Starting phenix.real_space_refine on Mon Dec 30 09:38:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c00_16347/12_2024/8c00_16347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c00_16347/12_2024/8c00_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/cci-nas-00/data/ceres_data/8c00_16347/12_2024/8c00_16347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c00_16347/12_2024/8c00_16347.map" model { file = "/net/cci-nas-00/data/ceres_data/8c00_16347/12_2024/8c00_16347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c00_16347/12_2024/8c00_16347.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 25.61, per 1000 atoms: 0.41 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 - 3.00 Amino acid : True - 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: 11.15 Conformation dependent library (CDL) restraints added in 3.5 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: 20.45 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: 49.58 Time building geometry restraints manager: 13.62 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: 0.00 - 2.09: 94731 2.09 - 4.17: 2593 4.17 - 6.26: 206 6.26 - 8.35: 33 8.35 - 10.43: 7 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: 39107 35.75 - 71.51: 2621 71.51 - 107.26: 302 107.26 - 143.02: 22 143.02 - 178.77: 23 Dihedral angle restraints: 42075 sinusoidal: 30295 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 42072 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 3.040 nonbonded pdb=" OG SER t 521 " pdb=" NE1 TRP t 525 " model vdw 2.100 3.120 nonbonded pdb=" O2' C 21568 " pdb=" OP2 A 21569 " model vdw 2.179 3.040 nonbonded pdb=" O2' A 2 197 " pdb=" O4' A 2 198 " model vdw 2.206 3.040 nonbonded pdb=" N6 A 2 219 " pdb=" O2 U 2 843 " model vdw 2.211 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 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: 0.080 Extract box with map and model: 1.940 Check model and map are aligned: 0.370 Set scattering table: 0.440 Process input model: 140.750 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 161.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 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 : 20.239 178.770 34557 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.44 % Favored : 96.26 % Rotamer: Outliers : 0.84 % Allowed : 3.49 % Favored : 95.67 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP t 778 HIS 0.010 0.002 HIS Z 29 PHE 0.023 0.002 PHE W 146 TYR 0.019 0.002 TYR d 89 ARG 0.039 0.003 ARG Y 3 *********************** 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 to be fit. rotamer outliers: 29 poor density : 469 time to evaluate : 3.677 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: B 35 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8890 (tm-30) REVERT: B 119 ASP cc_start: 0.9486 (m-30) cc_final: 0.9199 (m-30) REVERT: B 127 GLN cc_start: 0.9025 (mp10) cc_final: 0.8596 (mp10) REVERT: E 21 ASP cc_start: 0.8758 (t0) cc_final: 0.7598 (t0) REVERT: E 23 GLU cc_start: 0.9372 (mp0) cc_final: 0.8366 (mp0) REVERT: E 32 ASP cc_start: 0.8868 (m-30) cc_final: 0.8576 (m-30) REVERT: E 52 LYS cc_start: 0.9583 (mmmt) cc_final: 0.9268 (tppt) REVERT: E 118 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8003 (mt-10) REVERT: F 62 ASN cc_start: 0.9341 (m110) cc_final: 0.9100 (m-40) REVERT: H 56 LYS cc_start: 0.9545 (mttp) cc_final: 0.9340 (ttmt) REVERT: H 71 GLN cc_start: 0.8940 (tp40) cc_final: 0.8682 (tm-30) REVERT: H 90 ASN cc_start: 0.7880 (t0) cc_final: 0.7209 (t0) REVERT: I 5 SER cc_start: 0.9028 (t) cc_final: 0.8667 (p) REVERT: I 8 ASP cc_start: 0.8642 (m-30) cc_final: 0.8378 (m-30) REVERT: I 20 SER cc_start: 0.9331 (t) cc_final: 0.9058 (p) REVERT: I 23 GLN cc_start: 0.8780 (tt0) cc_final: 0.8555 (tm-30) REVERT: I 105 LEU cc_start: 0.9296 (mt) cc_final: 0.9084 (mt) REVERT: I 125 SER cc_start: 0.8737 (t) cc_final: 0.8349 (p) REVERT: I 143 ASP cc_start: 0.9196 (m-30) cc_final: 0.8820 (m-30) REVERT: L 8 THR cc_start: 0.9054 (m) cc_final: 0.8660 (p) REVERT: L 56 LEU cc_start: 0.9234 (mt) cc_final: 0.8922 (mm) REVERT: Q 49 ASN cc_start: 0.8312 (p0) cc_final: 0.7830 (p0) REVERT: Q 92 GLN cc_start: 0.8315 (pt0) cc_final: 0.8010 (pp30) REVERT: S 66 MET cc_start: 0.9461 (mmm) cc_final: 0.9190 (mmm) REVERT: S 250 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8311 (mt-10) REVERT: T 25 ARG cc_start: 0.9005 (mtp85) cc_final: 0.8729 (mtm-85) REVERT: U 50 ASP cc_start: 0.8990 (p0) cc_final: 0.8618 (p0) REVERT: U 85 PHE cc_start: 0.8721 (m-80) cc_final: 0.8433 (m-80) REVERT: f 5 GLN cc_start: 0.6597 (pt0) cc_final: 0.6271 (tt0) REVERT: f 36 LYS cc_start: 0.8493 (mtmt) cc_final: 0.7968 (tptt) REVERT: f 40 CYS cc_start: 0.7685 (m) cc_final: 0.7200 (p) REVERT: g 29 LYS cc_start: 0.8888 (mttm) cc_final: 0.8637 (mtmm) REVERT: g 54 ARG cc_start: 0.7127 (ppt-90) cc_final: 0.6728 (tpp-160) REVERT: p 95 GLU cc_start: 0.8436 (pt0) cc_final: 0.8012 (pm20) REVERT: r 152 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.5545 (ppp) REVERT: r 162 GLU cc_start: 0.8511 (tt0) cc_final: 0.7750 (tm-30) REVERT: r 166 MET cc_start: 0.8938 (mmt) cc_final: 0.8480 (mpm) REVERT: r 223 SER cc_start: 0.9421 (m) cc_final: 0.9217 (p) REVERT: t 559 MET cc_start: 0.8586 (ttm) cc_final: 0.8195 (ttt) outliers start: 29 outliers final: 7 residues processed: 490 average time/residue: 1.4830 time to fit residues: 925.5377 Evaluate side-chains 360 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 352 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain p residue 145 PHE Chi-restraints excluded: chain r residue 152 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 466 optimal weight: 4.9990 chunk 418 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 142 optimal weight: 30.0000 chunk 282 optimal weight: 0.0010 chunk 223 optimal weight: 9.9990 chunk 432 optimal weight: 40.0000 chunk 167 optimal weight: 20.0000 chunk 263 optimal weight: 8.9990 chunk 322 optimal weight: 4.9990 chunk 501 optimal weight: 0.0370 overall best weight: 