Starting phenix.real_space_refine on Sat Dec 9 04:04:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wts_32799/12_2023/7wts_32799.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wts_32799/12_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_32799/12_2023/7wts_32799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wts_32799/12_2023/7wts_32799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wts_32799/12_2023/7wts_32799.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wts_32799/12_2023/7wts_32799.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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-1.21rc1-5172/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: 23.56, per 1000 atoms: 0.38 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: 22.80 Conformation dependent library (CDL) restraints added in 4.1 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: 21.09 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: 48.95 Time building geometry restraints manager: 24.78 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: 37248 35.89 - 71.77: 3173 71.77 - 107.66: 453 107.66 - 143.54: 20 143.54 - 179.43: 27 Dihedral angle restraints: 40921 sinusoidal: 30046 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 40918 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 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: 0.050 Extract box with map and model: 11.340 Check model and map are aligned: 0.670 Set scattering table: 0.430 Process input model: 162.420 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 : 21.770 179.431 33885 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 % Allowed : 0.46 % Favored : 99.45 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP u 777 HIS 0.011 0.002 HIS r 6 PHE 0.028 0.003 PHE u 484 TYR 0.033 0.002 TYR N 18 ARG 0.011 0.001 ARG O 142 *********************** 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 : 3.458 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: 0.6634 time to fit residues: 475.2768 Evaluate side-chains 360 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 3.373 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1073 ------------------------------------------------------------------------------- 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: 3.9990 chunk 468 optimal weight: 0.0570 overall best weight: 2.4116 ------------------------------------------------------------------------------- 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 641 GLN ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 66239 Z= 0.245 Angle : 0.619 10.279 96518 Z= 0.316 Chirality : 0.038 0.320 11957 Planarity : 0.005 0.070 6768 Dihedral : 22.658 179.914 25933 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.75 % Rotamer: Outliers : 1.07 % Allowed : 7.29 % Favored : 91.64 % 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: -0.23 (0.13), residues: 3719 helix: 0.71 (0.14), residues: 1279 sheet: 0.11 (0.19), residues: 710 loop : -0.88 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 30 HIS 0.007 0.001 HIS I 22 PHE 0.029 0.002 PHE H 135 TYR 0.031 0.001 TYR x 238 ARG 0.009 0.001 ARG I 47 *********************** 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 427 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 392 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 406 average time/residue: 0.6539 time to fit residues: 437.2378 Evaluate side-chains 385 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 364 time to evaluate : 3.397 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4334 time to fit residues: 21.8795 ------------------------------------------------------------------------------- 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: 0.8980 chunk 145 optimal weight: 7.9990 chunk 389 optimal weight: 6.9990 chunk 319 optimal weight: 2.9990 chunk 129 optimal weight: 50.0000 chunk 469 optimal weight: 50.0000 chunk 507 optimal weight: 20.0000 chunk 418 optimal weight: 5.9990 chunk 465 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 chunk 376 optimal weight: 0.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 155 GLN x 217 ASN X 39 ASN W 91 ASN ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 256 HIS ** u 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 66239 Z= 0.236 Angle : 0.592 10.262 96518 Z= 0.302 Chirality : 0.038 0.326 11957 Planarity : 0.005 0.068 6768 Dihedral : 22.593 179.808 25933 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.70 % Allowed : 10.03 % Favored : 89.27 % 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: 0.06 (0.13), residues: 3719 helix: 1.11 (0.14), residues: 1282 sheet: 0.20 (0.20), residues: 688 loop : -0.81 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 30 HIS 0.007 0.001 HIS I 22 PHE 0.024 0.002 PHE X 84 TYR 0.026 0.001 TYR x 238 ARG 0.007 0.000 ARG I 47 *********************** 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 403 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 380 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 396 average time/residue: 0.6637 time to fit residues: 433.2434 Evaluate side-chains 349 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 338 time to evaluate : 3.473 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4408 time to fit residues: 13.6608 ------------------------------------------------------------------------------- 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: 5.9990 chunk 352 optimal weight: 0.5980 chunk 243 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 chunk 315 optimal weight: 3.9990 chunk 471 optimal weight: 10.0000 chunk 498 optimal weight: 0.9980 chunk 246 optimal weight: 9.9990 chunk 446 optimal weight: 20.0000 chunk 134 optimal weight: 30.