Starting phenix.real_space_refine (version: dev) on Thu Feb 23 17:52:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wts_32799/02_2023/7wts_32799.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wts_32799/02_2023/7wts_32799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wts_32799/02_2023/7wts_32799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wts_32799/02_2023/7wts_32799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wts_32799/02_2023/7wts_32799.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wts_32799/02_2023/7wts_32799.pdb" } resolution = 3.2 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= 0.011 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 Process input model Symmetric amino acids flipped Residue "E TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 61945 Number of models: 1 Model: "" Number of chains: 23 Chain: "2" Number of atoms: 31620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1481, 31620 Classifications: {'RNA': 1481} Modifications used: {'rna2p_pur': 115, 'rna2p_pyr': 85, 'rna3p_pur': 668, 'rna3p_pyr': 613} Link IDs: {'rna2p': 199, 'rna3p': 1281} Chain breaks: 16 Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "e" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 179 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "x" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1372 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "W" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1033 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "u" Number of atoms: 5060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5060 Classifications: {'peptide': 628} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 584} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "O" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1009 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} 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: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "r" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 940 Classifications: {'peptide': 118} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 106} Chain: "q" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1799 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "K" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 468 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain breaks: 1 Chain: "z" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 263 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "5" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 470 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "3" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2200 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 257} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 24.71, per 1000 atoms: 0.40 Number of scatterers: 61945 At special positions: 0 Unit cell: (213.918, 245.688, 201.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 P 1481 15.00 O 15604 8.00 N 11337 7.00 C 33394 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: 22.49 Conformation dependent library (CDL) restraints added in 3.4 seconds 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7036 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 31 sheets defined 38.5% alpha, 20.6% beta 473 base pairs and 810 stacking pairs defined. Time for finding SS restraints: 16.98 Creating SS restraints... Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'B' and resid 23 through 27 removed outlier: 4.239A pdb=" N LYS B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 23 through 27' Processing helix chain 'B' and resid 57 through 63 removed outlier: 3.676A pdb=" N GLY B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.575A pdb=" N VAL B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 177 removed outlier: 3.520A pdb=" N GLN B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.531A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) 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 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 4.029A pdb=" N CYS E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 50 Processing helix chain 'E' and resid 57 through 66 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 262 Processing helix chain 'e' and resid 30 through 42 removed outlier: 3.597A pdb=" N ARG e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 34 Processing helix chain 'H' and resid 36 through 41 removed outlier: 3.602A pdb=" N LEU H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG H 41 " --> pdb=" O LYS H 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 36 through 41' Processing helix chain 'H' and resid 68 through 75 removed outlier: 3.543A pdb=" N ILE H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 87 Processing helix chain 'H' and resid 117 through 120 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.998A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.911A pdb=" N VAL H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 182 Processing helix chain 'G' and resid 20 through 25 removed outlier: 3.533A pdb=" N LEU G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG G 25 " --> pdb=" O GLU G 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 20 through 25' 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 39 through 42 removed outlier: 3.955A pdb=" N GLY G 42 " --> pdb=" O ASP G 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 39 through 42' Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 152 through 157 removed outlier: 3.636A pdb=" N GLN G 155 " --> pdb=" O ASP G 152 