Starting phenix.real_space_refine on Mon Mar 25 16:16:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls6_23503/03_2024/7ls6_23503.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls6_23503/03_2024/7ls6_23503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls6_23503/03_2024/7ls6_23503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls6_23503/03_2024/7ls6_23503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls6_23503/03_2024/7ls6_23503.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls6_23503/03_2024/7ls6_23503.pdb" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.071 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 S 92 5.16 5 C 15964 2.51 5 N 4206 2.21 5 O 4835 1.98 5 H 25006 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50103 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3852 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 234} Chain: "B" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 3791 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "C" Number of atoms: 3676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3676 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 1 Chain: "D" Number of atoms: 3700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3700 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224} Chain: "E" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 3827 Classifications: {'peptide': 249} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 244} Chain: "F" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3614 Classifications: {'peptide': 234} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain: "G" Number of atoms: 3795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3795 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 9, 'TRANS': 235} Chain: "H" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1875 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 111} Chain breaks: 1 Chain: "I" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3101 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 3 Chain: "J" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2699 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 2 Chain: "K" Number of atoms: 3066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3066 Classifications: {'peptide': 191} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "O" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 3768 Classifications: {'peptide': 240} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 221} Chain breaks: 1 Chain: "P" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4133 Classifications: {'peptide': 257} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Chain: "L" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2723 Classifications: {'peptide': 177} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Chain: "M" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2483 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 3, 'TRANS': 156} Chain breaks: 3 Time building chain proxies: 20.18, per 1000 atoms: 0.40 Number of scatterers: 50103 At special positions: 0 Unit cell: (147.34, 131.44, 139.92, 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 92 16.00 O 4835 8.00 N 4206 7.00 C 15964 6.00 H 25006 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.72 Conformation dependent library (CDL) restraints added in 5.4 seconds 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5942 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 27 sheets defined 41.6% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.576A pdb=" N ALA A 31 " --> pdb=" O GLN A 27 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 109 Processing helix chain 'A' and resid 113 through 131 removed outlier: 3.639A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.516A pdb=" N ILE A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 215 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 237 through 251 Processing helix chain 'B' and resid 18 through 30 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 78 through 96 removed outlier: 3.563A pdb=" N LYS B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.964A pdb=" N ALA B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 184 through 199 removed outlier: 3.909A pdb=" N SER B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 249 removed outlier: 4.128A pdb=" N ALA B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.562A pdb=" N ALA C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 103 removed outlier: 3.642A pdb=" N ILE C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 125 removed outlier: 3.583A pdb=" N THR C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 removed outlier: 3.647A pdb=" N ALA C 172 " --> pdb=" O ASN C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 201 removed outlier: 4.164A pdb=" N GLU C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 231 through 242 removed outlier: 3.535A pdb=" N VAL C 240 " --> pdb=" O LYS C 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 78 through 100 removed outlier: 3.644A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 87 " --> pdb=" O ARG D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 187 through 201 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 226 through 238 removed outlier: 3.973A pdb=" N ASN D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 20 removed outlier: 4.174A pdb=" N ARG E 20 " --> pdb=" O PRO E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.605A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 removed outlier: 3.663A pdb=" N ILE E 64 " --> pdb=" O SER E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 104 removed outlier: 3.884A pdb=" N SER