEU h 130 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TYR h 132 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE h 105 " --> pdb=" O TYR h 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'i' and resid 84 through 89 Processing sheet with id=AB7, first strand: chain 'j' and resid 129 through 145 removed outlier: 5.424A pdb=" N ASP j 168 " --> pdb=" O MET j 130 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU j 166 " --> pdb=" O PRO j 132 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLN j 164 " --> pdb=" O PRO j 134 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR j 162 " --> pdb=" O PRO j 136 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS j 138 " --> pdb=" O ILE j 160 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE j 160 " --> pdb=" O LYS j 138 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG j 140 " --> pdb=" O PHE j 158 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE j 158 " --> pdb=" O ARG j 140 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR j 142 " --> pdb=" O PHE j 156 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE j 156 " --> pdb=" O TYR j 142 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'j' and resid 129 through 145 removed outlier: 5.424A pdb=" N ASP j 168 " --> pdb=" O MET j 130 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU j 166 " --> pdb=" O PRO j 132 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLN j 164 " --> pdb=" O PRO j 134 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR j 162 " --> pdb=" O PRO j 136 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS j 138 " --> pdb=" O ILE j 160 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE j 160 " --> pdb=" O LYS j 138 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG j 140 " --> pdb=" O PHE j 158 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE j 158 " --> pdb=" O ARG j 140 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR j 142 " --> pdb=" O PHE j 156 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE j 156 " --> pdb=" O TYR j 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'k' and resid 49 through 55 removed outlier: 5.772A pdb=" N VAL k 50 " --> pdb=" O ASP k 45 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP k 45 " --> pdb=" O VAL k 50 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA k 91 " --> pdb=" O PHE k 118 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ARG k 120 " --> pdb=" O ALA k 91 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL k 93 " --> pdb=" O ARG k 120 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL u 86 " --> pdb=" O ASP k 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'l' and resid 29 through 40 removed outlier: 6.549A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL l 37 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL l 52 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR l 39 " --> pdb=" O ARG l 50 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG l 50 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR l 95 " --> pdb=" O THR l 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'p' and resid 46 through 47 removed outlier: 5.684A pdb=" N LYS p 35 " --> pdb=" O ALA p 21 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA p 21 " --> pdb=" O LYS p 35 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL p 2 " --> pdb=" O GLN p 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'q' and resid 61 through 67 removed outlier: 7.003A pdb=" N GLN q 62 " --> pdb=" O VAL q 79 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL q 79 " --> pdb=" O GLN q 62 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN q 75 " --> pdb=" O ILE q 66 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE q 126 " --> pdb=" O GLN q 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 's' and resid 31 through 33 removed outlier: 5.984A pdb=" N ILE s 31 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N HIS s 52 " --> pdb=" O ILE s 31 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N THR s 33 " --> pdb=" O HIS s 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'v' and resid 210 through 217 removed outlier: 4.715A pdb=" N PHE v 227 " --> pdb=" O GLN v 216 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'v' and resid 249 through 250 Processing sheet with id=AC7, first strand: chain 'w' and resid 98 through 105 Processing sheet with id=AC8, first strand: chain 'w' and resid 98 through 105 Processing sheet with id=AC9, first strand: chain 'y' and resid 76 through 81 removed outlier: 3.754A pdb=" N GLU y 111 " --> pdb=" O PHE y 137 " (cutoff:3.500A) 1190 hydrogen bonds defined for protein. 3417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1123 hydrogen bonds 1874 hydrogen bond angles 0 basepair planarities 452 basepair parallelities 809 stacking parallelities Total time for adding SS restraints: 41.53 Time building geometry restraints manager: 22.