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL G 157 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 229 Processing helix chain 'Y' and resid 36 through 49 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 Processing helix chain 'Y' and resid 87 through 94 removed outlier: 3.574A pdb=" N HIS Y 94 " --> pdb=" O ARG Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 115 removed outlier: 3.540A pdb=" N ARG Y 107 " --> pdb=" O SER Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 116 through 117 No H-bonds generated for 'chain 'Y' and resid 116 through 117' Processing helix chain 'Y' and resid 118 through 125 removed outlier: 4.084A pdb=" N ALA Y 121 " --> pdb=" O ARG Y 118 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL Y 125 " --> pdb=" O LYS Y 122 " (cutoff:3.500A) Processing helix chain 'x' and resid 84 through 91 Processing helix chain 'x' and resid 92 through 103 Proline residue: x 98 - end of helix removed outlier: 3.731A pdb=" N HIS x 102 " --> pdb=" O PRO x 98 " (cutoff:3.500A) Processing helix chain 'x' and resid 127 through 143 removed outlier: 3.929A pdb=" N THR x 131 " --> pdb=" O VAL x 127 " (cutoff:3.500A) Processing helix chain 'x' and resid 145 through 155 removed outlier: 3.567A pdb=" N ALA x 149 " --> pdb=" O GLN x 145 " (cutoff:3.500A) Processing helix chain 'x' and resid 166 through 168 No H-bonds generated for 'chain 'x' and resid 166 through 168' Processing helix chain 'x' and resid 173 through 185 removed outlier: 3.551A pdb=" N SER x 177 " --> pdb=" O GLY x 173 " (cutoff:3.500A) Processing helix chain 'x' and resid 188 through 199 Processing helix chain 'x' and resid 214 through 231 removed outlier: 3.714A pdb=" N GLY x 231 " --> pdb=" O ASN x 227 " (cutoff:3.500A) Processing helix chain 'x' and resid 233 through 245 Processing helix chain 'X' and resid 9 through 23 Processing helix chain 'X' and resid 24 through 32 Processing helix chain 'X' and resid 89 through 94 removed outlier: 3.545A pdb=" N PHE X 93 " --> pdb=" O CYS X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'W' and resid 5 through 20 removed outlier: 3.589A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG W 20 " --> pdb=" O ASN W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.509A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 94 removed outlier: 4.290A pdb=" N GLU W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS W 88 " --> pdb=" O LYS W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 120 Processing helix chain 'u' and resid 49 through 75 removed outlier: 4.092A pdb=" N LEU u 75 " --> pdb=" O GLU u 71 " (cutoff:3.500A) Processing helix chain 'u' and resid 95 through 104 removed outlier: 3.540A pdb=" N ALA u 99 " --> pdb=" O SER u 95 " (cutoff:3.500A) Processing helix chain 'u' and resid 142 through 152 Processing helix chain 'u' and resid 167 through 181 Processing helix chain 'u' and resid 191 through 195 Processing helix chain 'u' and resid 196 through 213 removed outlier: 4.268A pdb=" N ILE u 201 " --> pdb=" O LEU u 197 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP u 202 " --> pdb=" O LYS u 198 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS u 209 " --> pdb=" O LYS u 205 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS u 213 " --> pdb=" O LYS u 209 " (cutoff:3.500A) Processing helix chain 'u' and resid 225 through 238 Processing helix chain 'u' and resid 244 through 250 removed outlier: 3.648A pdb=" N ARG u 250 " --> pdb=" O PHE u 246 " (cutoff:3.500A) Processing helix chain 'u' and resid 465 through 484 Processing helix chain 'u' and resid 495 through 500 Processing helix chain 'u' and resid 522 through 527 removed outlier: 3.707A pdb=" N ILE u 527 " --> pdb=" O TYR u 524 " (cutoff:3.500A) Processing helix chain 'u' and resid 532 through 547 Processing helix chain 'u' and resid 567 through 576 removed outlier: 3.610A pdb=" N GLU u 571 " --> pdb=" O VAL u 567 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN u 575 " --> pdb=" O GLU u 571 " (cutoff:3.500A) Processing helix chain 'u' and resid 720 through 726 removed outlier: 3.756A pdb=" N LEU u 724 " --> pdb=" O ARG u 720 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 89 Processing helix chain 'O' and resid 109 through 122 removed outlier: 3.732A pdb=" N GLN O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 43 Processing helix chain 'N' and resid 46 through 57 Processing helix chain 'N' and resid 62 through 68 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 105 Processing helix chain 'N' and resid 108 through 132 Processing helix chain 'N' and resid 146 through 150 Processing helix chain 'L' and resid 23 through 30 removed outlier: 3.706A pdb=" N LYS L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 52 removed outlier: 3.531A pdb=" N ILE L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 39 through 62 removed outlier: 4.004A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 Processing helix chain 'J' and resid 93 through 98 removed outlier: 3.809A pdb=" N ILE J 97 " --> pdb=" O LYS J 93 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU J 98 " --> pdb=" O LEU J 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 93 through 98' Processing helix chain 'J' and resid 101 through 108 removed outlier: 4.194A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 Processing helix chain 'J' and resid 122 through 132 Processing helix chain 'J' and resid 153 through 155 No H-bonds generated for 'chain 'J' and resid 153 through 155' Processing helix chain 'J' and resid 171 through 181 removed outlier: 3.566A pdb=" N LYS J 180 " --> pdb=" O LYS J 176 