E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 122 through 124 No H-bonds generated for 'chain 'E' and resid 122 through 124' Processing helix chain 'E' and resid 175 through 187 removed outlier: 3.528A pdb=" N ASN E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 208 removed outlier: 3.697A pdb=" N LEU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 248 Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.825A pdb=" N TYR F 6 " --> pdb=" O PHE F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 28 removed outlier: 3.684A pdb=" N ALA F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 32 Processing helix chain 'F' and resid 77 through 99 Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.509A pdb=" N HIS F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 175 removed outlier: 4.486A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 removed outlier: 3.614A pdb=" N ILE F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 183 No H-bonds generated for 'chain 'F' and resid 181 through 183' Processing helix chain 'F' and resid 185 through 199 Processing helix chain 'F' and resid 228 through 231 Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.870A pdb=" N GLU G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU G 32 " --> pdb=" O VAL G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.797A pdb=" N HIS G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 183 Processing helix chain 'G' and resid 188 through 205 removed outlier: 3.672A pdb=" N GLU G 205 " --> pdb=" O TYR G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 233 through 245 removed outlier: 3.600A pdb=" N LYS G 245 " --> pdb=" O ASP G 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 48 Processing helix chain 'H' and resid 53 through 58 Processing helix chain 'H' and resid 59 through 77 Processing helix chain 'H' and resid 78 through 95 Processing helix chain 'H' and resid 104 through 111 removed outlier: 3.523A pdb=" N ASP H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 123 Processing helix chain 'H' and resid 137 through 147 removed outlier: 3.840A pdb=" N LYS H 141 " --> pdb=" O ASP H 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 18 Processing helix chain 'I' and resid 77 through 100 removed outlier: 3.800A pdb=" N GLN I 86 " --> pdb=" O GLU I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 119 removed outlier: 3.549A pdb=" N ALA I 108 " --> pdb=" O ARG I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 146 No H-bonds generated for 'chain 'I' and resid 144 through 146' Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.597A pdb=" N ALA I 163 " --> pdb=" O GLY I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 191 Processing helix chain 'J' and resid 56 through 79 Processing helix chain 'J' and resid 83 through 97 Processing helix chain 'J' and resid 142 through 154 Processing helix chain 'J' and resid 159 through 173 Processing helix chain 'K' and resid 51 through 72 Processing helix chain 'K' and resid 76 through 95 removed outlier: 4.255A pdb=" N SER K 94 " --> pdb=" O LYS K 90 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG K 95 " --> pdb=" O SER K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 148 removed outlier: 4.797A pdb=" N TYR K 139 " --> pdb=" O TYR K 135 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N HIS K 146 " --> pdb=" O SER K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 172 removed outlier: 3.559A pdb=" N LYS K 170 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 47 Processing helix chain 'O' and resid 54 through 61 Proline residue: O 59 - end of helix Processing helix chain 'O' and resid 143 through 159 removed outlier: 3.922A pdb=" N GLY O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 206 Processing helix chain 'O' and resid 231 through 247 removed outlier: 4.308A pdb=" N GLN O 244 " --> pdb=" O ASP O 240 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP O 245 " --> pdb=" O LEU O 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 249 through 262 removed outlier: 3.685A pdb=" N LEU O 260 " --> pdb=" O GLU O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 275 removed outlier: 3.850A pdb=" N TYR O 275 " --> pdb=" O GLN O 271 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 13 through 26 Processing helix chain 'P' and resid 37 through 41 removed outlier: 4.648A pdb=" N TYR P 40 " --> pdb=" O ASP P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 93 No H-bonds generated for 'chain 'P' and resid 91 through 93' Processing helix chain 'P' and resid 94 through 102 removed outlier: 3.740A pdb=" N ILE P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 111 Processing helix chain 'P' and resid 124 through 126 No H-bonds generated for 'chain 'P' and resid 124 through 126' Processing helix chain 'P' and resid 146 through 148 No H-bonds generated for 'chain 'P' and resid 146 through 148' Processing helix chain 'P' and resid 151 through 159 removed outlier: 4.512A pdb=" N LEU P 157 " --> pdb=" O SER P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 191 Processing helix chain 'P' and resid 217 through 231 Processing helix chain 'P' and resid 246 through 254 removed outlier: 3.690A pdb=" N GLY P 251 " --> pdb=" O SER P 248 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR P 253 " --> pdb=" O GLN P 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 10 removed outlier: 4.275A pdb=" N VAL L 10 " --> pdb=" O ASP L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 146 removed outlier: 3.978A pdb=" N THR L 132 " --> pdb=" O GLN L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 165 removed outlier: 3.530A pdb=" N TYR L 165 " --> pdb=" O LEU L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 216 removed outlier: 