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 286 ASN ** u 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN r 7 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: 0.7388 moved from start: 0.1416 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 : 0.584 10.290 96518 Z= 0.298 Chirality : 0.037 0.319 11957 Planarity : 0.004 0.066 6768 Dihedral : 22.544 179.818 25933 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.13 % Allowed : 12.32 % Favored : 86.55 % 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: 0.23 (0.14), residues: 3719 helix: 1.33 (0.15), residues: 1281 sheet: 0.18 (0.20), residues: 693 loop : -0.71 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 30 HIS 0.007 0.001 HIS r 6 PHE 0.031 0.002 PHE X 84 TYR 0.023 0.001 TYR x 238 ARG 0.009 0.000 ARG I 92 *********************** 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 390 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 353 time to evaluate : 3.448 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 22 residues processed: 374 average time/residue: 0.6713 time to fit residues: 417.8172 Evaluate side-chains 356 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 334 time to evaluate : 3.373 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4549 time to fit residues: 23.1835 ------------------------------------------------------------------------------- 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: 0.9980 chunk 283 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 371 optimal weight: 8.9990 chunk 205 optimal weight: 0.0270 chunk 425 optimal weight: 0.7980 chunk 344 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 254 optimal weight: 0.0470 chunk 447 optimal weight: 30.0000 chunk 125 optimal weight: 50.0000 overall best weight: 1.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 70 HIS W 64 ASN ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 750 HIS N 36 GLN K1211 GLN ** 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: 0.7351 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 66239 Z= 0.162 Angle : 0.544 12.192 96518 Z= 0.277 Chirality : 0.035 0.295 11957 Planarity : 0.004 0.060 6768 Dihedral : 22.483 179.645 25933 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.73 % Allowed : 13.51 % Favored : 85.76 % 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: 0.40 (0.14), residues: 3719 helix: 1.53 (0.15), residues: 1283 sheet: 0.25 (0.20), residues: 683 loop : -0.66 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 30 HIS 0.006 0.001 HIS r 6 PHE 0.026 0.001 PHE 3 137 TYR 0.018 0.001 TYR x 238 ARG 0.007 0.000 ARG H 78 *********************** 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 386 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 362 time to evaluate : 3.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 377 average time/residue: 0.6551 time to fit residues: 411.0982 Evaluate side-chains 352 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 344 time to evaluate : 3.414 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5298 time to fit residues: 11.6959 ------------------------------------------------------------------------------- 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: 2.9990 chunk 449 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 292 optimal weight: 0.5980 chunk 123 optimal weight: 50.0000 chunk 499 optimal weight: 7.9990 chunk 414 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 68 GLN G 110 ASN x 106 GLN ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 750 HIS I 146 GLN ** 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: 0.7366 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 66239 Z= 0.186 Angle : 0.550 10.012 96518 Z= 0.280 Chirality : 0.035 0.304 11957 Planarity : 0.004 0.061 6768 Dihedral : 22.444 179.957 25933 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.76 % Allowed : 14.73 % Favored : 84.51 % 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: 0.47 (0.14), residues: 3719 helix: 1.62 (0.15), residues: 1282 sheet: 0.23 (0.20), residues: 681 loop : -0.60 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 30 HIS 0.007 0.001 HIS u 561 PHE 0.020 0.001 PHE H 135 TYR 0.018 0.001 TYR x 238 ARG 0.007 0.000 ARG H 78 *********************** 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 382 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 357 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 368 average time/residue: 0.6649 time to fit residues: 403.1284 Evaluate side-chains 359 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 343 time to evaluate : 3.414 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4556 time to fit residues: 17.9791 ------------------------------------------------------------------------------- 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: 0.0370 chunk 56 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 364 optimal weight: 8.9990 chunk 282 optimal weight: 1.9990 chunk 420 optimal weight: 0.0870 chunk 278 optimal weight: 0.8980 chunk 497 optimal weight: 30.0000 chunk 311 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 750 HIS r 7 ASN ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 66239 Z= 0.130 Angle : 0.521 9.328 96518 Z= 0.265 Chirality : 0.034 0.276 11957 Planarity : 0.004 0.055 6768 Dihedral : 22.377 179.963 25933 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.52 % Allowed : 15.07 % Favored : 84.42 % 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: 0.63 (0.14), residues: 3719 helix: 1.78 (0.15), residues: 1282 sheet: 0.25 (0.20), residues: 708 loop : -0.52 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 30 HIS 0.005 0.001 HIS r 6 PHE 0.017 0.001 PHE H 135 TYR 0.016 0.001 TYR x 238 ARG 0.008 0.000 ARG x 154 *********************** 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 387 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 370 time to evaluate : 3.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 382 average time/residue: 0.7121 time to fit residues: 452.4854 Evaluate side-chains 353 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 345 time to evaluate : 3.436 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4886 time to fit residues: 11.6810 ------------------------------------------------------------------------------- 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: 4.9990 chunk 198 optimal weight: 0.0070 chunk 297 optimal weight: 0.8980 chunk 149 optimal weight: 0.0870 chunk 97 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 316 optimal weight: 4.9990 chunk 338 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 46 optimal weight: 50.0000 chunk 390 optimal weight: 7.9990 overall best weight: 2.