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY J 181 " --> pdb=" O ASN J 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 29 Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 88 through 93 Processing helix chain 'I' and resid 106 through 118 Processing helix chain 'I' and resid 130 through 138 Processing helix chain 'I' and resid 142 through 154 Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 191 through 206 removed outlier: 3.518A pdb=" N LEU I 195 " --> pdb=" O GLU I 191 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS I 206 " --> pdb=" O ILE I 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 9 removed outlier: 3.552A pdb=" N HIS r 6 " --> pdb=" O LYS r 2 " (cutoff:3.500A) Processing helix chain 'r' and resid 38 through 46 removed outlier: 3.703A pdb=" N VAL r 42 " --> pdb=" O ASN r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 47 through 49 No H-bonds generated for 'chain 'r' and resid 47 through 49' Processing helix chain 'r' and resid 50 through 61 Processing helix chain 'r' and resid 77 through 90 Processing helix chain 'q' and resid 19 through 28 Processing helix chain 'q' and resid 29 through 47 removed outlier: 3.522A pdb=" N LEU q 47 " --> pdb=" O ALA q 43 " (cutoff:3.500A) Processing helix chain 'q' and resid 65 through 74 Processing helix chain 'q' and resid 84 through 94 removed outlier: 3.628A pdb=" N LEU q 88 " --> pdb=" O SER q 84 " (cutoff:3.500A) Processing helix chain 'q' and resid 105 through 108 Processing helix chain 'q' and resid 137 through 152 Processing helix chain 'q' and resid 167 through 181 removed outlier: 4.125A pdb=" N LEU q 171 " --> pdb=" O ASN q 167 " (cutoff:3.500A) Processing helix chain 'q' and resid 250 through 262 Processing helix chain 'K' and resid 1189 through 1215 Proline residue: K1209 - end of helix Processing helix chain 'K' and resid 1230 through 1234 Processing helix chain 'z' and resid 103 through 129 removed outlier: 3.626A pdb=" N LYS z 107 " --> pdb=" O PRO z 103 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS z 129 " --> pdb=" O ALA z 125 " (cutoff:3.500A) Processing helix chain '5' and resid 221 through 247 removed outlier: 3.915A pdb=" N ILE 5 247 " --> pdb=" O ARG 5 243 " (cutoff:3.500A) Processing helix chain '5' and resid 249 through 263 Processing helix chain '3' and resid 41 through 52 removed outlier: 3.597A pdb=" N ILE 3 45 " --> pdb=" O ASN 3 41 " (cutoff:3.500A) Processing helix chain '3' and resid 68 through 78 removed outlier: 3.686A pdb=" N VAL 3 72 " --> pdb=" O GLY 3 68 " (cutoff:3.500A) Processing helix chain '3' and resid 87 through 99 Processing helix chain '3' and resid 103 through 105 No H-bonds generated for 'chain '3' and resid 103 through 105' Processing helix chain '3' and resid 133 through 144 removed outlier: 3.835A pdb=" N PHE 3 137 " --> pdb=" O ILE 3 133 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL 3 138 " --> pdb=" O SER 3 134 " (cutoff:3.500A) Processing helix chain '3' and resid 157 through 164 Processing helix chain '3' and resid 173 through 182 Processing helix chain '3' and resid 192 through 196 removed outlier: 3.822A pdb=" N ASN 3 195 " --> pdb=" O GLY 3 192 " (cutoff:3.500A) Processing helix chain '3' and resid 219 through 231 Processing helix chain '3' and resid 237 through 243 Processing helix chain '3' and resid 244 through 263 Processing helix chain '3' and resid 271 through 284 Processing helix chain '3' and resid 289 through 293 removed outlier: 3.744A pdb=" N MET 3 293 " --> pdb=" O ALA 3 290 " (cutoff:3.500A) Processing helix chain '3' and resid 294 through 308 removed outlier: 3.511A pdb=" N PHE 3 298 " --> pdb=" O ASP 3 294 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AA2, first strand: chain 'b' and resid 54 through 55 removed outlier: 6.816A pdb=" N VAL b 54 " --> pdb=" O LEU b 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 50 removed outlier: 8.632A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LYS B 34 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N PHE B 100 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N CYS B 96 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL B 91 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR B 98 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU B 89 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N PHE B 100 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILE B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 50 removed outlier: 8.632A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LYS B 34 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N PHE B 100 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 13.616A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.133A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ARG B 213 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL B 212 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 140 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG B 136 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 9 through 10 removed outlier: 4.555A pdb=" N LEU E 9 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AA7, first strand: chain 'E' and resid 146 through 148 removed outlier: 5.959A pdb=" N ILE E 136 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL E 131 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS E 138 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE E 129 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.147A pdb=" N LYS E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS E 233 " --> pdb=" O LYS E 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 47 through 53 Processing