Starting phenix.real_space_refine (version: dev) on Fri Feb 24 03:35:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c00_16347/02_2023/8c00_16347.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c00_16347/02_2023/8c00_16347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c00_16347/02_2023/8c00_16347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c00_16347/02_2023/8c00_16347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c00_16347/02_2023/8c00_16347.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c00_16347/02_2023/8c00_16347.pdb" } resolution = 2.9 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= 0.000 sd= 0.002 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 "b PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 90": "OD1" <-> "OD2" 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: 63117 Number of models: 1 Model: "" Number of chains: 26 Chain: "2" Number of atoms: 30408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1425, 30408 Classifications: {'RNA': 1425} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 83, 'rna3p_pur': 653, 'rna3p_pyr': 571} Link IDs: {'rna2p': 201, 'rna3p': 1223} Chain breaks: 30 Chain: "B" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1588 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 902 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain breaks: 1 Chain: "F" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 973 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 118} Chain: "H" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1009 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1096 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "K" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "L" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 471 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "Q" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1709 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "S" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "T" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 216} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1481 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain: "V" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1462 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 1 Chain: "W" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "X" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1137 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 8, 'TRANS': 132} Chain: "Y" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "Z" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 926 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "b" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "c" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} Chain: "d" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1046 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "e" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 796 Classifications: {'peptide': 179} Incomplete info: {'backbone_only': 158} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain breaks: 5 Unresolved non-hydrogen bonds: 707 Unresolved non-hydrogen angles: 1025 Unresolved non-hydrogen dihedrals: 466 Unresolved non-hydrogen chiralities: 218 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 10, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 321 Chain: "f" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "g" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 257 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 4, 'TRANS': 25} Chain breaks: 1 Chain: "p" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1425 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 9, 'TRANS': 170} Chain: "r" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1574 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain breaks: 7 Chain: "t" Number of atoms: 4982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4982 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 29, 'TRANS': 589} Chain breaks: 5 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 65 Time building chain proxies: 25.48, per 1000 atoms: 0.40 Number of scatterers: 63117 At special positions: 0 Unit cell: (255.552, 172.304, 226.512, 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 78 16.00 P 1425 15.00 O 15807 8.00 N 11532 7.00 C 34275 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: 23.67 Conformation dependent library (CDL) restraints added in 3.8 seconds 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7518 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 41 sheets defined 41.6% alpha, 18.1% beta 444 base pairs and 751 stacking pairs defined. Time for finding SS restraints: 17.25 Creating SS restraints... Processing helix chain 'B' and resid 30 through 36 removed outlier: 3.619A pdb=" N ALA B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 88 through 98 removed outlier: 3.644A pdb=" N MET B 98 " --> pdb=" O THR B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 128 through 141 removed outlier: 3.689A pdb=" N VAL B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 184 removed outlier: 3.550A pdb=" N ALA B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 203 removed outlier: 3.709A pdb=" N GLU B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 225 removed outlier: 3.607A pdb=" N GLU B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 51 through 67 removed outlier: 4.050A pdb=" N GLY E 55 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 108 through 112 Processing helix chain 'E' and resid 115 through 120 removed outlier: 3.518A pdb=" N SER E 120 " --> pdb=" O GLY E 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 45 through 54 Proline residue: F 51 - end of helix Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 75 through 97 removed outlier: 3.561A pdb=" N TYR F 79 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG F 82 " --> pdb=" O VAL F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 113 removed outlier: 3.536A pdb=" N TYR F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 117 Processing helix chain 'H' and resid 27 through 33 removed outlier: 4.004A pdb=" N THR H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 51 Processing helix chain 'H' and resid 57 through 61 Processing helix chain 'H' and resid 62 through 67 Processing helix chain 'H' and resid 68 through 74 removed outlier: 3.528A pdb=" N GLN H 74 " --> pdb=" O VAL H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 111 through 119 Processing helix chain 'H' and resid 121 through 131 Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 10 through 26 Processing helix chain 'I' and resid 52 through 67 Processing helix chain 'I' and resid 72 through 80 Processing helix chain 'I' and resid 97 through 111 removed outlier: 4.171A pdb=" N ASN I 101 " --> pdb=" O SER I 97 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS I 103 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE I 111 " --> pdb=" O ALA I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 142 removed outlier: 3.543A pdb=" N ARG I 134 " --> pdb=" O ARG I 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 54 Processing helix chain 'K' and