3.594A pdb=" N ALA L 211 " --> pdb=" O GLY L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 242 Processing helix chain 'M' and resid 76 through 98 Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'M' and resid 161 through 171 Proline residue: M 167 - end of helix Processing helix chain 'M' and resid 195 through 207 removed outlier: 3.659A pdb=" N ILE M 200 " --> pdb=" O VAL M 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 removed outlier: 4.640A pdb=" N VAL A 225 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 74 removed outlier: 3.591A pdb=" N VAL A 82 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 154 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.688A pdb=" N GLY B 42 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.501A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 133 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'C' and resid 162 through 165 Processing sheet with id=AA7, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.687A pdb=" N LEU C 69 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP C 141 " --> pdb=" O GLY C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 161 through 164 Processing sheet with id=AA9, first strand: chain 'D' and resid 65 through 66 removed outlier: 3.613A pdb=" N SER D 65 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.707A pdb=" N VAL E 46 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN E 218 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS E 221 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.399A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.532A pdb=" N MET F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY F 136 " --> pdb=" O HIS F 143 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR F 154 " --> pdb=" O GLU F 146 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN F 152 " --> pdb=" O GLN F 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.694A pdb=" N LYS G 229 " --> pdb=" O TRP G 218 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 68 through 71 removed outlier: 5.033A pdb=" N VAL G 69 " --> pdb=" O CYS G 76 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS G 76 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET G 150 " --> pdb=" O TRP G 158 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP G 158 " --> pdb=" O MET G 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 63 through 67 removed outlier: 6.371A pdb=" N ILE I 70 " --> pdb=" O ILE I 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 243 through 247 removed outlier: 3.795A pdb=" N LYS I 243 " --> pdb=" O TYR J 199 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL I 247 " --> pdb=" O VAL J 195 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL J 195 " --> pdb=" O VAL I 247 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA J 185 " --> pdb=" O LEU J 200 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 43 through 45 Processing sheet with id=AC1, first strand: chain 'K' and resid 130 through 132 Processing sheet with id=AC2, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.637A pdb=" N THR K 42 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU K 116 " --> pdb=" O LEU K 128 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 35 through 37 removed outlier: 5.432A pdb=" N SER O 70 " --> pdb=" O SER O 126 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER O 126 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY O 72 " --> pdb=" O ILE O 124 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER O 134 " --> pdb=" O PRO O 123 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR O 49 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N PHE O 133 " --> pdb=" O THR O 49 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL O 51 " --> pdb=" O PHE O 133 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA O 50 " --> pdb=" O ILE O 166 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE O 168 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE O 52 " --> pdb=" O ILE O 168 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N THR O 170 " --> pdb=" O ILE O 52 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE O 165 " --> pdb=" O LYS O 215 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU O 217 " --> pdb=" O ILE O 165 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL O 167 " --> pdb=" O LEU O 217 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ALA O 219 " --> pdb=" O VAL O 167 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY O 169 " --> pdb=" O ALA O 219 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 193 through 194 Processing sheet with id=AC5, first strand: chain 'P' and resid 30 through 35 removed outlier: 6.938A pdb=" N VAL P 72 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALA P 35 " --> pdb=" O LEU P 70 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU P 70 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N CYS P 3 " --> pdb=" O PHE P 81 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE P 83 " --> pdb=" O CYS P 3 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL P 5 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLN P 85 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU P 4 " --> pdb=" O CYS P 116 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TRP P 118 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU P 6 " --> pdb=" O TRP P 118 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N SER P 120 " --> pdb=" O LEU P 6 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 201 through 204 removed outlier: 3.518A pdb=" N ASN L 251 " --> pdb=" O VAL L 91 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 110 through 111 removed outlier: 4.200A pdb=" N ILE L 187 " --> pdb=" O GLY L 199 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 155 through 159 Processing sheet with id=AC9, first strand: chain 'M' and resid 63 through 64 removed outlier: 4.001A pdb=" N VAL M 141 " --> pdb=" O GLU M 153 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU M 151 " --> pdb=" O SER M 143 " (cutoff:3.500A) 1324 hydrogen bonds defined for protein. 