sheet with id=AB1, first strand: chain 'H' and resid 185 through 188 removed outlier: 8.429A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS H 142 " --> pdb=" O ASP W 54 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU W 49 " --> pdb=" O ASN W 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.755A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN G 56 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU G 109 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY G 54 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU G 111 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE G 52 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE G 113 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL G 50 " --> pdb=" O ILE G 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AB4, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AB5, first strand: chain 'Y' and resid 6 through 9 Processing sheet with id=AB6, first strand: chain 'Y' and resid 6 through 9 removed outlier: 7.206A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'x' and resid 75 through 79 Processing sheet with id=AB8, first strand: chain 'x' and resid 159 through 164 Processing sheet with id=AB9, first strand: chain 'X' and resid 128 through 129 removed outlier: 5.399A pdb=" N VAL X 122 " --> pdb=" O ALA X 103 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA X 103 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AC2, first strand: chain 'W' and resid 71 through 74 removed outlier: 6.522A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'u' and resid 110 through 115 removed outlier: 3.560A pdb=" N ASN u 114 " --> pdb=" O ASN u 121 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN u 120 " --> pdb=" O SER u 137 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER u 137 " --> pdb=" O GLN u 120 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N HIS u 83 " --> pdb=" O PHE u 134 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR u 136 " --> pdb=" O HIS u 83 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL u 85 " --> pdb=" O THR u 136 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE u 156 " --> pdb=" O THR u 186 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA u 188 " --> pdb=" O ILE u 156 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE u 158 " --> pdb=" O ALA u 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'u' and resid 295 through 297 removed outlier: 6.819A pdb=" N ALA u 255 " --> pdb=" O TYR u 277 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N TYR u 277 " --> pdb=" O ALA u 255 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER u 263 " --> pdb=" O VAL u 269 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY u 270 " --> pdb=" O GLU u 564 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU u 564 " --> pdb=" O GLY u 270 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N SER u 563 " --> pdb=" O MET u 299 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N MET u 299 " --> pdb=" O SER u 563 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'u' and resid 621 through 625 removed outlier: 6.300A pdb=" N LYS u 669 " --> pdb=" O LEU u 678 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU u 678 " --> pdb=" O LYS u 669 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLY u 682 " --> pdb=" O ARG u 599 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ARG u 599 " --> pdb=" O GLY u 682 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU u 684 " --> pdb=" O VAL u 597 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL u 597 " --> pdb=" O LEU u 684 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE u 629 " --> pdb=" O GLN u 641 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LYS u 639 " --> pdb=" O GLN u 631 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ARG u 696 " --> pdb=" O LEU u 640 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE u 741 " --> pdb=" O SER u 754 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N SER u 754 " --> pdb=" O ILE u 741 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET u 710 " --> pdb=" O PHE u 707 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG u 714 " --> pdb=" O PRO u 703 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 52 through 56 removed outlier: 7.476A pdb=" N LEU O 93 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE O 129 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE O 95 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASP O 131 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU O 97 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 72 through 79 removed outlier: 16.421A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.535A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 16.051A pdb=" N VAL L 138 " --> pdb=" O HIS L 106 " (cutoff:3.500A) removed outlier: 13.678A pdb=" N ASN L 108 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AC9, first strand: chain 'I' and resid 37 through 38 removed outlier: 5.946A pdb=" N LYS I 37 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 62 through 67 removed outlier: 7.244A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE I 101 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N CYS I 100 " --> pdb=" O ILE I 175 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 27 through 32 removed outlier: 6.758A pdb=" N ALA r 27 " --> pdb=" O GLY r 96 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY r 96 " --> pdb=" O ALA r 27 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU r 29 " --> pdb=" O ILE r 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'r' and