3.0070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN 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 23 GLN I 77 ASN Q 157 GLN S 153 ASN T 10 ASN U 29 ASN U 161 GLN W 48 GLN Y 105 ASN Z 29 HIS Z 80 HIS b 12 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 603 GLN t 640 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1640 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= 0.218 Angle : 0.679 11.614 97570 Z= 0.359 Chirality : 0.043 0.338 11997 Planarity : 0.005 0.057 7195 Dihedral : 21.229 178.490 26434 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.37 % Favored : 97.48 % Rotamer: Outliers : 1.60 % Allowed : 9.19 % Favored : 89.22 % 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: 0.29 (0.13), residues: 4094 helix: 0.78 (0.13), residues: 1423 sheet: 0.16 (0.19), residues: 698 loop : -0.11 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 129 HIS 0.009 0.001 HIS F 21 PHE 0.017 0.002 PHE F 10 TYR 0.026 0.002 TYR p 117 ARG 0.015 0.001 ARG H 110 *********************** 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 454 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 399 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8850 (tm-30) REVERT: B 76 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8377 (ptm160) REVERT: B 127 GLN cc_start: 0.9017 (mp10) cc_final: 0.8584 (mp10) REVERT: E 21 ASP cc_start: 0.8772 (t0) cc_final: 0.8438 (t0) REVERT: E 32 ASP cc_start: 0.8979 (m-30) cc_final: 0.8642 (m-30) REVERT: E 111 MET cc_start: 0.8628 (mtm) cc_final: 0.8037 (mtm) REVERT: F 62 ASN cc_start: 0.9357 (m110) cc_final: 0.9078 (t0) REVERT: F 66 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8340 (mtt-85) REVERT: F 94 GLN cc_start: 0.9244 (tm-30) cc_final: 0.9024 (tm-30) REVERT: F 113 ASP cc_start: 0.8620 (t70) cc_final: 0.8384 (t0) REVERT: H 90 ASN cc_start: 0.7962 (t0) cc_final: 0.7224 (t0) REVERT: H 98 TYR cc_start: 0.8552 (m-80) cc_final: 0.8332 (m-80) REVERT: H 104 ASN cc_start: 0.8943 (m-40) cc_final: 0.8728 (m-40) REVERT: I 5 SER cc_start: 0.9277 (t) cc_final: 0.8749 (p) REVERT: I 125 SER cc_start: 0.8590 (t) cc_final: 0.8079 (p) REVERT: I 126 GLU cc_start: 0.8831 (pm20) cc_final: 0.8560 (pm20) REVERT: I 127 ASN cc_start: 0.8704 (m-40) cc_final: 0.8417 (t0) REVERT: I 138 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8698 (tp-100) REVERT: K 37 GLN cc_start: 0.8108 (tp-100) cc_final: 0.7865 (tp-100) REVERT: K 45 GLU cc_start: 0.8840 (mp0) cc_final: 0.8555 (mp0) REVERT: L 8 THR cc_start: 0.8924 (m) cc_final: 0.8520 (p) REVERT: L 40 ILE cc_start: 0.8673 (tp) cc_final: 0.8305 (tt) REVERT: L 56 LEU cc_start: 0.9025 (mt) cc_final: 0.8787 (mm) REVERT: L 58 GLU cc_start: 0.8225 (tp30) cc_final: 0.7907 (tm-30) REVERT: Q 49 ASN cc_start: 0.8322 (p0) cc_final: 0.7904 (p0) REVERT: Q 92 GLN cc_start: 0.8463 (pt0) cc_final: 0.8121 (pp30) REVERT: S 66 MET cc_start: 0.9250 (mmm) cc_final: 0.8854 (mmm) REVERT: U 50 ASP cc_start: 0.8901 (p0) cc_final: 0.8586 (p0) REVERT: U 85 PHE cc_start: 0.8640 (m-80) cc_final: 0.8407 (m-80) REVERT: V 195 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8345 (mpt90) REVERT: X 50 GLU cc_start: 0.8590 (mp0) cc_final: 0.8384 (mp0) REVERT: c 100 ASP cc_start: 0.8556 (m-30) cc_final: 0.8327 (m-30) REVERT: f 36 LYS cc_start: 0.8168 (mtmt) cc_final: 0.7710 (tttt) REVERT: f 42 ASN cc_start: 0.7911 (t0) cc_final: 0.7571 (t0) REVERT: g 29 LYS cc_start: 0.8876 (mttm) cc_final: 0.8634 (mtmm) REVERT: g 54 ARG cc_start: 0.7156 (ppt-90) cc_final: 0.6754 (tpp-160) REVERT: p 95 GLU cc_start: 0.8386 (pt0) cc_final: 0.8021 (pm20) REVERT: p 131 ASN cc_start: 0.8202 (t0) cc_final: 0.7852 (t0) REVERT: p 183 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8501 (tt0) REVERT: r 152 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.5653 (ppp) REVERT: r 261 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8297 (mm-40) REVERT: t 559 MET cc_start: 0.8428 (ttm) cc_final: 0.7958 (ttt) REVERT: t 777 MET cc_start: 0.7936 (mmm) cc_final: 0.7377 (mmm) outliers start: 55 outliers final: 13 residues processed: 428 average time/residue: 1.4229 time to fit residues: 786.3733 Evaluate side-chains 365 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 347 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain T residue 168 THR Chi-restraints excluded: chain U residue 105 THR Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain V residue 195 ARG Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain p residue 145 PHE Chi-restraints excluded: chain p residue 183 GLU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 152 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 278 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 417 optimal weight: 10.0000 chunk 341 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 502 optimal weight: 5.9990 chunk 542 optimal weight: 30.0000 chunk 447 optimal weight: 10.0000 chunk 497 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 402 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 ASN b 15 ASN g 46 ASN t 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 67275 Z= 0.338 Angle : 0.674 10.032 97570 Z= 0.356 Chirality : 0.044 0.518 11997 Planarity : 0.005 0.061 7195 Dihedral : 21.158 178.487 26426 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.08 % Favored : 96.78 % Rotamer: Outliers : 2.01 % Allowed : 11.66 % Favored : 86.34 % 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: 0.94 (0.14), residues: 1465 sheet: 0.09 (0.20), residues: 658 loop : -0.33 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 129 HIS 0.007 0.001 HIS W 124 PHE 0.020 0.002 PHE W 146 TYR 0.018 0.002 TYR r 170 ARG 0.009 0.001 ARG L 61 *********************** 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 432 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 363 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8852 (tm-30) REVERT: B 127 GLN cc_start: 0.9042 (mp10) cc_final: 0.8615 (mp10) REVERT: E 32 ASP cc_start: 0.9029 (m-30) cc_final: 0.8724 (m-30) REVERT: E 111 MET cc_start: 0.8565 (mtm) cc_final: 0.8277 (mtp) REVERT: E 118 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8196 (mm-30) REVERT: F 66 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8411 (mtt-85) REVERT: F 94 GLN cc_start: 0.9266 (tm-30) cc_final: 0.9044 (tm-30) REVERT: F 96 TYR cc_start: 0.9016 (m-10) cc_final: 0.8690 (m-10) REVERT: H 90 ASN cc_start: 0.7983 (t0) cc_final: 0.7181 (t0) REVERT: H 104 ASN cc_start: 0.8899 (m-40) cc_final: 0.8687 (m-40) REVERT: H 111 ASP cc_start: 0.8382 (t0) cc_final: 0.8043 (t0) REVERT: I 5 SER cc_start: 0.9287 (t) cc_final: 0.8947 (p) REVERT: I 125 SER cc_start: 0.8660 (t) cc_final: 0.8354 (p) REVERT: I 127 ASN cc_start: 0.8740 (m-40) cc_final: 0.8439 (t0) REVERT: K 84 GLU cc_start: 0.9285 (tm-30) cc_final: 0.9085 (tm-30) REVERT: L 8 THR cc_start: 0.8935 (m) cc_final: 0.8552 (p) REVERT: Q 49 ASN cc_start: 0.8371 (p0) cc_final: 0.7988 (p0) REVERT: Q 92 GLN cc_start: 0.8443 (pt0) cc_final: 0.8051 (pp30) REVERT: S 66 MET cc_start: 0.9309 (mmm) cc_final: 0.8968 (mmm) REVERT: U 50 ASP cc_start: 0.8907 (p0) cc_final: 0.8569 (p0) REVERT: V 195 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8343 (mpt90) REVERT: Z 66 ASP cc_start: 0.8899 (m-30) cc_final: 0.8694 (m-30) REVERT: f 36 LYS cc_start: 0.8360 (mtmt) cc_final: 0.7851 (tttt) REVERT: f 42 ASN cc_start: 0.8054 (t0) cc_final: 0.7685 (t0) REVERT: g 29 LYS cc_start: 0.8848 (mttm) cc_final: 0.8610 (mtmm) REVERT: g 54 ARG cc_start: 0.7167 (ppt-90) cc_final: 0.6891 (mpt180) REVERT: g 56 MET cc_start: 0.9054 (mtp) cc_final: 0.8847 (mmt) REVERT: p 95 GLU cc_start: 0.8445 (pt0) cc_final: 0.8095 (pm20) REVERT: p 131 ASN cc_start: 0.8212 (t0) cc_final: 0.7906 (t0) REVERT: p 183 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: r 152 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.5771 (ppp) REVERT: t 559 MET cc_start: 0.8506 (ttm) cc_final: 0.8062 (ttt) REVERT: t 777 MET cc_start: 0.8049 (mmm) cc_final: 0.7693 (mmm) outliers start: 69 outliers final: 28 residues processed: 399 average time/residue: 1.4208 time to fit residues: 732.8583 Evaluate side-chains 369 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 337 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain U residue 105 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain V residue 195 ARG Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain Y residue 145 THR Chi-restraints excluded: chain Y residue 150 VAL Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain p residue 145 PHE Chi-restraints excluded: chain p residue 183 GLU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 152 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 496 optimal weight: 10.0000 chunk 377 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 239 optimal weight: 0.8980 chunk 337 optimal weight: 1.9990 chunk 503 optimal weight: 9.9990 chunk 533 optimal weight: 20.0000 chunk 263 optimal weight: 3.9990 chunk 477 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN E 128 HIS ** F 93 HIS ** 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 r 222 ASN r 261 GLN t 53 GLN t 60 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2174 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 : 0.594 12.745 97570 Z= 0.313 Chirality : 0.039 0.396 11997 Planarity : 0.004 0.060 7195 Dihedral : 21.119 179.586 26426 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.27 % Favored : 97.56 % Rotamer: Outliers : 1.98 % Allowed : 12.53 % Favored : 85.49 % 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: 0.42 (0.13), residues: 4094 helix: 1.24 (0.14), residues: 1461 sheet: 0.12 (0.19), residues: 687 loop : -0.33 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 129 HIS 0.006 0.001 HIS Q 232 PHE 0.017 0.001 PHE F 10 TYR 0.021 0.001 TYR F 92 ARG 0.009 0.000 ARG B 143 *********************** 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 429 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 361 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8853 (tm-30) REVERT: B 127 GLN cc_start: 0.9009 (mp10) cc_final: 0.8538 (mp10) REVERT: E 21 ASP cc_start: 0.8763 (t0) cc_final: 0.8554 (t0) REVERT: E 32 ASP cc_start: 0.9085 (m-30) cc_final: 0.8750 (m-30) REVERT: E 111 MET cc_start: 0.8539 (mtm) cc_final: 0.8016 (mtm) REVERT: F 66 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8556 (mtt-85) REVERT: H 90 ASN cc_start: 0.7830 (t0) cc_final: 0.6960 (t0) REVERT: H 96 LYS cc_start: 0.8933 (mtpm) cc_final: 0.8596 (mtmm) REVERT: H 98 TYR cc_start: 0.8663 (m-80) cc_final: 0.8328 (m-80) REVERT: H 108 LYS cc_start: 0.8991 (mmmm) cc_final: 0.8650 (mmmm) REVERT: I 125 SER cc_start: 0.8658 (t) cc_final: 0.8191 (p) REVERT: I 126 GLU cc_start: 0.8848 (pm20) cc_final: 0.8629 (pm20) REVERT: I 127 ASN cc_start: 0.8798 (m-40) cc_final: 0.8502 (t0) REVERT: K 37 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7877 (tp-100) REVERT: K 84 GLU cc_start: 0.9239 (tm-30) cc_final: 0.9010 (tm-30) REVERT: L 8 THR cc_start: 0.8970 (m) cc_final: 0.8509 (p) REVERT: Q 49 ASN cc_start: 0.8372 (p0) cc_final: 0.7962 (p0) REVERT: Q 92 GLN cc_start: 0.8464 (pt0) cc_final: 0.8134 (pp30) REVERT: U 50 ASP cc_start: 0.8905 (p0) cc_final: 0.8601 (p0) REVERT: V 195 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8312 (mpt90) REVERT: Z 47 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8673 (mttp) REVERT: f 36 LYS cc_start: 0.8328 (mtmt) cc_final: 0.7800 (tptt) REVERT: f 42 ASN cc_start: 0.8081 (t0) cc_final: 0.7709 (t0) REVERT: g 29 LYS cc_start: 0.8816 (mttm) cc_final: 0.8592 (mtmm) REVERT: g 56 MET cc_start: 0.9038 (mtp) cc_final: 0.8657 (mmt) REVERT: p 95 GLU cc_start: 0.8378 (pt0) cc_final: 0.8072 (pm20) REVERT: p 131 ASN cc_start: 0.8210 (t0) cc_final: 0.7893 (t0) REVERT: p 183 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8659 (tt0) REVERT: r 152 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.5898 (ppp) REVERT: r 162 GLU cc_start: 0.9236 (pt0) cc_final: 0.8894 (pm20) REVERT: r 222 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8246 (p0) REVERT: r 236 MET cc_start: 0.9115 (tpp) cc_final: 0.8908 (mmp) REVERT: t 559 MET cc_start: 0.8461 (ttm) cc_final: 0.8244 (ttt) REVERT: t 777 MET cc_start: 0.8128 (mmm) cc_final: 0.7751 (mmm) outliers start: 68 outliers final: 21 residues processed: 403 average time/residue: 1.4003 time to fit residues: 733.4482 Evaluate side-chains 363 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 336 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 12 GLN Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain V residue 195 ARG Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Y residue 150 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain p residue 145 PHE Chi-restraints excluded: chain p residue 183 GLU Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain r residue 222 ASN Chi-restraints excluded: chain t residue 154 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 444 optimal weight: 0.9980 chunk 302 optimal weight: 0.0980 chunk 7 optimal weight: 10.0000 chunk 397 optimal weight: 8.9990 chunk 220 optimal weight: 40.0000 chunk 455 optimal weight: 0.1980 chunk 368 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 chunk 478 optimal weight: 40.0000 chunk 134 optimal weight: 40.0000 overall best weight: 1.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN F 103 ASN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 HIS ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN g 46 ASN t 60 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 67275 Z= 0.155 Angle : 0.568 13.003 97570 Z= 0.298 Chirality : 0.038 0.409 11997 Planarity : 0.004 0.060 7195 Dihedral : 21.044 179.806 26426 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.59 % Favored : 97.24 % Rotamer: Outliers : 2.06 % Allowed : 13.46 % Favored : 84.48 % 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: 0.58 (0.13), residues: 4094 helix: 1.43 (0.14), residues: 1461 sheet: 0.19 (0.20), residues: 689 loop : -0.28 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 129 HIS 0.004 0.001 HIS Q 232 PHE 0.017 0.001 PHE F 10 TYR 0.015 0.001 TYR F 92 ARG 0.013 0.000 ARG L 61 *********************** 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 440 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 369 time to evaluate : 3.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8834 (tm-30) REVERT: B 122 ASN cc_start: 0.9025 (OUTLIER) cc_final: 0.8750 (t0) REVERT: B 127 GLN cc_start: 0.9009 (mp10) cc_final: 0.8552 (mp10) REVERT: E 111 MET cc_start: 0.8464 (mtm) cc_final: 0.7932 (mtm) REVERT: F 66 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8559 (mtt-85) REVERT: H 90 ASN cc_start: 0.7718 (t0) cc_final: 0.6812 (t0) REVERT: H 96 LYS cc_start: 0.8947 (mtpm) cc_final: 0.8665 (mtmm) REVERT: H 98 TYR cc_start: 0.8637 (m-80) cc_final: 0.8272 (m-80) REVERT: H 108 LYS cc_start: 0.9012 (mmmm) cc_final: 0.8646 (mmmm) REVERT: H 117 LYS cc_start: 0.8906 (ttpp) cc_final: 0.8638 (ttpp) REVERT: I 109 GLU cc_start: 0.8858 (pt0) cc_final: 0.8634 (pp20) REVERT: I 125 SER cc_start: 0.8636 (t) cc_final: 0.8343 (p) REVERT: I 126 GLU cc_start: 0.8895 (pm20) cc_final: 0.8683 (pm20) REVERT: I 127 ASN cc_start: 0.8805 (m-40) cc_final: 0.8545 (t0) REVERT: K 37 GLN cc_start: 0.8227 (tp-100) cc_final: 0.7979 (tp-100) REVERT: K 48 ASP cc_start: 0.9218 (p0) cc_final: 0.8878 (p0) REVERT: L 8 THR cc_start: 0.8989 (m) cc_final: 0.8517 (p) REVERT: L 58 GLU cc_start: 0.8258 (tp30) cc_final: 0.7841 (tp30) REVERT: Q 49 ASN cc_start: 0.8407 (p0) cc_final: 0.7994 (p0) REVERT: Q 92 GLN cc_start: 0.8428 (pt0) cc_final: 0.8135 (pp30) REVERT: U 50 ASP cc_start: 0.8881 (p0) cc_final: 0.8591 (p0) REVERT: V 195 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8207 (mpt90) REVERT: W 172 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8675 (t) REVERT: Z 66 ASP cc_start: 0.8882 (m-30) cc_final: 0.8620 (m-30) REVERT: Z 72 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8595 (tppt) REVERT: Z 124 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7346 (m-30) REVERT: f 36 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7818 (tptt) REVERT: f 42 ASN cc_start: 0.8122 (t0) cc_final: 0.7747 (t0) REVERT: g 29 LYS cc_start: 0.8817 (mttm) cc_final: 0.8586 (mtmm) REVERT: g 56 MET cc_start: 0.9037 (mtp) cc_final: 0.8627 (mmt) REVERT: p 131 ASN cc_start: 0.8254 (t0) cc_final: 0.7950 (t0) REVERT: r 152 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.5713 (ppp) REVERT: r 222 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8133 (p0) REVERT: t 559 MET cc_start: 0.8493 (ttm) cc_final: 0.8269 (ttp) REVERT: t 777 MET cc_start: 0.8158 (mmm) cc_final: 0.7779 (mmm) outliers start: 71 outliers final: 25 residues processed: 411 average time/residue: 1.4011 time to fit residues: 747.3293 Evaluate side-chains 369 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 337 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain V residue 195 ARG Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain Y residue 150 VAL Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain Z residue 124 ASP Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain p residue 145 PHE Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain r residue 222 ASN Chi-restraints excluded: chain t residue 104 LEU Chi-restraints excluded: chain t residue 154 VAL 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: 30.0000 chunk 105 optimal weight: 40.0000 chunk 313 optimal weight: 0.9990 chunk 131 optimal weight: 20.0000 chunk 534 optimal weight: 20.0000 chunk 443 optimal weight: 0.0470 chunk 247 optimal weight: 0.0670 chunk 44 optimal weight: 20.0000 chunk 176 optimal weight: 0.1980 chunk 280 optimal weight: 9.9990 overall best weight: 2.2620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 GLN ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 107 GLN g 46 ASN ** r 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 67275 Z= 0.170 Angle : 0.569 13.848 97570 Z= 0.297 Chirality : 0.038 0.444 11997 Planarity : 0.004 0.060 