resid 55 through 57 No H-bonds generated for 'chain 'K' and resid 55 through 57' Processing helix chain 'K' and resid 61 through 69 Processing helix chain 'K' and resid 72 through 86 removed outlier: 4.152A pdb=" N ILE K 78 " --> pdb=" O SER K 74 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG K 81 " --> pdb=" O ARG K 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 25 Processing helix chain 'Q' and resid 57 through 62 Processing helix chain 'Q' and resid 70 through 75 Processing helix chain 'Q' and resid 76 through 80 Processing helix chain 'Q' and resid 106 through 114 removed outlier: 3.572A pdb=" N MET Q 113 " --> pdb=" O LYS Q 109 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL Q 114 " --> pdb=" O LEU Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 176 Processing helix chain 'Q' and resid 180 through 189 Processing helix chain 'Q' and resid 191 through 202 removed outlier: 4.196A pdb=" N LYS Q 195 " --> pdb=" O GLU Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 224 through 231 removed outlier: 3.969A pdb=" N LEU Q 228 " --> pdb=" O ASP Q 224 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 19 Processing helix chain 'S' and resid 37 through 41 Processing helix chain 'S' and resid 44 through 51 Processing helix chain 'S' and resid 57 through 66 Processing helix chain 'S' and resid 117 through 119 No H-bonds generated for 'chain 'S' and resid 117 through 119' Processing helix chain 'S' and resid 133 through 135 No H-bonds generated for 'chain 'S' and resid 133 through 135' Processing helix chain 'S' and resid 247 through 259 Processing helix chain 'T' and resid 20 through 25 Processing helix chain 'T' and resid 42 through 46 Processing helix chain 'T' and resid 59 through 61 No H-bonds generated for 'chain 'T' and resid 59 through 61' Processing helix chain 'T' and resid 137 through 146 Processing helix chain 'T' and resid 152 through 156 removed outlier: 3.844A pdb=" N ASP T 155 " --> pdb=" O ASP T 152 " (cutoff:3.500A) Processing helix chain 'T' and resid 180 through 225 removed outlier: 3.609A pdb=" N VAL T 195 " --> pdb=" O ARG T 191 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 226 No H-bonds generated for 'chain 'T' and resid 226 through 226' Processing helix chain 'U' and resid 4 through 8 Processing helix chain 'U' and resid 14 through 31 Processing helix chain 'U' and resid 33 through 38 Processing helix chain 'U' and resid 52 through 54 No H-bonds generated for 'chain 'U' and resid 52 through 54' Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.750A pdb=" N PHE U 70 " --> pdb=" O SER U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 85 removed outlier: 3.598A pdb=" N LEU U 77 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG U 79 " --> pdb=" O THR U 75 " (cutoff:3.500A) Processing helix chain 'U' and resid 113 through 116 Processing helix chain 'U' and resid 117 through 130 removed outlier: 4.002A pdb=" N VAL U 130 " --> pdb=" O LEU U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 158 through 164 removed outlier: 4.113A pdb=" N ASP U 163 " --> pdb=" O GLN U 160 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TYR U 164 " --> pdb=" O GLN U 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 165 through 178 removed outlier: 3.853A pdb=" N ALA U 171 " --> pdb=" O GLU U 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 25 through 29 removed outlier: 3.714A pdb=" N GLU V 28 " --> pdb=" O ARG V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 51 No H-bonds generated for 'chain 'V' and resid 49 through 51' Processing helix chain 'V' and resid 88 through 94 Processing helix chain 'V' and resid 106 through 117 Processing helix chain 'V' and resid 136 through 147 removed outlier: 3.806A pdb=" N LYS V 142 " --> pdb=" O ASN V 138 " (cutoff:3.500A) Processing helix chain 'V' and resid 148 through 150 No H-bonds generated for 'chain 'V' and resid 148 through 150' Processing helix chain 'V' and resid 153 through 158 Processing helix chain 'V' and resid 172 through 177 Processing helix chain 'V' and resid 186 through 198 Processing helix chain 'W' and resid 20 through 35 removed outlier: 3.514A pdb=" N ALA W 26 " --> pdb=" O SER W 22 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 60 removed outlier: 3.807A pdb=" N ILE W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 83 removed outlier: 3.868A pdb=" N VAL W 83 " --> pdb=" O ARG W 79 " (cutoff:3.500A) Processing helix chain 'W' and resid 92 through 100 removed outlier: 3.510A pdb=" N LEU W 97 " --> pdb=" O ASP W 94 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS W 100 " --> pdb=" O LEU W 97 " (cutoff:3.500A) Processing helix chain 'W' and resid 101 through 106 Processing helix chain 'W' and resid 108 through 116 removed outlier: 3.782A pdb=" N TYR W 114 " --> pdb=" O GLN W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 131 removed outlier: 3.509A pdb=" N VAL W 127 " --> pdb=" O HIS W 123 " (cutoff:3.500A) Processing helix chain 'W' and resid 151 through 154 removed outlier: 3.794A pdb=" N LYS W 154 " --> pdb=" O ASP W 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 151 through 154' Processing helix chain 'W' and resid 170 through 185 Processing helix chain 'X' and resid 45 through 51 removed outlier: 3.518A pdb=" N ILE X 49 " --> pdb=" O PRO X 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'Y' and resid 46 through 58 removed outlier: 3.512A pdb=" N VAL Y 52 " --> pdb=" O SER Y 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 62 through 67 Processing helix chain 'Y' and resid 70 through 78 Processing helix chain 'Y' and resid 85 through 105 removed outlier: 3.593A pdb=" N GLU Y 103 " --> pdb=" O ARG Y 99 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG Y 104 " --> pdb=" O LYS Y 100 " (cutoff:3.500A) Processing helix chain 'Y' and resid 108 through 132 removed outlier: 3.660A pdb=" N ILE Y 116 " --> pdb=" O LYS Y 112 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU Y 117 " --> pdb=" O PHE Y 113 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR Y 128 " --> pdb=" O ARG Y 124 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 151 removed outlier: 4.702A pdb=" N SER Y 147 " --> pdb=" O SER Y 143 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA Y 148 " --> pdb=" O ALA Y 144 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 48 removed outlier: 3.725A pdb=" N VAL Z 48 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 54 Processing helix chain 'Z' and resid 56 through 75 Processing helix chain 'Z' and resid 95 through 107 Processing helix chain 'b' and resid 5 through 20 removed outlier: 3.717A pdb=" N ASP b 9 " --> pdb=" O SER b 5 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 44 removed outlier: 3.588A pdb=" N HIS b 44 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 84 No H-bonds generated for 'chain 'b' and resid 82 through 84' Processing helix chain 'b' and resid 85 through 94 Processing helix chain 'b' and resid 113 through 120 Processing helix chain 'c' and resid 11 through 24 removed outlier: 4.240A pdb=" N TRP c 24 " --> pdb=" O ARG c 20 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 35 Processing helix chain 'c' and resid 35 through 40 removed outlier: 3.557A pdb=" N LYS c 