resid 115 through 116 removed outlier: 6.390A pdb=" N TYR q 56 " --> pdb=" O GLY q 118 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE q 120 " --> pdb=" O TYR q 56 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU q 58 " --> pdb=" O ILE q 120 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ASP q 117 " --> pdb=" O GLY q 156 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG q 158 " --> pdb=" O ASP q 117 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '3' and resid 107 through 111 removed outlier: 6.152A pdb=" N VAL 3 81 " --> pdb=" O GLN 3 108 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU 3 110 " --> pdb=" O VAL 3 81 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA 3 83 " --> pdb=" O LEU 3 110 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL 3 59 " --> pdb=" O THR 3 124 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL 3 126 " --> pdb=" O VAL 3 59 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU 3 61 " --> pdb=" O VAL 3 126 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASN 3 128 " --> pdb=" O LEU 3 61 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL 3 63 " --> pdb=" O ASN 3 128 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS 3 125 " --> pdb=" O ILE 3 152 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N MET 3 154 " --> pdb=" O CYS 3 125 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA 3 127 " --> pdb=" O MET 3 154 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N GLN 3 156 " --> pdb=" O ALA 3 127 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER 3 204 " --> pdb=" O LYS 3 190 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS 3 190 " --> pdb=" O SER 3 204 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL 3 206 " --> pdb=" O LEU 3 188 " (cutoff:3.500A) 1310 hydrogen bonds defined for protein. 3720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1169 hydrogen bonds 1810 hydrogen bond angles 0 basepair planarities 473 basepair parallelities 810 stacking parallelities Total time for adding SS restraints: 51.69 Time building geometry restraints manager: 24.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8053 1.32 - 1.45: 25910 1.45 - 1.58: 29127 1.58 - 1.70: 2946 1.70 - 1.83: 203 Bond restraints: 66239 Sorted by residual: bond pdb=" C1' G 21639 " pdb=" N9 G 21639 " ideal model delta sigma weight residual 1.465 1.594 -0.129 1.50e-02 4.44e+03 7.44e+01 bond pdb=" C ASP u 348 " pdb=" N PRO u 349 " ideal model delta sigma weight residual 1.331 1.392 -0.061 1.27e-02 6.20e+03 2.31e+01 bond pdb=" C LYS B 34 " pdb=" N ALA B 35 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.86e-02 2.89e+03 9.32e+00 bond pdb=" O3' C 21703 " pdb=" P C 21704 " ideal model delta sigma weight residual 1.607 1.648 -0.041 1.50e-02 4.44e+03 7.46e+00 bond pdb=" N VAL 3 202 " pdb=" CA VAL 3 202 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.38e-02 5.25e+03 7.39e+00 ... (remaining 66234 not shown) Histogram of bond angle deviations from ideal: 94.12 - 102.42: 2006 102.42 - 110.73: 30792 110.73 - 119.04: 30337 119.04 - 127.35: 30061 127.35 - 135.65: 3322 Bond angle restraints: 96518 Sorted by residual: angle pdb=" CA GLN G 197 " pdb=" CB GLN G 197 " pdb=" CG GLN G 197 " ideal model delta sigma weight residual 114.10 126.12 -12.02 2.00e+00 2.50e-01 3.61e+01 angle pdb=" C VAL J 137 " pdb=" N ARG J 138 " pdb=" CA ARG J 138 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 angle pdb=" C3' U 21494 " pdb=" O3' U 21494 " pdb=" P G 21495 " ideal model delta sigma weight residual 120.20 127.56 -7.36 1.50e+00 4.44e-01 2.41e+01 angle pdb=" C CYS O 54 " pdb=" N ARG O 55 " pdb=" CA ARG O 55 " ideal model delta sigma weight residual 121.40 128.55 -7.15 1.52e+00 4.33e-01 2.22e+01 angle pdb=" N GLN G 197 " pdb=" CA GLN G 197 " pdb=" CB GLN G 197 " ideal model delta sigma weight residual 110.39 118.16 -7.77 1.66e+00 3.63e-01 2.19e+01 ... (remaining 96513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 35413 35.89 - 71.77: 1302 71.77 - 107.66: 111 107.66 - 143.54: 20 143.54 - 179.43: 27 Dihedral angle restraints: 36873 sinusoidal: 25998 harmonic: 10875 Sorted by residual: dihedral pdb=" O4' U 2 427 " pdb=" C1' U 2 427 " pdb=" N1 U 2 427 " pdb=" C2 U 2 427 " ideal model delta sinusoidal sigma weight residual 200.00 21.34 178.66 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 16.63 -176.63 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 2 853 " pdb=" C1' C 2 853 " pdb=" N1 C 2 853 " pdb=" C2 C 2 853 " ideal model delta sinusoidal sigma weight residual -160.00 5.85 -165.85 1 1.50e+01 4.44e-03 8.40e+01 ... (remaining 36870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 11114 0.086 - 0.171: 769 0.171 - 0.257: 55 0.257 - 0.343: 16 0.343 - 0.428: 3 Chirality restraints: 11957 Sorted by residual: chirality pdb=" CB ILE L 40 " pdb=" CA ILE L 40 " pdb=" CG1 ILE L 40 " pdb=" CG2 ILE L 40 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" C3' G 2 114 " pdb=" C4' G 2 114 " pdb=" O3' G 2 114 " pdb=" C2' G 2 114 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C1' U 2 918 " pdb=" O4' U 2 918 " pdb=" C2' U 2 918 " pdb=" N1 U 2 918 " both_signs ideal model delta sigma weight residual False 2.47 2.11 0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 11954 not shown) Planarity restraints: 6768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 21837 " -0.025 2.00e-02 2.50e+03 2.94e-02 2.59e+01 pdb=" N9 G 21837 " 0.010 2.00e-02 2.50e+03 pdb=" C8 G 21837 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G 21837 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G 21837 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G 