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7934 1.33 - 1.46: 25174 1.46 - 1.59: 23253 1.59 - 1.72: 2812 1.72 - 1.85: 127 Bond restraints: 59300 Sorted by residual: bond pdb=" CA ALA x 88 " pdb=" CB ALA x 88 " ideal model delta sigma weight residual 1.534 1.643 -0.109 1.18e-02 7.18e+03 8.46e+01 bond pdb=" CA ALA x 88 " pdb=" C ALA x 88 " ideal model delta sigma weight residual 1.521 1.614 -0.092 1.17e-02 7.31e+03 6.23e+01 bond pdb=" CA ILE b 35 " pdb=" CB ILE b 35 " ideal model delta sigma weight residual 1.540 1.607 -0.067 1.36e-02 5.41e+03 2.43e+01 bond pdb=" N ALA x 88 " pdb=" CA ALA x 88 " ideal model delta sigma weight residual 1.462 1.504 -0.042 9.50e-03 1.11e+04 1.99e+01 bond pdb=" CA VAL i 168 " pdb=" CB VAL i 168 " ideal model delta sigma weight residual 1.539 1.591 -0.052 1.20e-02 6.94e+03 1.85e+01 ... (remaining 59295 not shown) Histogram of bond angle deviations from ideal: 96.96 - 105.18: 7398 105.18 - 113.41: 36136 113.41 - 121.63: 29244 121.63 - 129.85: 13619 129.85 - 138.08: 1030 Bond angle restraints: 87427 Sorted by residual: angle pdb=" C GLY k 97 " pdb=" N PRO k 98 " pdb=" CA PRO k 98 " ideal model delta sigma weight residual 119.87 132.84 -12.97 1.04e+00 9.25e-01 1.56e+02 angle pdb=" C LYS c 119 " pdb=" N PRO c 120 " pdb=" CA PRO c 120 " ideal model delta sigma weight residual 119.56 129.50 -9.94 1.01e+00 9.80e-01 9.68e+01 angle pdb=" C ALA x 88 " pdb=" N PRO x 89 " pdb=" CA PRO x 89 " ideal model delta sigma weight residual 120.13 109.17 10.96 1.13e+00 7.83e-01 9.40e+01 angle pdb=" N GLY s 82 " pdb=" CA GLY s 82 " pdb=" C GLY s 82 " ideal model delta sigma weight residual 112.65 124.38 -11.73 1.30e+00 5.92e-01 8.14e+01 angle pdb=" N ASN m 52 " pdb=" CA ASN m 52 " pdb=" C ASN m 52 " ideal model delta sigma weight residual 111.30 121.78 -10.48 1.36e+00 5.41e-01 5.94e+01 ... (remaining 87422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 30923 35.91 - 71.83: 1419 71.83 - 107.74: 104 107.74 - 143.66: 16 143.66 - 179.57: 5 Dihedral angle restraints: 32467 sinusoidal: 23871 harmonic: 8596 Sorted by residual: dihedral pdb=" CA TRP t 173 " pdb=" C TRP t 173 " pdb=" N TYR t 174 " pdb=" CA TYR t 174 " ideal model delta harmonic sigma weight residual 180.00 135.36 44.64 0 5.00e+00 4.00e-02 7.97e+01 dihedral pdb=" O4' C a 702 " pdb=" C1' C a 702 " pdb=" N1 C a 702 " pdb=" C2 C a 702 " ideal model delta sinusoidal sigma weight residual 200.00 56.99 143.01 1 1.50e+01 4.44e-03 7.67e+01 dihedral pdb=" O4' U a 336 " pdb=" C1' U a 336 " pdb=" N1 U a 336 " pdb=" C2 U a 336 " ideal model delta sinusoidal sigma weight residual 200.00 58.72 141.28 1 1.50e+01 4.44e-03 7.60e+01 ... (remaining 32464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 10473 0.096 - 0.192: 483 0.192 - 0.289: 27 0.289 - 0.385: 5 0.385 - 0.481: 1 Chirality restraints: 10989 Sorted by residual: chirality pdb=" CB ILE i 107 " pdb=" CA ILE i 107 " pdb=" CG1 ILE i 107 " pdb=" CG2 ILE i 107 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" CA ILE b 35 " pdb=" N ILE b 35 " pdb=" C ILE b 35 " pdb=" CB ILE b 35 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CB ILE s 41 " pdb=" CA ILE s 41 " pdb=" CG1 ILE s 41 " pdb=" CG2 ILE s 41 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 10986 not shown) Planarity restraints: 5570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA g 152 " -0.026 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C ALA g 152 " 0.088 2.00e-02 2.50e+03 pdb=" O ALA g 152 " -0.034 2.00e-02 2.50e+03 pdb=" N HIS g 153 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G a1006 " 0.024 2.00e-02 2.50e+03 2.54e-02 1.94e+01 pdb=" N9 G a1006 " -0.023 2.00e-02 2.50e+03 pdb=" C8 G a1006 " 0.017 2.00e-02 2.50e+03 pdb=" N7 G a1006 " 0.013 2.00e-02 2.50e+03 pdb=" C5 G a1006 " -0.046 2.00e-02 2.50e+03 pdb=" C6 G a1006 " -0.043 2.00e-02 2.50e+03 pdb=" O6 G a1006 " 0.034 2.00e-02 2.50e+03 pdb=" N1 G a1006 " 0.031 2.00e-02 2.50e+03 pdb=" C2 G a1006 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G a1006 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G a1006 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G a1006 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA i 174 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO i 175 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO i 175 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO i 175 " 0.047 5.00e-02 4.00e+02 ... (remaining 5567 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 199 2.40 - 3.02: 28994 3.02 - 3.65: 93384 3.65 - 4.27: 152294 4.27 - 4.90: 210564 Nonbonded interactions: 485435 Sorted by model distance: nonbonded pdb=" OP1 A a 707 " pdb="MG MG a1544 " model vdw 1.774 2.170 nonbonded pdb=" O6 G a1057 " pdb="MG MG a1637 " model vdw 1.776 2.170 nonbonded pdb=" OP2 A a1059 " pdb="MG MG a1526 " model vdw 1.816 2.170 nonbonded pdb=" OP1 G a1172 " pdb="MG MG a1539 " model vdw 1.837 2.170 nonbonded pdb=" OP2 U a1032 " pdb="MG MG a1513 " model vdw 1.840 2.170 ... (remaining 485430 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.950 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 137.960 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.150 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.109 59300 Z= 0.510 Angle : 1.155 14.342 87427 Z= 0.685 Chirality : 0.047 0.481 10989 Planarity : 0.005 0.078 5570 Dihedral : 16.658 179.571 26901 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.90 % Favored : 94.85 % Rotamer Outliers : 7.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.13), residues: 2756 helix: -3.09 (0.10), residues: 1140 sheet: -0.66 (0.21), residues: 470 loop : -1.95 (0.15), residues: 1146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 997 time to evaluate : 2.871 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 outliers start: 174 outliers final: 58 residues processed: 1112 average time/residue: 0.6711 time to fit residues: 1164.2872 Evaluate side-chains 707 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 649 time to evaluate : 2.907 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.4184 time to fit residues: 48.7025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 367 optimal weight: 7.9990 chunk 329 optimal weight: 0.7980 chunk 182 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 340 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 253 optimal weight: 9.9990 chunk 395 optimal weight: 9.