39 " --> pdb=" O GLY c 35 " (cutoff:3.500A) Processing helix chain 'c' and resid 89 through 96 removed outlier: 3.520A pdb=" N VAL c 96 " --> pdb=" O LEU c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 132 through 137 Processing helix chain 'd' and resid 16 through 18 No H-bonds generated for 'chain 'd' and resid 16 through 18' Processing helix chain 'd' and resid 36 through 48 Processing helix chain 'd' and resid 51 through 53 No H-bonds generated for 'chain 'd' and resid 51 through 53' Processing helix chain 'd' and resid 78 through 86 Processing helix chain 'd' and resid 87 through 94 Processing helix chain 'd' and resid 104 through 116 Processing helix chain 'd' and resid 125 through 132 Processing helix chain 'e' and resid 214 through 219 Processing helix chain 'e' and resid 220 through 227 removed outlier: 4.218A pdb=" N TRP e 224 " --> pdb=" O LEU e 221 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR e 225 " --> pdb=" O LYS e 222 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY e 227 " --> pdb=" O TRP e 224 " (cutoff:3.500A) Processing helix chain 'e' and resid 230 through 235 Processing helix chain 'e' and resid 236 through 240 removed outlier: 5.201A pdb=" N ARG e 240 " --> pdb=" O PRO e 237 " (cutoff:3.500A) Processing helix chain 'e' and resid 241 through 246 Processing helix chain 'e' and resid 247 through 254 Proline residue: e 251 - end of helix Processing helix chain 'e' and resid 255 through 266 Processing helix chain 'e' and resid 275 through 280 Processing helix chain 'e' and resid 282 through 294 Processing helix chain 'e' and resid 300 through 310 Processing helix chain 'e' and resid 313 through 322 Processing helix chain 'e' and resid 323 through 326 Processing helix chain 'e' and resid 332 through 343 removed outlier: 3.632A pdb=" N VAL e 341 " --> pdb=" O ILE e 337 " (cutoff:3.500A) Processing helix chain 'e' and resid 348 through 360 removed outlier: 4.270A pdb=" N ALA e 354 " --> pdb=" O LEU e 350 " (cutoff:3.500A) Processing helix chain 'e' and resid 371 through 376 Processing helix chain 'e' and resid 377 through 379 No H-bonds generated for 'chain 'e' and resid 377 through 379' Processing helix chain 'e' and resid 384 through 394 Processing helix chain 'e' and resid 415 through 424 Processing helix chain 'f' and resid 11 through 17 removed outlier: 3.515A pdb=" N ARG f 17 " --> pdb=" O ALA f 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 32 through 45 removed outlier: 3.567A pdb=" N LEU g 38 " --> pdb=" O ALA g 34 " (cutoff:3.500A) Processing helix chain 'p' and resid 102 through 122 removed outlier: 4.322A pdb=" N THR p 107 " --> pdb=" O PRO p 103 " (cutoff:3.500A) Proline residue: p 108 - end of helix removed outlier: 4.833A pdb=" N THR p 114 " --> pdb=" O ARG p 110 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LYS p 115 " --> pdb=" O ASN p 111 " (cutoff:3.500A) Proline residue: p 118 - end of helix Processing helix chain 'p' and resid 149 through 164 Processing helix chain 'p' and resid 167 through 172 Processing helix chain 'p' and resid 172 through 177 removed outlier: 3.661A pdb=" N ARG p 176 " --> pdb=" O ILE p 172 " (cutoff:3.500A) Processing helix chain 'p' and resid 188 through 190 No H-bonds generated for 'chain 'p' and resid 188 through 190' Processing helix chain 'p' and resid 195 through 207 Processing helix chain 'p' and resid 210 through 220 Processing helix chain 'p' and resid 237 through 253 removed outlier: 3.500A pdb=" N SER p 246 " --> pdb=" O MET p 242 " (cutoff:3.500A) Processing helix chain 'p' and resid 255 through 270 removed outlier: 3.623A pdb=" N VAL p 259 " --> pdb=" O PRO p 255 " (cutoff:3.500A) Processing helix chain 'p' and resid 271 through 272 No H-bonds generated for 'chain 'p' and resid 271 through 272' Processing helix chain 'r' and resid 78 through 78 No H-bonds generated for 'chain 'r' and resid 78 through 78' Processing helix chain 'r' and resid 79 through 84 Processing helix chain 'r' and resid 85 through 92 Processing helix chain 'r' and resid 155 through 156 No H-bonds generated for 'chain 'r' and resid 155 through 156' Processing helix chain 'r' and resid 158 through 158 No H-bonds generated for 'chain 'r' and resid 158 through 158' Processing helix chain 'r' and resid 159 through 172 Processing helix chain 'r' and resid 198 through 200 No H-bonds generated for 'chain 'r' and resid 198 through 200' Processing helix chain 'r' and resid 205 through 223 removed outlier: 3.611A pdb=" N ILE r 217 " --> pdb=" O LEU r 213 " (cutoff:3.500A) Processing helix chain 'r' and resid 264 through 283 Processing helix chain 't' and resid 23 through 31 Processing helix chain 't' and resid 50 through 74 removed outlier: 3.609A pdb=" N GLN t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 77 No H-bonds generated for 'chain 't' and resid 75 through 77' Processing helix chain 't' and resid 96 through 108 removed outlier: 4.115A pdb=" N ILE t 100 " --> pdb=" O ASP t 96 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS t 107 " --> pdb=" O LYS t 103 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA t 108 " --> pdb=" O LEU t 104 " (cutoff:3.500A) Processing helix chain 't' and resid 109 through 114 removed outlier: 6.862A pdb=" N GLY t 112 " --> pdb=" O ASP t 109 " (cutoff:3.500A) Processing helix chain 't' and resid 144 through 155 removed outlier: 3.515A pdb=" N LEU t 149 " --> pdb=" O PHE t 145 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL t 154 " --> pdb=" O ASP t 150 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA t 155 " --> pdb=" O CYS t 151 " (cutoff:3.500A) Processing helix chain 't' and resid 172 through 184 removed outlier: 3.672A pdb=" N ILE t 177 " --> pdb=" O GLY t 173 " (cutoff:3.500A) Processing helix chain 't' and resid 194 through 199 Processing helix chain 't' and resid 201 through 220 removed outlier: 3.631A pdb=" N HIS t 218 " --> pdb=" O SER t 214 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE t 219 " --> pdb=" O TYR t 215 " (cutoff:3.500A) Processing helix chain 't' and resid 231 through 245 Processing helix chain 't' and resid 250 through 255 Processing helix chain 't' and resid 464 through 482 removed outlier: 3.814A pdb=" N GLN t 468 " --> pdb=" O GLU t 464 " (cutoff:3.500A) Processing helix chain 't' and resid 493 through 499 Processing helix chain 't' and resid 533 through 548 removed outlier: 3.841A pdb=" N ARG t 540 " --> pdb=" O ASN t 536 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN t 547 " --> pdb=" O LYS t 543 " (cutoff:3.500A) Processing helix chain 't' and resid 564 through 571 removed outlier: 3.642A pdb=" N GLU t 569 " --> pdb=" O PHE t 566 " (cutoff:3.500A) Processing helix chain 't' and resid 585 through 589 removed outlier: 4.164A pdb=" N HIS t 589 " --> pdb=" O LEU t 586 " (cutoff:3.500A) Processing helix chain 't' and resid 723 through 730 Processing sheet with id=AA1, first strand: chain 'B' and resid 144 through 148 Processing sheet with id=AA2, first strand: chain 'E' and resid 16 through 17 Processing sheet with id=AA3, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.278A pdb=" N VAL E 76 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N TYR E 97 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR E 78 " --> pdb=" O TYR E 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 6 through 12 removed outlier: 6.070A pdb=" N LEU F 28 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N VAL F 67 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS F 30 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 14 through 17 Processing sheet with id=AA6, first strand: chain 'I' and resid 82 through 84 Processing sheet with id=AA7, first strand: chain 'I' and resid 114 through 116 Processing sheet with id=AA8, first strand: chain 'K' and resid 59 through 60 removed outlier: 3.546A pdb=" N SER K 93 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR K 102 " --> pdb=" O PRO K 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 40 through 44 removed outlier: 6.919A pdb=" N VAL L 25 " --> pdb=" O ARG L 18 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG L 18 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLN L 27 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU L 31 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL L 12 " --> pdb=" O GLU L 31 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 42 through 49 removed outlier: 4.160A pdb=" N GLY Q 44 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N LEU Q 96 " --> pdb=" O TRP Q 29 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP Q 31 " --> pdb=" O LEU Q 96 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR Q 98 " --> pdb=" O ASP Q 31 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS Q 33 " --> pdb=" O THR Q 98 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N PHE Q 100 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASN Q 99 " --> pdb=" O VAL Q 88 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL Q 88 " --> pdb=" O ASN Q 99 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS Q 101 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU Q 86 " --> pdb=" O HIS Q 101 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET Q 103 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE Q 84 " --> pdb=" O MET Q 103 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE Q 105 " --> pdb=" O ARG Q 82 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG Q 82 " --> pdb=" O PHE Q 105 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL Q 88 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ARG Q 64 " --> pdb=" O VAL Q 88 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 42 through 49 removed outlier: 4.160A pdb=" N GLY Q 44 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N LEU Q 96 " --> pdb=" O TRP Q 29 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP Q 31 " --> pdb=" O LEU Q 96 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR Q 98 " --> pdb=" O ASP Q 31 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS Q 33 " --> pdb=" O THR Q 98 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N PHE Q 100 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) removed outlier: 13.669A pdb=" N ASN Q 99 " --> pdb=" O LYS Q 219 " (cutoff:3.500A) removed outlier: 13.261A pdb=" N LYS Q 219 " --> pdb=" O ASN Q 99 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N HIS Q 101 " --> pdb=" O LEU Q 217 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU Q 217 " --> pdb=" O HIS Q 101 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE Q 105 " --> pdb=" O ARG Q 213 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N ARG Q 213 " --> pdb=" O PHE Q 105 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE Q 210 " --> pdb=" O ILE Q 140 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE Q 140 " --> pdb=" O ILE Q 210 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL Q 212 " --> pdb=" O PHE Q 138 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE Q 138 " --> pdb=" O VAL Q 212 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS Q 214 " --> pdb=" O ARG Q 136 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG Q 136 " --> pdb=" O LYS Q 214 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LYS Q 216 " --> pdb=" O VAL Q 134 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL Q 134 " --> pdb=" O LYS Q 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 9 through 10 removed outlier: 4.491A pdb=" N LEU S 9 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 42 through 43 Processing sheet with id=AB5, first strand: chain 'S' and resid 75 through 76 Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.720A pdb=" N TYR S 138 " --> pdb=" O VAL S 129 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL S 129 " --> pdb=" O TYR S 138 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL S 140 " --> pdb=" O LYS S 127 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP S 171 " --> pdb=" O LYS S 161 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP S 163 " --> pdb=" O ILE S 169 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE S 169 " --> pdb=" O ASP S 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 217 through 221 removed outlier: 6.747A pdb=" N LEU S 207 " --> pdb=" O LYS S 198 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS S 198 " --> pdb=" O LEU S 207 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS S 209 " --> pdb=" O VAL S 196 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU S 180 " --> pdb=" O ILE S 228 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU S 230 " --> pdb=" O LYS S 233 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'T' and resid 13 through 17 removed outlier: 6.465A pdb=" N LYS T 2 " --> pdb=" O LEU T 109 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU T 111 " --> pdb=" O LYS T 2 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN T 4 " --> pdb=" O LEU T 111 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE T 113 " --> pdb=" O ASN T 4 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER T 6 " --> pdb=" O ILE T 113 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS T 115 " --> pdb=" O SER T 6 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY T 54 " --> pdb=" O ALA T 110 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL T 112 " --> pdb=" O ILE T 52 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE T 52 " --> pdb=" O VAL T 112 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL T 114 " --> pdb=" O PHE T 50 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N PHE T 50 " --> pdb=" O VAL T 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'T' and resid 72 through 77 Processing sheet with id=AC1, first strand: chain 'T' and resid 160 through 164 Processing sheet with id=AC2, first strand: chain 'U' and resid 45 through 50 removed outlier: 3.795A pdb=" N SER U 45 " --> pdb=" O PHE U 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 181 through 184 removed outlier: 3.792A pdb=" N GLY U 137 " --> pdb=" O LEU U 153 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE b 50 " --> pdb=" O TYR U 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 37 through 38 removed outlier: 6.480A pdb=" N ARG V 42 " --> pdb=" O LEU V 58 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 62 through 66 removed outlier: 5.311A pdb=" N ARG V 77 " --> pdb=" O ASP V 105 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN V 103 " --> pdb=" O ALA V 79 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL V 81 " --> pdb=" O ILE V 101 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE V 101 " --> pdb=" O VAL V 81 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLY V 181 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN V 64 " --> pdb=" O GLY V 181 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE V 183 " --> pdb=" O ASN V 64 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER V 66 " --> pdb=" O ILE V 183 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 139 through 140 Processing sheet with id=AC7, first strand: chain 'X' and resid 70 through 77 removed outlier: 18.445A pdb=" N ILE X 70 " --> pdb=" O LEU X 91 " (cutoff:3.500A) removed outlier: 15.677A pdb=" N LEU X 91 " --> pdb=" O ILE X 70 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N THR X 72 " --> pdb=" O ALA X 89 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA X 89 " --> pdb=" O THR X 72 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL X 85 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG X 99 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N PHE X 137 " --> pdb=" O ASN X 106 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N VAL X 139 " --> pdb=" O PRO X 108 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N HIS X 110 " --> pdb=" O VAL X 139 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N LYS X 141 " --> pdb=" O HIS X 110 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR X 124 " --> pdb=" O VAL X 140 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL X 142 " --> pdb=" O ILE X 122 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE X 122 " --> pdb=" O VAL X 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Z' and resid 38 through 40 removed outlier: 7.096A pdb=" N VAL Z 30 " --> pdb=" O ILE Z 39 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL Z 79 " --> pdb=" O GLY Z 113 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE Z 115 " --> pdb=" O VAL Z 79 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL Z 81 " --> pdb=" O ILE Z 115 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASP Z 117 " --> pdb=" O VAL Z 81 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE Z 83 " --> pdb=" O ASP Z 117 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 71 through 74 removed outlier: 5.493A pdb=" N ILE b 125 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N THR b 105 " --> pdb=" O ILE b 125 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY b 127 " --> pdb=" O ILE b 103 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'c' and resid 130 through 131 removed outlier: 6.617A pdb=" N LEU c 103 " --> pdb=" O VAL c 125 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL c 127 " --> pdb=" O GLU c 101 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU c 101 " --> pdb=" O VAL c 127 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL c 53 " --> pdb=" O GLN c 75 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN c 75 " --> pdb=" O VAL c 53 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU c 55 " --> pdb=" O ARG c 73 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE c 122 " --> pdb=" O THR c 84 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 6 through 15 removed outlier: 4.777A pdb=" N VAL d 12 " --> pdb=" O GLN d 22 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLN d 22 " --> pdb=" O VAL d 12 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER d 14 " --> pdb=" O ARG d 20 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ARG d 20 " --> pdb=" O SER d 14 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS d 68 " --> pdb=" O THR d 62 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR d 62 " --> pdb=" O LYS d 68 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL d 70 " --> pdb=" O PHE d 60 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE d 60 " --> pdb=" O VAL d 70 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'f' and resid 43 through 47 Processing sheet with id=AD4, first strand: chain 'f' and resid 64 through 65 Processing sheet with id=AD5, first strand: chain 'p' and resid 96 through 100 Processing sheet with id=AD6, first strand: chain 'p' and resid 180 through 186 Processing sheet with id=AD7, first strand: chain 'r' and resid 107 through 110 removed outlier: 3.778A pdb=" N ASP r 181 " --> pdb=" O VAL r 188 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'r' and resid 195 through 196 removed outlier: 3.509A pdb=" N TYR r 195 " --> pdb=" O ILE r 237 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'r' and resid 225 through 226 Processing sheet with id=AE1, first strand: chain 't' and resid 123 through 128 removed outlier: 3.520A pdb=" N ILE t 88 " --> pdb=" O ILE t 138 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE t 85 " --> pdb=" O PHE t 157 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL t 159 " --> pdb=" O ILE t 85 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR t 87 " --> pdb=" O VAL t 159 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLY t 161 " --> pdb=" O THR t 87 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL t 89 " --> pdb=" O GLY t 161 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 't' and resid 258 through 260 Processing sheet with id=AE3, first strand: chain 't' and resid 263 through 265 removed outlier: 3.700A pdb=" N PHE t 263 " --> pdb=" O GLU t 279 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ARG t 556 " --> pdb=" O LYS t 308 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LYS t 308 " --> pdb=" O ARG t 556 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG t 558 " --> pdb=" O ILE t 306 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE t 306 " --> pdb=" O ARG t 558 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE t 560 " --> pdb=" O ASN t 304 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 't' and resid 629 through 630 removed outlier: 3.718A pdb=" N ASN t 690 " --> pdb=" O ASN t 595 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER t 597 " --> pdb=" O PHE t 688 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE t 688 " --> pdb=" O SER t 597 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N GLN t 599 " --> pdb=" O GLY t 686 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLY t 686 " --> pdb=" O GLN t 599 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU t 682 " --> pdb=" O LYS t 671 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS t 671 " --> pdb=" O LEU t 682 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG t 621 " --> pdb=" O TYR t 618 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 't' and resid 640 through 641 removed outlier: 6.328A pdb=" N HIS t 640 " --> pdb=" O ALA t 698 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG t 700 " --> pdb=" O HIS t 640 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU t 697 " --> pdb=" O MET t 777 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE t 745 " --> pdb=" O THR t 758 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR t 758 " --> pdb=" O ILE t 745 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU t 747 " --> pdb=" O LYS t 756 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS t 756 " --> pdb=" O GLU t 747 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR t 754 " --> pdb=" O LEU t 749 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE t 755 " --> pdb=" O VAL t 717 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR t 716 " --> pdb=" O PHE t 708 " (cutoff:3.500A) 1401 hydrogen bonds defined for protein. 