3765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.88 Time building geometry restraints manager: 42.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 24966 1.03 - 1.23: 46 1.23 - 1.42: 10649 1.42 - 1.62: 14769 1.62 - 1.81: 144 Bond restraints: 50574 Sorted by residual: bond pdb=" ND1 HIS A 15 " pdb=" HD1 HIS A 15 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" ND1 HIS L 241 " pdb=" HD1 HIS L 241 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.62e+01 bond pdb=" N GLY M 29 " pdb=" CA GLY M 29 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.05e+00 bond pdb=" N TYR D 4 " pdb=" CA TYR D 4 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" N THR G 2 " pdb=" CA THR G 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 50569 not shown) Histogram of bond angle deviations from ideal: 74.75 - 86.63: 3 86.63 - 98.50: 0 98.50 - 110.38: 50679 110.38 - 122.26: 33280 122.26 - 134.13: 7449 Bond angle restraints: 91411 Sorted by residual: angle pdb=" N ALA P 69 " pdb=" CA ALA P 69 " pdb=" HA ALA P 69 " ideal model delta sigma weight residual 110.00 75.00 35.00 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C ALA P 69 " pdb=" CA ALA P 69 " pdb=" HA ALA P 69 " ideal model delta sigma weight residual 109.00 74.75 34.25 3.00e+00 1.11e-01 1.30e+02 angle pdb=" CB ALA P 69 " pdb=" CA ALA P 69 " pdb=" HA ALA P 69 " ideal model delta sigma weight residual 109.00 75.28 33.72 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C GLN I 173 " pdb=" N ASP I 174 " pdb=" CA ASP I 174 " ideal model delta sigma weight residual 121.54 133.45 -11.91 1.91e+00 2.74e-01 3.89e+01 angle pdb=" CA ARG E 122 " pdb=" C ARG E 122 " pdb=" N PHE E 123 " ideal model delta sigma weight residual 118.43 125.01 -6.58 1.33e+00 5.65e-01 2.45e+01 ... (remaining 91406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 21847 17.93 - 35.85: 1418 35.85 - 53.78: 369 53.78 - 71.71: 100 71.71 - 89.63: 28 Dihedral angle restraints: 23762 sinusoidal: 12928 harmonic: 10834 Sorted by residual: dihedral pdb=" CA MET L 172 " pdb=" C MET L 172 " pdb=" N GLY L 173 " pdb=" CA GLY L 173 " ideal model delta harmonic sigma weight residual 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA LEU I 4 " pdb=" C LEU I 4 " pdb=" N SER I 5 " pdb=" CA SER I 5 " ideal model delta harmonic sigma weight residual -180.00 -155.67 -24.33 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PRO P 238 " pdb=" C PRO P 238 " pdb=" N PRO P 239 " pdb=" CA PRO P 239 " ideal model delta harmonic sigma weight residual 0.00 -21.72 21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 23759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3507 0.069 - 0.138: 390 0.138 - 0.207: 5 0.207 - 0.276: 0 0.276 - 0.346: 1 Chirality restraints: 3903 Sorted by residual: chirality pdb=" CA ALA P 69 " pdb=" N ALA P 69 " pdb=" C ALA P 69 " pdb=" CB ALA P 69 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA ASN O 58 " pdb=" N ASN O 58 " pdb=" C ASN O 58 " pdb=" CB ASN O 58 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA VAL H 41 " pdb=" N VAL H 41 " pdb=" C VAL H 41 " pdb=" CB VAL H 41 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.57e-01 ... (remaining 3900 not shown) Planarity restraints: 7503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 99 " -0.241 9.50e-02 1.11e+02 8.08e-02 7.75e+00 pdb=" NE ARG B 99 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 99 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 99 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 99 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 99 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 99 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG B 99 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG B 99 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 106 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO J 107 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 107 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 107 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA P 237 " 0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO P 238 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO P 238 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO P 238 " 0.024 5.00e-02 4.00e+02 ... (remaining 7500 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 871 2.09 - 2.71: 85637 2.71 - 3.34: 149529 3.34 - 3.97: 190907 3.97 - 4.60: 304415 Nonbonded interactions: 731359 Sorted by model distance: nonbonded pdb=" H SER M 195 " pdb=" OE2 GLU M 198 " model vdw 1.458 1.850 nonbonded pdb=" OD2 ASP G 84 " pdb="HH12 ARG G 130 " model vdw 1.583 1.850 nonbonded pdb=" O LEU P 189 " pdb=" H LEU P 193 " model vdw 1.591 1.850 nonbonded pdb=" HG1 THR E 36 " pdb=" O SER E 174 " model vdw 1.591 1.850 nonbonded pdb=" OE1 GLN M 154 " pdb=" H GLN M 154 " model vdw 1.603 1.850 ... (remaining 731354 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 0.720 Extract box with map and model: 12.390 Check model and map are aligned: 0.680 Set scattering table: 0.390 Process input model: 151.520 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.003 0.079 25568 Z= 0.174 Angle : 0.545 11.906 34577 Z= 0.311 Chirality : 0.041 0.346 3903 Planarity : 0.004 0.107 4438 Dihedral : 13.118 89.634 9408 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 0.90 (0.15), residues: 3148 helix: 1.52 (0.16), residues: 1144 sheet: -0.02 (0.18), residues: 739 loop : 0.28 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 130 HIS 0.012 0.001 HIS M 98 PHE 0.021 0.001 PHE L 115 TYR 0.017 0.001 TYR M 94 ARG 0.013 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 3.