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 78 ASN ** b 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 ASN ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 GLN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 277 ASN g 20 ASN ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 ASN h 30 ASN h 75 ASN i 81 GLN ** i 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 153 GLN j 149 HIS j 151 HIS ** k 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 10 ASN ** m 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 136 HIS m 138 GLN n 72 ASN n 81 HIS o 43 HIS ** p 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 70 ASN ** q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 98 GLN s 47 HIS ** u 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 101 ASN u 133 HIS u 140 ASN ** v 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 162 GLN w 168 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 59300 Z= 0.339 Angle : 0.715 9.041 87427 Z= 0.368 Chirality : 0.040 0.402 10989 Planarity : 0.006 0.098 5570 Dihedral : 15.537 178.231 21128 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.56 % Favored : 96.19 % Rotamer Outliers : 5.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % 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: -1.58 (0.14), residues: 2756 helix: -0.66 (0.14), residues: 1151 sheet: -0.31 (0.22), residues: 482 loop : -1.68 (0.16), residues: 1123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 745 time to evaluate : 2.823 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 outliers start: 127 outliers final: 68 residues processed: 811 average time/residue: 0.5670 time to fit residues: 754.0578 Evaluate side-chains 659 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 591 time to evaluate : 2.806 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.4065 time to fit residues: 55.0627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 219 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 328 optimal weight: 0.6980 chunk 268 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 395 optimal weight: 10.0000 chunk 427 optimal weight: 8.9990 chunk 352 optimal weight: 20.0000 chunk 392 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 317 optimal weight: 8.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 107 ASN b 144 GLN ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 16 GLN c 98 ASN ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 211 ASN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 ASN ** i 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 117 GLN ** k 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 138 GLN n 29 GLN n 60 HIS p 13 GLN ** p 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 59 GLN s 47 HIS ** t 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 68 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.089 59300 Z= 0.464 Angle : 0.764 11.506 87427 Z= 0.389 Chirality : 0.042 0.361 10989 Planarity : 0.006 0.083 5570 Dihedral : 15.604 178.203 21128 Min Nonbonded Distance : 1.377 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.64 % Favored : 95.21 % Rotamer Outliers : 5.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % 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: -1.10 (0.15), residues: 2756 helix: -0.16 (0.14), residues: 1164 sheet: -0.21 (0.23), residues: 475 loop : -1.48 (0.17), residues: 1117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 621 time to evaluate : 2.861 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 outliers start: 139 outliers final: 74 residues processed: 704 average time/residue: 0.5804 time to fit residues: 672.0676 Evaluate side-chains 636 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 562 time to evaluate : 2.867 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.4278 time to fit residues: 61.8014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 390 optimal weight: 2.9990 chunk 297 optimal weight: 0.3980 chunk 205 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 265 optimal weight: 0.6980 chunk 397 optimal weight: 0.4980 chunk 420 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 376 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 93 GLN c 16 GLN c 98 ASN ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 HIS d 133 GLN d 176 ASN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 269 GLN g 24 ASN ** i 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 204 GLN j 164 GLN ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 84 HIS ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 140 ASN w 168 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 59300 Z= 0.155 Angle : 0.593 9.333 87427 Z= 0.305 Chirality : 0.035 0.354 10989 Planarity : 0.005 0.055 5570 Dihedral : 15.059 178.777 21128 Min Nonbonded Distance : 1.613 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.81 % Favored : 96.01 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % 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: -0.53 (0.15), residues: 2756 helix: 