3855 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1072 hydrogen bonds 1692 hydrogen bond angles 0 basepair planarities 444 basepair parallelities 751 stacking parallelities Total time for adding SS restraints: 37.06 Time building geometry restraints manager: 25.86 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: 8662 1.32 - 1.44: 25131 1.44 - 1.57: 30535 1.57 - 1.69: 2819 1.69 - 1.81: 128 Bond restraints: 67275 Sorted by residual: bond pdb=" C4' C 21711 " pdb=" O4' C 21711 " ideal model delta sigma weight residual 1.454 1.425 0.029 1.50e-02 4.44e+03 3.84e+00 bond pdb=" C3' U 2 9 " pdb=" C2' U 2 9 " ideal model delta sigma weight residual 1.525 1.552 -0.027 1.50e-02 4.44e+03 3.21e+00 bond pdb=" C2' A 2 198 " pdb=" C1' A 2 198 " ideal model delta sigma weight residual 1.529 1.502 0.027 1.50e-02 4.44e+03 3.19e+00 bond pdb=" C3' A 21750 " pdb=" C2' A 21750 " ideal model delta sigma weight residual 1.525 1.552 -0.027 1.50e-02 4.44e+03 3.17e+00 bond pdb=" C4' C 2 402 " pdb=" O4' C 2 402 " ideal model delta sigma weight residual 1.451 1.424 0.027 1.50e-02 4.44e+03 3.17e+00 ... (remaining 67270 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.08: 8339 106.08 - 113.12: 38364 113.12 - 120.16: 24643 120.16 - 127.19: 22958 127.19 - 134.23: 3266 Bond angle restraints: 97570 Sorted by residual: angle pdb=" C2' G 2 143 " pdb=" C1' G 2 143 " pdb=" N9 G 2 143 " ideal model delta sigma weight residual 112.00 121.43 -9.43 1.50e+00 4.44e-01 3.95e+01 angle pdb=" C3' G 2 514 " pdb=" O3' G 2 514 " pdb=" P A 2 515 " ideal model delta sigma weight residual 120.20 129.12 -8.92 1.50e+00 4.44e-01 3.54e+01 angle pdb=" C5' U 2 9 " pdb=" C4' U 2 9 " pdb=" O4' U 2 9 " ideal model delta sigma weight residual 109.10 117.09 -7.99 1.50e+00 4.44e-01 2.84e+01 angle pdb=" C4' G 2 514 " pdb=" C3' G 2 514 " pdb=" O3' G 2 514 " ideal model delta sigma weight residual 109.40 117.37 -7.97 1.50e+00 4.44e-01 2.82e+01 angle pdb=" C2' C 21653 " pdb=" C1' C 21653 " pdb=" N1 C 21653 " ideal model delta sigma weight residual 112.00 119.78 -7.78 1.50e+00 4.44e-01 2.69e+01 ... (remaining 97565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 36418 35.75 - 71.51: 702 71.51 - 107.26: 98 107.26 - 143.02: 22 143.02 - 178.77: 23 Dihedral angle restraints: 37263 sinusoidal: 25483 harmonic: 11780 Sorted by residual: dihedral pdb=" C5' A 21492 " pdb=" C4' A 21492 " pdb=" C3' A 21492 " pdb=" O3' A 21492 " ideal model delta sinusoidal sigma weight residual 147.00 66.87 80.13 1 8.00e+00 1.56e-02 1.24e+02 dihedral pdb=" C4' A 21492 " pdb=" C3' A 21492 " pdb=" C2' A 21492 " pdb=" C1' A 21492 " ideal model delta sinusoidal sigma weight residual -35.00 33.39 -68.39 1 8.00e+00 1.56e-02 9.48e+01 dihedral pdb=" O4' C 21796 " pdb=" C1' C 21796 " pdb=" N1 C 21796 " pdb=" C2 C 21796 " ideal model delta sinusoidal sigma weight residual 200.00 26.19 173.81 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 37260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 11241 0.106 - 0.212: 702 0.212 - 0.318: 42 0.318 - 0.423: 8 0.423 - 0.529: 4 Chirality restraints: 11997 Sorted by residual: chirality pdb=" C4' U 2 9 " pdb=" C5' U 2 9 " pdb=" O4' U 2 9 " pdb=" C3' U 2 9 " both_signs ideal model delta sigma weight residual False -2.50 -1.97 -0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" C3' G 2 514 " pdb=" C4' G 2 514 " pdb=" O3' G 2 514 " pdb=" C2' G 2 514 " both_signs ideal model delta sigma weight residual False -2.74 -2.23 -0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" C1' G 2 143 " pdb=" O4' G 2 143 " pdb=" C2' G 2 143 " pdb=" N9 G 2 143 " both_signs ideal model delta sigma weight residual False 2.46 2.01 0.44 2.00e-01 2.50e+01 4.94e+00 ... (remaining 11994 not shown) Planarity restraints: 7195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 21690 " 0.048 2.00e-02 2.50e+03 3.63e-02 3.96e+01 pdb=" N9 G 21690 " -0.100 2.00e-02 2.50e+03 pdb=" C8 G 21690 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G 21690 " 0.006 2.00e-02 2.50e+03 pdb=" C5 G 21690 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G 21690 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G 21690 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G 21690 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 21690 " -0.007 2.00e-02 2.50e+03 pdb=" N2 G 21690 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G 21690 " -0.007 2.00e-02 2.50e+03 pdb=" C4 G 21690 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Y 3 " 0.443 9.50e-02 1.11e+02 2.00e-01 2.93e+01 pdb=" NE ARG Y 3 " -0.040 2.00e-02 2.50e+03 pdb=" CZ ARG Y 3 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG Y 3 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG Y 3 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 143 " -0.059 2.00e-02 2.50e+03 3.12e-02 2.91e+01 pdb=" N9 G 2 143 " 0.088 2.00e-02 2.50e+03 pdb=" C8 G 2 143 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G 2 143 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G 2 143 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G 2 143 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G 2 143 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G 2 143 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G 2 143 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G 2 143 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G 2 143 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G 2 143 " -0.016 2.00e-02 2.50e+03 ... (remaining 7192 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1704 2.65 - 3.21: 54449 3.21 - 3.78: 103589 3.78 - 4.34: 147917 4.34 - 4.90: 209040 Nonbonded interactions: 516699 Sorted by model distance: nonbonded pdb=" OP2 U 21206 " pdb=" O2' C 21207 " model vdw 2.091 2.440 nonbonded pdb=" OG SER t 521 " pdb=" NE1 TRP t 525 " model vdw 2.100 2.520 nonbonded pdb=" O2' C 21568 " pdb=" OP2 A 21569 " model vdw 2.179 2.440 nonbonded pdb=" O2' A 2 197 " pdb=" O4' A 2 198 " model vdw 2.206 2.440 nonbonded pdb=" N6 A 2 219 " pdb=" O2 U 2 843 " model vdw 2.211 2.520 ... (remaining 516694 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 1425 5.49 5 S 78 5.16 5 C 34275 2.51 5 N 11532 2.21 5 O 15807 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: 3.750 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: 15.870 Check model and map are aligned: 0.670 Process input model: 149.000 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.420 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 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 : 0.007 0.076 67275 Z= 0.411 Angle : 0.824 10.432 97570 Z= 0.479 Chirality : 0.055 0.529 11997 Planarity : 0.010 0.200 7195 Dihedral : 14.516 178.770 29745 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.44 % Favored : 96.26 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.72 (0.12), residues: 4094 helix: -0.78 (0.12), residues: 1372 sheet: 0.09 (0.19), residues: 661 loop : -0.30 (0.13), residues: 2061 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 