7195 Dihedral : 21.002 178.420 26426 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.49 % Favored : 97.34 % Rotamer: Outliers : 1.89 % Allowed : 14.36 % Favored : 83.75 % 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: 0.63 (0.13), residues: 4094 helix: 1.54 (0.14), residues: 1466 sheet: 0.14 (0.19), residues: 709 loop : -0.28 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 129 HIS 0.005 0.001 HIS p 232 PHE 0.017 0.001 PHE F 10 TYR 0.019 0.001 TYR F 92 ARG 0.013 0.000 ARG L 61 *********************** 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 419 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 354 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8827 (tm-30) REVERT: B 127 GLN cc_start: 0.8966 (mp10) cc_final: 0.8499 (mp10) REVERT: E 21 ASP cc_start: 0.8696 (t0) cc_final: 0.8480 (t0) REVERT: E 88 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7924 (mp0) REVERT: E 111 MET cc_start: 0.8401 (mtm) cc_final: 0.7898 (mtm) REVERT: F 62 ASN cc_start: 0.9209 (t0) cc_final: 0.8985 (t0) REVERT: F 66 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8613 (mtt-85) REVERT: H 96 LYS cc_start: 0.8939 (mtpm) cc_final: 0.8639 (mtmm) REVERT: H 98 TYR cc_start: 0.8597 (m-80) cc_final: 0.8220 (m-80) REVERT: H 108 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8655 (mmmm) REVERT: I 125 SER cc_start: 0.8637 (t) cc_final: 0.8354 (p) REVERT: I 127 ASN cc_start: 0.8792 (m-40) cc_final: 0.8469 (t0) REVERT: I 131 ASP cc_start: 0.9058 (m-30) cc_final: 0.8833 (m-30) REVERT: K 37 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7869 (tp-100) REVERT: K 48 ASP cc_start: 0.9216 (p0) cc_final: 0.8818 (p0) REVERT: K 93 SER cc_start: 0.8869 (t) cc_final: 0.8373 (p) REVERT: L 8 THR cc_start: 0.8990 (m) cc_final: 0.8489 (p) REVERT: Q 49 ASN cc_start: 0.8383 (p0) cc_final: 0.7992 (p0) REVERT: Q 92 GLN cc_start: 0.8418 (pt0) cc_final: 0.8160 (pp30) REVERT: U 50 ASP cc_start: 0.8880 (p0) cc_final: 0.8610 (p0) REVERT: V 195 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8299 (mpt90) REVERT: W 172 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8687 (t) REVERT: Z 72 LYS cc_start: 0.8872 (ttmm) cc_final: 0.8612 (tppt) REVERT: c 55 GLU cc_start: 0.8362 (pt0) cc_final: 0.7997 (pp20) REVERT: f 36 LYS cc_start: 0.8466 (mtmt) cc_final: 0.8031 (tttt) REVERT: f 42 ASN cc_start: 0.8125 (t0) cc_final: 0.7678 (t0) REVERT: g 29 LYS cc_start: 0.8781 (mttm) cc_final: 0.8553 (mtmm) REVERT: g 56 MET cc_start: 0.9039 (mtp) cc_final: 0.8656 (mmt) REVERT: p 131 ASN cc_start: 0.8227 (t0) cc_final: 0.7941 (t0) REVERT: r 152 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.5735 (ppp) REVERT: r 236 MET cc_start: 0.8882 (mmt) cc_final: 0.8570 (mmp) REVERT: t 307 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: t 559 MET cc_start: 0.8455 (ttm) cc_final: 0.8230 (ttp) REVERT: t 777 MET cc_start: 0.8163 (mmm) cc_final: 0.7767 (mmm) outliers start: 65 outliers final: 30 residues processed: 394 average time/residue: 1.4318 time to fit residues: 729.2263 Evaluate side-chains 369 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 334 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain V residue 195 ARG Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain Y residue 150 VAL Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain Z residue 124 ASP Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain p residue 145 PHE Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain t residue 104 LEU Chi-restraints excluded: chain t residue 154 VAL Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 307 GLU 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: 4.9990 chunk 390 optimal weight: 0.9980 chunk 302 optimal weight: 0.2980 chunk 449 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 chunk 532 optimal weight: 6.9990 chunk 332 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 245 optimal weight: 0.7980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** b 98 GLN g 46 ASN ** r 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 67275 Z= 0.169 Angle : 0.573 14.025 97570 Z= 0.298 Chirality : 0.037 0.490 11997 Planarity : 0.004 0.073 7195 Dihedral : 20.970 178.879 26426 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.59 % Favored : 97.24 % Rotamer: Outliers : 1.69 % Allowed : 15.12 % Favored : 83.20 % 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: 0.63 (0.13), residues: 4094 helix: 1.55 (0.14), residues: 1471 sheet: 0.16 (0.19), residues: 709 loop : -0.32 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 129 HIS 0.005 0.001 HIS p 232 PHE 0.015 0.001 PHE F 10 TYR 0.013 0.001 TYR F 92 ARG 0.017 0.000 ARG L 61 *********************** 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 407 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 349 time to evaluate : 3.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8809 (tm-30) REVERT: B 122 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8718 (t0) REVERT: B 127 GLN cc_start: 0.8934 (mp10) cc_final: 0.8474 (mp10) REVERT: E 88 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7893 (mp0) REVERT: E 111 MET cc_start: 0.8386 (mtm) cc_final: 0.7876 (mtm) REVERT: F 62 ASN cc_start: 0.9251 (t0) cc_final: 0.8941 (t0) REVERT: F 66 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8606 (mtt-85) REVERT: H 60 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8617 (mp0) REVERT: H 96 LYS cc_start: 0.8937 (mtpm) cc_final: 0.8644 (mtmm) REVERT: H 98 TYR cc_start: 0.8597 (m-80) cc_final: 0.8220 (m-80) REVERT: H 108 LYS cc_start: 0.8967 (mmmm) cc_final: 0.8629 (mmmm) REVERT: I 125 SER cc_start: 0.8685 (t) cc_final: 0.8260 (p) REVERT: I 127 ASN cc_start: 0.8835 (m-40) cc_final: 0.8544 (t0) REVERT: K 48 ASP cc_start: 0.9177 (p0) cc_final: 0.8831 (p0) REVERT: K 93 SER cc_start: 0.8839 (t) cc_final: 0.8319 (p) REVERT: L 8 THR cc_start: 0.8989 (m) cc_final: 0.8396 (p) REVERT: L 56 LEU cc_start: 0.8864 (mp) cc_final: 0.8554 (mm) REVERT: L 58 GLU cc_start: 0.7476 (tp30) cc_final: 0.6549 (tp30) REVERT: Q 49 ASN cc_start: 0.8372 (p0) cc_final: 0.7998 (p0) REVERT: Q 92 GLN cc_start: 0.8405 (pt0) cc_final: 0.8147 (pp30) REVERT: U 50 ASP cc_start: 0.8912 (p0) cc_final: 0.8630 (p0) REVERT: V 195 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8246 (mpt90) REVERT: W 172 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8692 (t) REVERT: Z 72 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8610 (tppt) REVERT: Z 116 GLU cc_start: 0.8240 (tp30) cc_final: 0.7923 (tp30) REVERT: c 55 GLU cc_start: 0.8397 (pt0) cc_final: 0.8014 (pp20) REVERT: f 36 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8044 (tptt) REVERT: f 42 ASN cc_start: 0.8167 (t0) cc_final: 0.7752 (t0) REVERT: g 29 LYS cc_start: 0.8779 (mttm) cc_final: 0.8546 (mtmm) REVERT: g 56 MET cc_start: 0.9052 (mtp) cc_final: 0.8694 (mmt) REVERT: p 131 ASN cc_start: 0.8227 (t0) cc_final: 0.7964 (t0) REVERT: r 152 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.5782 (ppp) REVERT: r 236 MET cc_start: 0.8801 (mmt) cc_final: 0.8450 (mmp) REVERT: t 307 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: t 559 MET cc_start: 0.8452 (ttm) cc_final: 0.8228 (ttp) REVERT: t 777 MET cc_start: 0.8208 (mmm) cc_final: 0.7815 (mmm) outliers start: 58 outliers final: 30 residues processed: 384 average time/residue: 1.4317 time to fit residues: 712.6744 Evaluate side-chains 365 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 329 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain V residue 195 ARG Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain Y residue 150 VAL Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain Z residue 124 ASP Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain p residue 145 PHE Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain t residue 104 LEU Chi-restraints excluded: chain t residue 154 VAL Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 307 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 329 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 338 optimal weight: 0.9980 chunk 362 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 418 optimal weight: 0.8980 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 ** 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 210 GLN ** b 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 46 ASN ** r 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2671 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= 0.219 Angle : 0.596 14.623 97570 Z= 0.310 Chirality : 0.038 0.456 11997 Planarity : 0.004 0.064 7195 Dihedral : 20.954 179.094 26426 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.88 % Favored : 96.95 % Rotamer: Outliers : 1.63 % Allowed : 15.84 % Favored : 82.53 % 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: 0.55 (0.13), residues: 4094 helix: 1.53 (0.14), residues: 1477 sheet: 0.11 (0.19), residues: 707 loop : -0.40 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 129 HIS 0.006 0.001 HIS p 232 PHE 0.016 0.001 PHE F 10 TYR 0.016 0.001 TYR K 59 ARG 0.016 0.000 ARG L 61 *********************** 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 397 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 341 time to evaluate : 3.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8800 (tm-30) REVERT: B 127 GLN cc_start: 0.8927 (mp10) cc_final: 0.8475 (mp10) REVERT: E 21 ASP cc_start: 0.8733 (t0) cc_final: 0.8498 (t0) REVERT: E 35 LYS cc_start: 0.8743 (mtmm) cc_final: 0.8282 (mtmm) REVERT: E 80 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8148 (mtp) REVERT: E 88 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7929 (mp0) REVERT: E 111 MET cc_start: 0.8395 (mtm) cc_final: 0.7998 (mtt) REVERT: F 62 ASN cc_start: 0.9283 (t0) cc_final: 0.8942 (t0) REVERT: F 66 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8595 (mtt-85) REVERT: H 60 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8715 (mp0) REVERT: H 96 LYS cc_start: 0.8925 (mtpm) cc_final: 0.8565 (mtmm) REVERT: H 98 TYR cc_start: 0.8604 (m-80) cc_final: 0.8206 (m-80) REVERT: H 108 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8511 (mmmm) REVERT: I 125 SER cc_start: 0.8775 (t) cc_final: 0.8296 (p) REVERT: I 127 ASN cc_start: 0.8869 (m-40) cc_final: 0.8534 (t0) REVERT: I 131 ASP cc_start: 0.9072 (m-30) cc_final: 0.8864 (m-30) REVERT: K 37 GLN cc_start: 0.8368 (tp-100) cc_final: 0.8099 (tp-100) REVERT: K 68 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8231 (pmm-80) REVERT: K 93 SER cc_start: 0.8835 (t) cc_final: 0.8326 (p) REVERT: Q 49 ASN cc_start: 0.8398 (p0) cc_final: 0.8023 (p0) REVERT: Q 92 GLN cc_start: 0.8427 (pt0) cc_final: 0.8138 (pp30) REVERT: U 50 ASP cc_start: 0.8919 (p0) cc_final: 0.8634 (p0) REVERT: V 195 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8248 (mpt90) REVERT: W 172 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8744 (t) REVERT: Z 72 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8631 (tppt) REVERT: Z 116 GLU cc_start: 0.8335 (tp30) cc_final: 0.8018 (tp30) REVERT: Z 124 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7318 (m-30) REVERT: c 55 GLU cc_start: 0.8421 (pt0) cc_final: 0.8066 (pp20) REVERT: f 36 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8116 (tttt) REVERT: f 42 ASN cc_start: 0.8152 (t0) cc_final: 0.7676 (t0) REVERT: g 29 LYS cc_start: 0.8792 (mttm) cc_final: 0.8549 (mtmm) REVERT: g 56 MET cc_start: 0.9055 (mtp) cc_final: 0.8717 (mmt) REVERT: p 131 ASN cc_start: 0.8234 (t0) cc_final: 0.7959 (t0) REVERT: r 152 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.5842 (ppp) REVERT: r 236 MET cc_start: 0.8840 (mmt) cc_final: 0.8484 (mmp) REVERT: t 307 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: t 559 MET cc_start: 0.8460 (ttm) cc_final: 0.8235 (ttp) REVERT: t 777 MET cc_start: 0.8213 (mmm) cc_final: 0.7747 (mmm) outliers start: 56 outliers final: 33 residues processed: 374 average time/residue: 1.4375 time to fit residues: 699.0712 Evaluate side-chains 370 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 329 