21837 " 0.026 2.00e-02 2.50e+03 pdb=" O6 G 21837 " -0.032 2.00e-02 2.50e+03 pdb=" N1 G 21837 " -0.014 2.00e-02 2.50e+03 pdb=" C2 G 21837 " 0.075 2.00e-02 2.50e+03 pdb=" N2 G 21837 " -0.046 2.00e-02 2.50e+03 pdb=" N3 G 21837 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G 21837 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21701 " 0.014 2.00e-02 2.50e+03 3.32e-02 2.48e+01 pdb=" N1 C 21701 " -0.009 2.00e-02 2.50e+03 pdb=" C2 C 21701 " -0.080 2.00e-02 2.50e+03 pdb=" O2 C 21701 " 0.046 2.00e-02 2.50e+03 pdb=" N3 C 21701 " 0.009 2.00e-02 2.50e+03 pdb=" C4 C 21701 " -0.021 2.00e-02 2.50e+03 pdb=" N4 C 21701 " 0.020 2.00e-02 2.50e+03 pdb=" C5 C 21701 " 0.010 2.00e-02 2.50e+03 pdb=" C6 C 21701 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 918 " -0.049 2.00e-02 2.50e+03 2.58e-02 1.50e+01 pdb=" N1 U 2 918 " 0.044 2.00e-02 2.50e+03 pdb=" C2 U 2 918 " 0.026 2.00e-02 2.50e+03 pdb=" O2 U 2 918 " 0.006 2.00e-02 2.50e+03 pdb=" N3 U 2 918 " -0.024 2.00e-02 2.50e+03 pdb=" C4 U 2 918 " 0.006 2.00e-02 2.50e+03 pdb=" O4 U 2 918 " -0.018 2.00e-02 2.50e+03 pdb=" C5 U 2 918 " 0.006 2.00e-02 2.50e+03 pdb=" C6 U 2 918 " 0.003 2.00e-02 2.50e+03 ... (remaining 6765 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 1472 2.64 - 3.21: 48482 3.21 - 3.77: 114981 3.77 - 4.34: 153939 4.34 - 4.90: 216680 Nonbonded interactions: 535554 Sorted by model distance: nonbonded pdb=" O4 U 2 749 " pdb=" O6 G 2 793 " model vdw 2.076 3.040 nonbonded pdb=" O4 U 2 678 " pdb=" N7 A 21027 " model vdw 2.133 3.120 nonbonded pdb=" O2' A 2 671 " pdb=" OP2 G 21089 " model vdw 2.136 2.440 nonbonded pdb=" N4 C 2 748 " pdb=" N6 A 2 794 " model vdw 2.194 3.200 nonbonded pdb=" O2' C 21811 " pdb=" OE1 GLN u 63 " model vdw 2.197 2.440 ... (remaining 535549 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1481 5.49 5 S 129 5.16 5 C 33394 2.51 5 N 11337 2.21 5 O 15604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.030 Extract box with map and model: 12.850 Check model and map are aligned: 0.660 Process input model: 160.110 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.430 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:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.005 0.129 66239 Z= 0.325 Angle : 0.855 13.999 96518 Z= 0.436 Chirality : 0.046 0.428 11957 Planarity : 0.006 0.079 6768 Dihedral : 16.372 179.431 29837 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.06 % Twisted Proline : 0.55 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 3719 helix: -0.26 (0.14), residues: 1248 sheet: -0.11 (0.19), residues: 730 loop : -1.14 (0.13), residues: 1741 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 437 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 439 average time/residue: 0.6655 time to fit residues: 471.0719 Evaluate side-chains 360 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 3.483 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 435 optimal weight: 8.9990 chunk 391 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 133 optimal weight: 30.0000 chunk 263 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 chunk 404 optimal weight: 0.0040 chunk 156 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 301 optimal weight: 9.9990 chunk 468 optimal weight: 0.0570 overall best weight: 2.8116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 83 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 GLN G 70 HIS G 186 GLN x 115 ASN ** x 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 301 GLN u 617 HIS ** u 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 HIS I 99 ASN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 66239 Z= 0.275 Angle : 0.638 10.445 96518 Z= 0.325 Chirality : 0.039 0.324 11957 Planarity : 0.005 0.073 6768 Dihedral : 15.812 179.988 21885 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.28 % Favored : 96.69 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.06 % Twisted Proline : 0.55 % Twisted General : 0.03 % 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: -0.28 (0.13), residues: 3719 helix: 0.67 (0.14), residues: 1279 sheet: 0.10 (0.19), residues: 710 loop : -0.90 (0.14), residues: 1730 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 386 time to evaluate : 3.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 24 residues processed: 400 average time/residue: 0.6537 time to fit residues: 426.4537 Evaluate side-chains 391 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 367 time to evaluate : 3.500 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4265 time to fit residues: 23.9183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 260 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 389 optimal weight: 5.9990 chunk 319 optimal weight: 0.9990 chunk 129 optimal weight: 50.0000 chunk 469 optimal weight: 50.0000 chunk 507 optimal weight: 9.9990 chunk 418 optimal weight: 4.9990 chunk 465 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 376 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 19 HIS ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS G 70 HIS G 81 HIS x 217 ASN X 39 ASN W 91 ASN ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 256 HIS u 641 GLN ** u 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 262 GLN ** 3 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 66239 Z= 0.352 Angle : 0.678 10.293 96518 Z= 0.343 Chirality : 0.042 0.348 11957 Planarity : 0.006 0.076 6768 Dihedral : 15.925 179.902 21885 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.45 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.06 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.13), residues: 3719 helix: 0.96 (0.14), residues: 1273 sheet: 0.05 (0.19), residues: 703 loop : -0.88 (0.14), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 381 time to evaluate : 3.603 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 405 average time/residue: 0.6720 time to fit residues: 447.7995 Evaluate side-chains 363 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 347 time to evaluate : 3.697 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4895 time to fit residues: 19.5894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 463 optimal weight: 0.3980 chunk 352 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 315 optimal weight: 3.9990 chunk 471 optimal weight: 50.0000 chunk 498 optimal weight: 8.9990 chunk 246 optimal weight: 1.9990 chunk 446 optimal weight: 30.0000 chunk 134 optimal weight: 30.