469 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 7 residues processed: 490 average time/residue: 1.4946 time to fit residues: 935.6468 Evaluate side-chains 348 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 341 time to evaluate : 3.667 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 4 average time/residue: 0.5001 time to fit residues: 8.0665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 466 optimal weight: 7.9990 chunk 418 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 282 optimal weight: 1.9990 chunk 223 optimal weight: 0.0010 chunk 432 optimal weight: 0.0370 chunk 167 optimal weight: 5.9990 chunk 263 optimal weight: 8.9990 chunk 322 optimal weight: 7.9990 chunk 501 optimal weight: 3.9990 overall best weight: 2.2070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN B 131 GLN B 200 ASN F 21 HIS ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 HIS ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 ASN Q 157 GLN S 153 ASN T 10 ASN U 29 ASN U 161 GLN V 64 ASN W 48 GLN Y 105 ASN Z 29 HIS Z 80 HIS b 12 ASN b 15 ASN c 18 HIS c 27 ASN d 110 GLN ** f 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 46 ASN p 239 HIS r 90 ASN ** r 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN t 134 ASN t 205 GLN t 237 ASN t 294 HIS t 589 HIS t 640 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 67275 Z= 0.183 Angle : 0.658 11.798 97570 Z= 0.349 Chirality : 0.042 0.326 11997 Planarity : 0.004 0.051 7195 Dihedral : 13.741 177.261 21607 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.25 % Favored : 97.61 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.32 (0.13), residues: 4094 helix: 0.79 (0.13), residues: 1435 sheet: 0.23 (0.19), residues: 682 loop : -0.11 (0.14), residues: 1977 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 379 time to evaluate : 4.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 18 residues processed: 406 average time/residue: 1.4462 time to fit residues: 760.7117 Evaluate side-chains 347 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 329 time to evaluate : 3.749 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 9 average time/residue: 0.6298 time to fit residues: 13.7991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 278 optimal weight: 3.9990 chunk 155 optimal weight: 30.0000 chunk 417 optimal weight: 7.9990 chunk 341 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 502 optimal weight: 10.0000 chunk 542 optimal weight: 30.0000 chunk 447 optimal weight: 8.9990 chunk 497 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 402 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 ASN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 ASN S 258 GLN g 46 ASN r 90 ASN r 164 GLN t 127 HIS t 603 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 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 : 0.007 0.053 67275 Z= 0.414 Angle : 0.700 11.146 97570 Z= 0.370 Chirality : 0.046 0.401 11997 Planarity : 0.005 0.064 7195 Dihedral : 13.900 177.058 21607 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.35 % Favored : 96.51 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.13), residues: 4094 helix: 0.99 (0.14), residues: 1449 sheet: 0.08 (0.20), residues: 664 loop : -0.38 (0.14), residues: 1981 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 348 time to evaluate : 3.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 35 residues processed: 386 average time/residue: 1.4138 time to fit residues: 709.1290 Evaluate side-chains 356 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 321 time to evaluate : 3.619 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 20 residues processed: 15 average time/residue: 0.5220 time to fit residues: 18.1776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 496 optimal weight: 7.9990 chunk 377 optimal weight: 10.0000 chunk 260 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 337 optimal weight: 0.0980 chunk 503 optimal weight: 6.9990 chunk 533 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 477 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 46 ASN p 232 HIS t 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 67275 Z= 0.224 Angle : 0.608 12.017 97570 Z= 0.321 Chirality : 0.040 0.386 11997 Planarity : 0.004 0.058 7195 Dihedral : 13.692 178.631 21607 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.64 % Favored : 97.19 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.38 (0.13), residues: 4094 helix: 1.28 (0.14), residues: 1454 sheet: 0.06 (0.19), residues: 691 loop : -0.40 (0.14), residues: 1949 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 350 time to evaluate : 3.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 38 residues processed: 397 average time/residue: 1.4233 time to fit residues: 739.4684 Evaluate side-chains 361 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 323 time to evaluate : 3.682 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 24 residues processed: 15 average time/residue: 0.6267 time to fit residues: 20.0691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 444 optimal weight: 6.9990 chunk 302 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 397 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 chunk 455 optimal weight: 8.9990 chunk 368 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 478 optimal weight: 6.9990 chunk 134 optimal weight: 40.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN g 46 ASN r 222 ASN t 127 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 67275 Z= 0.210 Angle : 0.584 12.904 97570 Z= 0.308 Chirality : 0.039 0.386 11997 Planarity : 0.004 0.056 7195 Dihedral : 13.548 179.904 21607 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.10 % Favored : 96.75 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.51 (0.13), residues: 4094 helix: 1.49 (0.14), residues: 1448 sheet: 0.11 (0.19), residues: 693 loop : -0.39 (0.14), residues: 1953 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 339 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 42 residues processed: 400 average time/residue: 1.4137 time to fit residues: 739.0075 Evaluate side-chains 365 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 323 time to evaluate : 3.704 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 30 residues processed: 13 average time/residue: 0.7930 time to fit residues: 20.1430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 179 optimal weight: 20.0000 chunk 480 optimal weight: 7.9990 chunk 105 optimal weight: 40.0000 chunk 313 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 534 optimal weight: 20.0000 chunk 443 optimal weight: 1.9990 chunk 247 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 280 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 201 GLN T 210 GLN b 98 GLN b 120 HIS f 9 HIS g 46 ASN r 164 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 67275 Z= 0.384 Angle : 0.673 12.736 97570 Z= 0.353 Chirality : 0.044 0.394 11997 Planarity : 0.005 0.068 7195 Dihedral : 13.725 178.995 21607 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.76 % Favored : 96.07 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.29 (0.13), residues: 4094 helix: 1.42 (0.14), residues: 1446 sheet: -0.01 (0.19), residues: 682 loop : -0.63 (0.14), residues: 1966 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 333 time to evaluate : 3.