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 115 ASN ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 66239 Z= 0.223 Angle : 0.567 9.926 96518 Z= 0.287 Chirality : 0.036 0.370 11957 Planarity : 0.004 0.060 6768 Dihedral : 22.370 179.596 25933 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.40 % Allowed : 15.77 % Favored : 83.84 % 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: 0.57 (0.14), residues: 3719 helix: 1.75 (0.15), residues: 1278 sheet: 0.17 (0.20), residues: 706 loop : -0.54 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 30 HIS 0.007 0.001 HIS I 22 PHE 0.019 0.001 PHE B 100 TYR 0.015 0.001 TYR x 238 ARG 0.010 0.000 ARG H 78 *********************** 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 365 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 352 time to evaluate : 3.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 360 average time/residue: 0.6663 time to fit residues: 395.9680 Evaluate side-chains 351 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 341 time to evaluate : 3.450 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4519 time to fit residues: 13.0606 ------------------------------------------------------------------------------- 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: 50.0000 chunk 476 optimal weight: 7.9990 chunk 434 optimal weight: 7.9990 chunk 463 optimal weight: 6.9990 chunk 278 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 chunk 363 optimal weight: 0.0770 chunk 142 optimal weight: 8.9990 chunk 418 optimal weight: 4.9990 chunk 438 optimal weight: 6.9990 chunk 461 optimal weight: 7.9990 overall best weight: 3.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 750 HIS I 52 ASN I 167 GLN ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 66239 Z= 0.344 Angle : 0.648 10.580 96518 Z= 0.327 Chirality : 0.041 0.345 11957 Planarity : 0.005 0.073 6768 Dihedral : 22.458 179.692 25933 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 0.40 % Allowed : 15.83 % Favored : 83.78 % 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: 0.34 (0.14), residues: 3719 helix: 1.55 (0.15), residues: 1278 sheet: 0.07 (0.20), residues: 712 loop : -0.68 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 30 HIS 0.010 0.001 HIS I 22 PHE 0.028 0.002 PHE J 159 TYR 0.027 0.002 TYR x 238 ARG 0.010 0.001 ARG H 78 *********************** 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 359 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 346 time to evaluate : 3.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 350 average time/residue: 0.7166 time to fit residues: 416.8649 Evaluate side-chains 344 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 335 time to evaluate : 3.468 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4959 time to fit residues: 12.8517 ------------------------------------------------------------------------------- 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: 4.9990 chunk 490 optimal weight: 6.9990 chunk 299 optimal weight: 0.9990 chunk 232 optimal weight: 0.9990 chunk 340 optimal weight: 8.9990 chunk 514 optimal weight: 8.9990 chunk 473 optimal weight: 0.9980 chunk 409 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 316 optimal weight: 5.9990 chunk 251 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 GLN ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 66239 Z= 0.143 Angle : 0.540 13.472 96518 Z= 0.275 Chirality : 0.035 0.287 11957 Planarity : 0.004 0.060 6768 Dihedral : 22.365 179.942 25933 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.15 % Allowed : 15.86 % Favored : 83.99 % 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: 0.59 (0.14), residues: 3719 helix: 1.78 (0.15), residues: 1277 sheet: 0.18 (0.20), residues: 706 loop : -0.54 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 30 HIS 0.005 0.001 HIS r 6 PHE 0.022 0.001 PHE H 135 TYR 0.020 0.001 TYR x 238 ARG 0.011 0.000 ARG H 78 ********************** 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 354 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 349 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 350 average time/residue: 0.6742 time to fit residues: 386.0022 Evaluate side-chains 342 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 340 time to evaluate : 3.384 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4624 time to fit residues: 5.8911 ------------------------------------------------------------------------------- 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: 4.9990 chunk 436 optimal weight: 9.9990 chunk 125 optimal weight: 50.0000 chunk 377 optimal weight: 0.0870 chunk 60 optimal weight: 20.0000 chunk 113 optimal weight: 60.0000 chunk 410 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 421 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 301 GLN ** u 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 750 HIS N 36 GLN ** I 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.158748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.129162 restraints weight = 107100.401| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.44 r_work: 0.3315 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2113 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= 0.318 Angle : 0.636 10.482 96518 Z= 0.320 Chirality : 0.039 0.334 11957 Planarity : 0.005 0.069 6768 Dihedral : 22.409 179.852 25933 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.15 % Allowed : 16.19 % Favored : 83.65 % Cbeta Deviations : 0.03 % 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: 0.42 (0.14), residues: 3719 helix: 1.66 (0.15), residues: 1277 sheet: 0.07 (0.20), residues: 705 loop : -0.65 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 30 HIS 0.009 0.001 HIS I 22 PHE 0.033 0.002 PHE J 159 TYR 0.026 0.002 TYR x 238 ARG 0.010 0.001 ARG H 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9619.31 seconds wall clock time: 172 minutes 57.92 seconds (10377.92 seconds total)