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 ASN G 70 HIS ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 750 HIS ** r 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 66239 Z= 0.185 Angle : 0.566 10.162 96518 Z= 0.289 Chirality : 0.036 0.306 11957 Planarity : 0.004 0.064 6768 Dihedral : 15.723 179.917 21885 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.06 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.13), residues: 3719 helix: 1.30 (0.14), residues: 1278 sheet: 0.18 (0.20), residues: 688 loop : -0.74 (0.14), residues: 1753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 372 time to evaluate : 3.480 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 17 residues processed: 387 average time/residue: 0.6552 time to fit residues: 416.7886 Evaluate side-chains 364 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 347 time to evaluate : 3.498 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4466 time to fit residues: 18.8375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 415 optimal weight: 0.9990 chunk 283 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 205 optimal weight: 0.8980 chunk 425 optimal weight: 2.9990 chunk 344 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 254 optimal weight: 0.0770 chunk 447 optimal weight: 50.0000 chunk 125 optimal weight: 50.0000 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 70 HIS G 110 ASN ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 286 ASN ** u 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 750 HIS N 36 GLN K1211 GLN 3 248 GLN ** 3 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 66239 Z= 0.209 Angle : 0.570 11.000 96518 Z= 0.290 Chirality : 0.036 0.308 11957 Planarity : 0.004 0.064 6768 Dihedral : 15.671 179.863 21885 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.67 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.06 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3719 helix: 1.42 (0.15), residues: 1281 sheet: 0.20 (0.20), residues: 678 loop : -0.70 (0.14), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 360 time to evaluate : 3.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 379 average time/residue: 0.6593 time to fit residues: 410.7897 Evaluate side-chains 371 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 355 time to evaluate : 3.455 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4457 time to fit residues: 17.8238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 167 optimal weight: 0.5980 chunk 449 optimal weight: 40.0000 chunk 98 optimal weight: 7.9990 chunk 292 optimal weight: 1.9990 chunk 123 optimal weight: 50.0000 chunk 499 optimal weight: 10.0000 chunk 414 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 70 HIS G 155 GLN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 750 HIS ** 3 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 66239 Z= 0.296 Angle : 0.623 10.324 96518 Z= 0.316 Chirality : 0.039 0.332 11957 Planarity : 0.005 0.070 6768 Dihedral : 15.749 179.904 21885 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.06 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.14), residues: 3719 helix: 1.47 (0.15), residues: 1273 sheet: 0.06 (0.20), residues: 700 loop : -0.75 (0.14), residues: 1746 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 359 time to evaluate : 3.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 17 residues processed: 373 average time/residue: 0.6850 time to fit residues: 423.1180 Evaluate side-chains 352 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 335 time to evaluate : 3.490 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4595 time to fit residues: 19.2510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 481 optimal weight: 0.0010 chunk 56 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 chunk 364 optimal weight: 0.9980 chunk 282 optimal weight: 2.9990 chunk 420 optimal weight: 0.6980 chunk 278 optimal weight: 10.0000 chunk 497 optimal weight: 50.0000 chunk 311 optimal weight: 6.9990 chunk 303 optimal weight: 0.9980 chunk 229 optimal weight: 0.0470 overall best weight: 0.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 165 ASN G 70 HIS x 106 GLN ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 750 HIS ** 3 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 66239 Z= 0.127 Angle : 0.541 10.051 96518 Z= 0.277 Chirality : 0.034 0.331 11957 Planarity : 0.004 0.058 6768 Dihedral : 15.606 179.890 21885 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.06 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3719 helix: 1.69 (0.15), residues: 1272 sheet: 0.19 (0.20), residues: 680 loop : -0.61 (0.14), residues: 1767 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 365 time to evaluate : 3.