0.50 (0.15), residues: 1145 sheet: -0.15 (0.22), residues: 490 loop : -1.27 (0.17), residues: 1121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 705 time to evaluate : 2.876 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 outliers start: 71 outliers final: 25 residues processed: 738 average time/residue: 0.5785 time to fit residues: 706.3075 Evaluate side-chains 622 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 597 time to evaluate : 2.817 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.4128 time to fit residues: 22.7585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 350 optimal weight: 0.0570 chunk 238 optimal weight: 4.9990 chunk 6 optimal weight: 50.0000 chunk 313 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 358 optimal weight: 8.9990 chunk 290 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 377 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 overall best weight: 3.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 16 GLN ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 160 ASN ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 78 GLN n 18 GLN n 29 GLN ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 59300 Z= 0.283 Angle : 0.624 12.423 87427 Z= 0.320 Chirality : 0.036 0.362 10989 Planarity : 0.005 0.057 5570 Dihedral : 14.998 177.524 21128 Min Nonbonded Distance : 1.499 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.39 % Favored : 95.43 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % 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: -0.45 (0.15), residues: 2756 helix: 0.51 (0.15), residues: 1162 sheet: 0.01 (0.23), residues: 473 loop : -1.24 (0.18), residues: 1121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 625 time to evaluate : 2.847 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 outliers start: 78 outliers final: 43 residues processed: 665 average time/residue: 0.5681 time to fit residues: 624.4889 Evaluate side-chains 616 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 573 time to evaluate : 2.815 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4064 time to fit residues: 36.3165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 141 optimal weight: 10.0000 chunk 378 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 420 optimal weight: 8.9990 chunk 349 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 211 ASN ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 81 GLN ** i 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 164 GLN ** k 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 43 HIS ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.071 59300 Z= 0.425 Angle : 0.729 14.377 87427 Z= 0.370 Chirality : 0.040 0.347 10989 Planarity : 0.006 0.064 5570 Dihedral : 15.331 173.075 21128 Min Nonbonded Distance : 1.423 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.26 % Favored : 94.56 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % 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: -0.66 (0.16), residues: 2756 helix: 0.30 (0.15), residues: 1155 sheet: -0.14 (0.24), residues: 469 loop : -1.27 (0.18), residues: 1132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 593 time to evaluate : 2.873 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 outliers start: 64 outliers final: 37 residues processed: 615 average time/residue: 0.5628 time to fit residues: 574.5731 Evaluate side-chains 590 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 553 time to evaluate : 2.783 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.4046 time to fit residues: 31.4304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 405 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 chunk 307 optimal weight: 0.6980 chunk 238 optimal weight: 0.8980 chunk 354 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 419 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 16 GLN ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 45 GLN ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 59300 Z= 0.171 Angle : 0.601 14.758 87427 Z= 0.308 Chirality : 0.034 0.292 10989 Planarity : 0.005 0.064 5570 Dihedral : 14.872 179.505 21128 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.99 % Favored : 95.79 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % 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: -0.34 (0.16), residues: 2756 helix: 0.59 (0.15), residues: 1150 sheet: 0.06 (0.24), residues: 483 loop : -1.14 (0.19), residues: 1123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 662 time to evaluate : 2.794 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 outliers start: 36 outliers final: 18 residues processed: 677 average time/residue: 0.5811 time to fit residues: 647.2443 Evaluate side-chains 610 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 592 time to evaluate : 2.794 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4113 time to fit residues: 17.2313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 259 optimal weight: 0.0970 chunk 167 optimal weight: 30.0000 chunk 250 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 266 optimal weight: 7.9990 chunk 285 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 329 optimal weight: 6.