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain K residue 68 ARG Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain U residue 105 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain V residue 195 ARG Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Y residue 29 SER Chi-restraints excluded: chain Y residue 150 VAL Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain Z residue 124 ASP Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain p residue 145 PHE Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain p residue 186 GLU Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain t residue 104 LEU Chi-restraints excluded: chain t residue 154 VAL Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 307 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 483 optimal weight: 9.9990 chunk 509 optimal weight: 9.9990 chunk 465 optimal weight: 5.9990 chunk 495 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 389 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 448 optimal weight: 10.0000 chunk 468 optimal weight: 6.9990 chunk 494 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 44 GLN ** 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 ** b 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 HIS g 46 ASN r 164 GLN ** r 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 67275 Z= 0.367 Angle : 0.685 14.489 97570 Z= 0.356 Chirality : 0.044 0.438 11997 Planarity : 0.005 0.061 7195 Dihedral : 21.031 178.456 26426 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.66 % Favored : 96.14 % Rotamer: Outliers : 1.86 % Allowed : 15.73 % Favored : 82.41 % 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: 0.36 (0.13), residues: 4094 helix: 1.40 (0.14), residues: 1458 sheet: 0.04 (0.20), residues: 683 loop : -0.53 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP V 67 HIS 0.011 0.001 HIS p 232 PHE 0.022 0.002 PHE W 146 TYR 0.017 0.001 TYR d 89 ARG 0.020 0.001 ARG L 61 *********************** 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 405 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 341 time to evaluate : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8799 (tm-30) REVERT: B 127 GLN cc_start: 0.8980 (mp10) cc_final: 0.8552 (mp10) REVERT: E 28 MET cc_start: 0.8725 (tpp) cc_final: 0.8131 (tmm) REVERT: E 35 LYS cc_start: 0.8898 (mtmm) cc_final: 0.8682 (mtmm) REVERT: E 80 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8157 (mtt) REVERT: F 62 ASN cc_start: 0.9336 (t0) cc_final: 0.9043 (t0) REVERT: F 66 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8582 (mtt-85) REVERT: H 56 LYS cc_start: 0.8918 (tppp) cc_final: 0.8352 (mmmm) REVERT: H 60 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8605 (mp0) REVERT: H 96 LYS cc_start: 0.8877 (mtpm) cc_final: 0.8488 (mtmm) REVERT: H 98 TYR cc_start: 0.8618 (m-80) cc_final: 0.8251 (m-80) REVERT: H 108 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8493 (mmmm) REVERT: I 109 GLU cc_start: 0.8908 (pm20) cc_final: 0.8645 (pm20) REVERT: I 125 SER cc_start: 0.8860 (t) cc_final: 0.8286 (p) REVERT: I 127 ASN cc_start: 0.8863 (m-40) cc_final: 0.8523 (t0) REVERT: I 131 ASP cc_start: 0.9055 (m-30) cc_final: 0.8839 (m-30) REVERT: K 37 GLN cc_start: 0.8370 (tp-100) cc_final: 0.8076 (tp-100) REVERT: K 68 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8228 (pmm-80) REVERT: Q 49 ASN cc_start: 0.8467 (p0) cc_final: 0.8130 (p0) REVERT: Q 92 GLN cc_start: 0.8489 (pt0) cc_final: 0.8082 (pp30) REVERT: S 258 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8609 (tm-30) REVERT: U 50 ASP cc_start: 0.8961 (p0) cc_final: 0.8669 (p0) REVERT: V 195 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8335 (mpt90) REVERT: Z 116 GLU cc_start: 0.8450 (tp30) cc_final: 0.8199 (tp30) REVERT: Z 124 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: b 23 ARG cc_start: 0.8650 (mmp-170) cc_final: 0.8270 (mmm160) REVERT: c 98 GLU cc_start: 0.8646 (mp0) cc_final: 0.8379 (tp30) REVERT: f 36 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8118 (tptt) REVERT: f 42 ASN cc_start: 0.8159 (t0) cc_final: 0.7741 (t0) REVERT: g 29 LYS cc_start: 0.8819 (mttm) cc_final: 0.8553 (mtmm) REVERT: g 56 MET cc_start: 0.9087 (mtp) cc_final: 0.8802 (mmt) REVERT: p 131 ASN cc_start: 0.8241 (t0) cc_final: 0.7958 (t0) REVERT: r 152 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.6002 (ppp) REVERT: t 307 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: t 559 MET cc_start: 0.8512 (ttm) cc_final: 0.8290 (ttp) REVERT: t 777 MET cc_start: 0.8112 (mmm) cc_final: 0.7532 (mmm) outliers start: 64 outliers final: 35 residues processed: 380 average time/residue: 1.4409 time to fit residues: 710.8639 Evaluate side-chains 373 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 331 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain K residue 68 ARG Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain U residue 105 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain V residue 195 ARG Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 150 VAL Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain Z residue 124 ASP Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 57 VAL Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain p residue 145 PHE Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain t residue 154 VAL Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 307 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 325 optimal weight: 4.9990 chunk 524 optimal weight: 30.0000 chunk 319 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 364 optimal weight: 1.9990 chunk 549 optimal weight: 20.0000 chunk 506 optimal weight: 5.9990 chunk 437 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 338 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 ASN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 46 ASN r 164 GLN t 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 67275 Z= 0.210 Angle : 0.634 15.015 97570 Z= 0.330 Chirality : 0.040 0.471 11997 Planarity : 0.004 0.076 7195 Dihedral : 21.042 178.818 26426 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.83 % Favored : 96.97 % Rotamer: Outliers : 1.16 % Allowed : 16.63 % Favored : 82.21 % 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: 1.41 (0.14), residues: 1470 sheet: 0.01 (0.19), residues: 706 loop : -0.51 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 129 HIS 0.005 0.001 HIS F 93 PHE 0.016 0.001 PHE F 10 TYR 0.012 0.001 TYR F 92 ARG 0.018 0.000 ARG L 61 ********************** 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 379 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 339 time to evaluate : 4.