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 373 average time/residue: 0.6628 time to fit residues: 404.4616 Evaluate side-chains 355 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 350 time to evaluate : 3.520 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4424 time to fit residues: 8.5026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 307 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 297 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 316 optimal weight: 0.8980 chunk 338 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 chunk 46 optimal weight: 50.0000 chunk 390 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 165 ASN G 70 HIS ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 750 HIS ** 3 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 66239 Z= 0.232 Angle : 0.579 10.192 96518 Z= 0.294 Chirality : 0.037 0.313 11957 Planarity : 0.004 0.062 6768 Dihedral : 15.605 179.992 21885 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.06 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3719 helix: 1.65 (0.15), residues: 1276 sheet: 0.13 (0.20), residues: 691 loop : -0.62 (0.14), residues: 1752 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 361 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 371 average time/residue: 0.6670 time to fit residues: 408.5911 Evaluate side-chains 354 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 343 time to evaluate : 3.477 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4585 time to fit residues: 13.8235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 452 optimal weight: 30.0000 chunk 476 optimal weight: 30.0000 chunk 434 optimal weight: 7.9990 chunk 463 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 201 optimal weight: 0.6980 chunk 363 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 418 optimal weight: 1.9990 chunk 438 optimal weight: 3.9990 chunk 461 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN H 68 GLN H 165 ASN G 70 HIS ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 ASN ** 3 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 66239 Z= 0.314 Angle : 0.647 11.112 96518 Z= 0.328 Chirality : 0.040 0.338 11957 Planarity : 0.005 0.072 6768 Dihedral : 15.731 179.952 21885 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.06 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3719 helix: 1.40 (0.15), residues: 1284 sheet: 0.05 (0.20), residues: 696 loop : -0.75 (0.14), residues: 1739 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 348 time to evaluate : 3.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 352 average time/residue: 0.6603 time to fit residues: 381.1995 Evaluate side-chains 341 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 338 time to evaluate : 3.507 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4583 time to fit residues: 6.8279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 304 optimal weight: 1.9990 chunk 490 optimal weight: 0.9980 chunk 299 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 340 optimal weight: 0.9980 chunk 514 optimal weight: 8.9990 chunk 473 optimal weight: 1.9990 chunk 409 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 GLN G 70 HIS x 196 ASN ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 301 GLN u 750 HIS ** 3 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 66239 Z= 0.162 Angle : 0.561 10.124 96518 Z= 0.287 Chirality : 0.035 0.292 11957 Planarity : 0.004 0.059 6768 Dihedral : 15.573 179.519 21885 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.06 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.14), residues: 3719 helix: 1.60 (0.15), residues: 1283 sheet: 0.14 (0.20), residues: 683 loop : -0.61 (0.14), residues: 1753 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7438 Ramachandran restraints generated. 3719 Oldfield, 0 Emsley, 3719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 342 time to evaluate : 3.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 347 average time/residue: 0.6712 time to fit residues: 381.6154 Evaluate side-chains 341 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 335 time to evaluate : 3.470 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4545 time to fit residues: 9.3747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 325 optimal weight: 10.0000 chunk 436 optimal weight: 7.9990 chunk 125 optimal weight: 50.0000 chunk 377 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 113 optimal weight: 60.0000 chunk 410 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 421 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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** G 70 HIS x 196 ASN ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN L 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.157035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.135443 restraints weight = 106599.555| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.36 r_work: 0.3522 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.078 66239 Z= 0.461 Angle : 0.741 11.207 96518 Z= 0.370 Chirality : 0.045 0.367 11957 Planarity : 0.006 0.078 6768 Dihedral : 15.861 179.815 21885 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.46 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.06 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 3719 helix: 1.26 (0.14), residues: 1288 sheet: -0.00 (0.19), residues: 703 loop : -0.82 (0.14), residues: 1728 =============================================================================== Job complete usr+sys time: 9070.01 seconds wall clock time: 163 minutes 40.24 seconds (9820.24 seconds total)