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 211 ASN ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN ** k 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 58 GLN ** t 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 59300 Z= 0.366 Angle : 0.685 12.610 87427 Z= 0.348 Chirality : 0.038 0.396 10989 Planarity : 0.005 0.061 5570 Dihedral : 15.009 174.633 21128 Min Nonbonded Distance : 1.380 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.04 % Favored : 94.78 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % 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: -0.46 (0.16), residues: 2756 helix: 0.48 (0.15), residues: 1160 sheet: 0.03 (0.24), residues: 466 loop : -1.21 (0.19), residues: 1130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 585 time to evaluate : 2.896 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 outliers start: 58 outliers final: 38 residues processed: 607 average time/residue: 0.5761 time to fit residues: 579.9481 Evaluate side-chains 601 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 563 time to evaluate : 2.813 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4088 time to fit residues: 32.5989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 381 optimal weight: 7.9990 chunk 401 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 chunk 390 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 306 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 353 optimal weight: 2.9990 chunk 369 optimal weight: 0.9980 chunk 389 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 167 ASN ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 31 ASN ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 58 GLN ** t 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 141 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 59300 Z= 0.223 Angle : 0.634 20.198 87427 Z= 0.323 Chirality : 0.035 0.412 10989 Planarity : 0.005 0.071 5570 Dihedral : 14.898 176.810 21128 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.54 % Favored : 95.28 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % 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: -0.48 (0.16), residues: 2756 helix: 0.48 (0.15), residues: 1165 sheet: -0.04 (0.24), residues: 477 loop : -1.23 (0.19), residues: 1114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 611 time to evaluate : 2.843 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 outliers start: 21 outliers final: 8 residues processed: 619 average time/residue: 0.5643 time to fit residues: 580.7115 Evaluate side-chains 591 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 583 time to evaluate : 2.868 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4158 time to fit residues: 9.5358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 256 optimal weight: 8.9990 chunk 413 optimal weight: 0.8980 chunk 252 optimal weight: 0.8980 chunk 195 optimal weight: 0.7980 chunk 287 optimal weight: 10.0000 chunk 433 optimal weight: 2.9990 chunk 398 optimal weight: 3.9990 chunk 345 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 chunk 211 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 ASN ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 96 HIS ** m 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 59300 Z= 0.166 Angle : 0.609 19.098 87427 Z= 0.311 Chirality : 0.034 0.425 10989 Planarity : 0.004 0.057 5570 Dihedral : 14.619 179.962 21128 Min Nonbonded Distance : 1.484 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.54 % Favored : 95.28 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % 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: -0.41 (0.16), residues: 2756 helix: 0.48 (0.15), residues: 1165 sheet: 0.06 (0.24), residues: 468 loop : -1.14 (0.18), residues: 1123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 639 time to evaluate : 2.790 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 outliers start: 15 outliers final: 7 residues processed: 644 average time/residue: 0.5595 time to fit residues: 600.4908 Evaluate side-chains 615 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 608 time to evaluate : 2.850 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5008 time to fit residues: 9.4259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 274 optimal weight: 10.0000 chunk 367 optimal weight: 0.4980 chunk 105 optimal weight: 7.9990 chunk 318 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 345 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 354 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 235 ASN c 107 ASN ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN ** k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.058975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.045598 restraints weight = 313059.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.046465 restraints weight = 124488.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.046964 restraints weight = 79373.985| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 59300 Z= 0.317 Angle : 0.677 19.135 87427 Z= 0.344 Chirality : 0.037 0.411 10989 Planarity : 0.005 0.057 5570 Dihedral : 14.792 174.596 21128 Min Nonbonded Distance : 1.334 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.37 % Favored : 94.48 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % 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: -0.53 (0.16), residues: 2756 helix: 0.38 (0.15), residues: 1156 sheet: -0.08 (0.24), residues: 468 loop : -1.17 (0.19), residues: 1132 =============================================================================== Job complete usr+sys time: 10823.99 seconds wall clock time: 192 minutes 33.24 seconds (11553.24 seconds total)