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8795 (tm-30) REVERT: B 127 GLN cc_start: 0.8977 (mp10) cc_final: 0.8551 (mp10) REVERT: E 21 ASP cc_start: 0.8729 (t0) cc_final: 0.8262 (t0) REVERT: E 23 GLU cc_start: 0.9433 (mp0) cc_final: 0.9166 (mp0) REVERT: E 28 MET cc_start: 0.8751 (tpp) cc_final: 0.8133 (tmm) REVERT: E 35 LYS cc_start: 0.8872 (mtmm) cc_final: 0.8429 (mtmm) REVERT: E 80 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8175 (mtt) REVERT: F 62 ASN cc_start: 0.9339 (t0) cc_final: 0.9017 (t0) REVERT: F 66 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8583 (mtt-85) REVERT: H 60 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8628 (mp0) REVERT: H 64 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8777 (tm-30) REVERT: H 96 LYS cc_start: 0.8860 (mtpm) cc_final: 0.8509 (mtmm) REVERT: H 98 TYR cc_start: 0.8631 (m-80) cc_final: 0.8269 (m-80) REVERT: H 108 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8639 (mmmm) REVERT: I 125 SER cc_start: 0.8816 (t) cc_final: 0.8268 (p) REVERT: I 127 ASN cc_start: 0.8845 (m-40) cc_final: 0.8537 (t0) REVERT: I 131 ASP cc_start: 0.9042 (m-30) cc_final: 0.8836 (m-30) REVERT: K 37 GLN cc_start: 0.8341 (tp-100) cc_final: 0.8078 (tp-100) REVERT: K 68 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8209 (pmm-80) REVERT: K 93 SER cc_start: 0.8836 (t) cc_final: 0.8318 (p) REVERT: Q 49 ASN cc_start: 0.8460 (p0) cc_final: 0.8096 (p0) REVERT: Q 92 GLN cc_start: 0.8484 (pt0) cc_final: 0.8116 (pp30) REVERT: S 258 GLN cc_start: 0.8878 (tp-100) cc_final: 0.8608 (tm-30) REVERT: U 50 ASP cc_start: 0.8948 (p0) cc_final: 0.8660 (p0) REVERT: V 195 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8274 (mpt90) REVERT: Z 72 LYS cc_start: 0.8899 (ttmm) cc_final: 0.8657 (tppt) REVERT: Z 73 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8532 (tm-30) REVERT: Z 116 GLU cc_start: 0.8423 (tp30) cc_final: 0.8165 (tp30) REVERT: Z 124 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7305 (m-30) REVERT: c 55 GLU cc_start: 0.8367 (pt0) cc_final: 0.7963 (pp20) REVERT: c 98 GLU cc_start: 0.8551 (mp0) cc_final: 0.8265 (tp30) REVERT: f 36 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8140 (tmtt) REVERT: f 42 ASN cc_start: 0.8101 (t0) cc_final: 0.7651 (t0) REVERT: g 29 LYS cc_start: 0.8793 (mttm) cc_final: 0.8556 (mtmm) REVERT: g 56 MET cc_start: 0.9097 (mtp) cc_final: 0.8815 (mmt) REVERT: p 131 ASN cc_start: 0.8266 (t0) cc_final: 0.7952 (t0) REVERT: r 152 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6007 (ppp) REVERT: r 236 MET cc_start: 0.8809 (mmp) cc_final: 0.8567 (mmp) REVERT: t 307 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: t 559 MET cc_start: 0.8483 (ttm) cc_final: 0.8260 (ttp) REVERT: t 777 MET cc_start: 0.8110 (mmm) cc_final: 0.7524 (mmm) outliers start: 40 outliers final: 32 residues processed: 365 average time/residue: 1.4622 time to fit residues: 689.0406 Evaluate side-chains 370 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 331 time to evaluate : 3.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain K residue 68 ARG Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 126 THR Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain U residue 105 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 67 TRP Chi-restraints excluded: chain V residue 195 ARG Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain Y residue 150 VAL Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain Z residue 124 ASP Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain d residue 62 THR Chi-restraints excluded: chain p residue 145 PHE Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain p residue 193 LEU Chi-restraints excluded: chain r residue 100 THR Chi-restraints excluded: chain r residue 152 MET Chi-restraints excluded: chain r residue 153 HIS Chi-restraints excluded: chain r residue 222 ASN Chi-restraints excluded: chain t residue 154 VAL Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 307 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 347 optimal weight: 7.9990 chunk 466 optimal weight: 2.9990 chunk 134 optimal weight: 40.0000 chunk 403 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 121 optimal weight: 20.0000 chunk 438 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 450 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 46 ASN ** r 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.059813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.038243 restraints weight = 269389.676| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 1.71 r_work: 0.2584 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 67275 Z= 0.402 Angle : 0.702 14.362 97570 Z= 0.364 Chirality : 0.044 0.443 11997 Planarity : 0.005 0.067 7195 Dihedral : 21.045 178.709 26426 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.76 % Favored : 96.04 % Rotamer: Outliers : 1.45 % Allowed : 16.40 % Favored : 82.15 % 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: 0.25 (0.13), residues: 4094 helix: 1.35 (0.14), residues: 1453 sheet: -0.04 (0.19), residues: 698 loop : -0.63 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V 67 HIS 0.011 0.001 HIS p 232 PHE 0.022 0.002 PHE W 146 TYR 0.017 0.001 TYR d 89 ARG 0.018 0.001 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13996.65 seconds wall clock time: 245 minutes 39.39 seconds (14739.39 seconds total)