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 52 residues processed: 393 average time/residue: 1.4517 time to fit residues: 750.5516 Evaluate side-chains 372 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 320 time to evaluate : 3.697 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 37 residues processed: 15 average time/residue: 0.7348 time to fit residues: 21.8793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 514 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 304 optimal weight: 0.1980 chunk 390 optimal weight: 2.9990 chunk 302 optimal weight: 7.9990 chunk 449 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 chunk 532 optimal weight: 9.9990 chunk 332 optimal weight: 0.9990 chunk 324 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 138 ASN g 46 ASN r 164 GLN r 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 67275 Z= 0.175 Angle : 0.583 13.441 97570 Z= 0.305 Chirality : 0.038 0.426 11997 Planarity : 0.004 0.058 7195 Dihedral : 13.480 179.540 21607 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.71 % Favored : 97.14 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.48 (0.13), residues: 4094 helix: 1.61 (0.14), residues: 1449 sheet: 0.08 (0.19), residues: 683 loop : -0.54 (0.14), residues: 1962 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 347 time to evaluate : 3.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 42 residues processed: 397 average time/residue: 1.4112 time to fit residues: 729.7466 Evaluate side-chains 371 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 329 time to evaluate : 3.730 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 34 residues processed: 8 average time/residue: 0.8812 time to fit residues: 15.1139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 329 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 chunk 317 optimal weight: 9.9990 chunk 160 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 338 optimal weight: 7.9990 chunk 362 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 418 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 138 ASN g 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 67275 Z= 0.219 Angle : 0.594 14.137 97570 Z= 0.311 Chirality : 0.039 0.420 11997 Planarity : 0.004 0.049 7195 Dihedral : 13.434 179.373 21607 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.25 % Favored : 96.58 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.46 (0.13), residues: 4094 helix: 1.60 (0.14), residues: 1456 sheet: 0.08 (0.19), residues: 688 loop : -0.58 (0.14), residues: 1950 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 337 time to evaluate : 3.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 51 residues processed: 383 average time/residue: 1.4539 time to fit residues: 725.2616 Evaluate side-chains 375 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 324 time to evaluate : 3.775 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 37 residues processed: 15 average time/residue: 0.8614 time to fit residues: 24.2872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 483 optimal weight: 20.0000 chunk 509 optimal weight: 10.0000 chunk 465 optimal weight: 2.9990 chunk 495 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 389 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 448 optimal weight: 0.0980 chunk 468 optimal weight: 9.9990 chunk 494 optimal weight: 1.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 ASN ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 46 ASN r 222 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 67275 Z= 0.257 Angle : 0.618 14.260 97570 Z= 0.323 Chirality : 0.040 0.385 11997 Planarity : 0.004 0.072 7195 Dihedral : 13.454 179.436 21607 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.37 % Favored : 96.48 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.38 (0.13), residues: 4094 helix: 1.56 (0.14), residues: 1456 sheet: 0.02 (0.19), residues: 694 loop : -0.63 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 332 time to evaluate : 3.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 45 residues processed: 374 average time/residue: 1.4515 time to fit residues: 711.2221 Evaluate side-chains 368 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 323 time to evaluate : 3.931 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 37 residues processed: 8 average time/residue: 0.6882 time to fit residues: 13.2886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 325 optimal weight: 10.0000 chunk 524 optimal weight: 3.9990 chunk 319 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 364 optimal weight: 1.9990 chunk 549 optimal weight: 10.0000 chunk 506 optimal weight: 6.9990 chunk 437 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 338 optimal weight: 5.9990 chunk 268 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 ASN ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 46 ASN r 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 67275 Z= 0.267 Angle : 0.633 14.355 97570 Z= 0.330 Chirality : 0.040 0.423 11997 Planarity : 0.004 0.050 7195 Dihedral : 13.464 179.816 21607 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.49 % Favored : 96.34 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.38 (0.13), residues: 4094 helix: 1.56 (0.14), residues: 1444 sheet: 0.06 (0.19), residues: 696 loop : -0.64 (0.14), residues: 1954 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 327 time to evaluate : 3.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 45 residues processed: 368 average time/residue: 1.4246 time to fit residues: 688.2246 Evaluate side-chains 366 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 321 time to evaluate : 3.722 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 38 residues processed: 8 average time/residue: 0.8664 time to fit residues: 14.7471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 347 optimal weight: 0.9990 chunk 466 optimal weight: 3.9990 chunk 134 optimal weight: 40.0000 chunk 403 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 121 optimal weight: 20.0000 chunk 438 optimal weight: 0.0010 chunk 183 optimal weight: 4.9990 chunk 450 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 GLN ** Y 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.061553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.040335 restraints weight = 270268.593| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.65 r_work: 0.2668 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 67275 Z= 0.183 Angle : 0.596 15.326 97570 Z= 0.309 Chirality : 0.037 0.383 11997 Planarity : 0.004 0.085 7195 Dihedral : 13.340 179.725 21607 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.13 % Favored : 96.75 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.13), residues: 4094 helix: 1.64 (0.14), residues: 1443 sheet: 0.10 (0.19), residues: 697 loop : -0.56 (0.14), residues: 1954 =============================================================================== Job complete usr+sys time: 14119.00 seconds wall clock time: 248 minutes 30.11 seconds (14910.11 seconds total)