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6826 (mt-10) REVERT: L 195 THR cc_start: 0.7779 (m) cc_final: 0.7530 (m) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.8476 time to fit residues: 449.4698 Evaluate side-chains 247 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 HIS F 91 GLN K 63 ASN M 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 25568 Z= 0.360 Angle : 0.578 6.672 34577 Z= 0.318 Chirality : 0.044 0.336 3903 Planarity : 0.004 0.066 4438 Dihedral : 4.958 25.474 3456 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.10 % Allowed : 4.62 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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 (0.15), residues: 3148 helix: 1.45 (0.15), residues: 1165 sheet: -0.28 (0.18), residues: 754 loop : 0.03 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 159 HIS 0.012 0.001 HIS M 98 PHE 0.017 0.002 PHE F 179 TYR 0.017 0.001 TYR J 69 ARG 0.010 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 261 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6946 (mt-10) REVERT: L 195 THR cc_start: 0.8019 (m) cc_final: 0.7763 (m) outliers start: 30 outliers final: 28 residues processed: 282 average time/residue: 0.8639 time to fit residues: 390.1171 Evaluate side-chains 266 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 238 time to evaluate : 3.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 135 ASP Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain O residue 172 ASP Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 111 ASN Chi-restraints excluded: chain M residue 198 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 308 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 HIS D 167 ASN K 112 ASN K 166 GLN M 111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 25568 Z= 0.448 Angle : 0.588 6.672 34577 Z= 0.323 Chirality : 0.045 0.330 3903 Planarity : 0.004 0.070 4438 Dihedral : 5.036 24.489 3456 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.47 % Allowed : 6.30 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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 (0.15), residues: 3148 helix: 1.32 (0.15), residues: 1170 sheet: -0.46 (0.18), residues: 754 loop : -0.18 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 159 HIS 0.009 0.001 HIS H 139 PHE 0.020 0.002 PHE P 44 TYR 0.018 0.001 TYR J 69 ARG 0.012 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 245 time to evaluate : 3.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7068 (mt-10) outliers start: 40 outliers final: 35 residues processed: 276 average time/residue: 0.8436 time to fit residues: 367.9873 Evaluate side-chains 268 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 233 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 214 GLU Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 135 ASP Chi-restraints excluded: chain J residue 157 ASN Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 166 GLN Chi-restraints excluded: chain O residue 172 ASP Chi-restraints excluded: chain L residue 115 PHE Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 155 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 286 optimal weight: 0.8980 chunk 303 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 chunk 271 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25568 Z= 0.246 Angle : 0.521 6.428 34577 Z= 0.283 Chirality : 0.042 0.325 3903 Planarity : 0.004 0.065 4438 Dihedral : 4.850 24.238 3456 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.25 % Allowed : 7.51 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 0.53 (0.15), residues: 3148 helix: 1.52 (0.15), residues: 1166 sheet: -0.48 (0.18), residues: 743 loop : -0.09 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.006 0.001 HIS H 139 PHE 0.018 0.001 PHE P 44 TYR 0.014 0.001 TYR J 69 ARG 0.005 0.000 ARG M 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 249 time to evaluate : 3.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6997 (mt-10) REVERT: E 208 MET cc_start: 0.8362 (ttp) cc_final: 0.8009 (mtm) REVERT: H 89 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7001 (mm-30) outliers start: 34 outliers final: 30 residues processed: 274 average time/residue: 0.8113 time to fit residues: 354.9979 Evaluate side-chains 265 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 235 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 135 ASP Chi-restraints excluded: chain J residue 157 ASN Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain O residue 172 ASP Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain M residue 34 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 25568 Z= 0.363 Angle : 0.549 6.517 34577 Z= 0.299 Chirality : 0.043 0.328 3903 Planarity : 0.004 0.059 4438 Dihedral : 4.851 24.601 3456 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.76 % Allowed : 7.69 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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 (0.15), residues: 3148 helix: 1.52 (0.15), residues: 1163 sheet: -0.61 (0.18), residues: 739 loop : -0.21 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 130 HIS 0.007 0.001 HIS M 98 PHE 0.017 0.001 PHE P 44 TYR 0.017 0.001 TYR J 69 ARG 0.007 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 241 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 9 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: H 66 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7226 (tm-30) REVERT: H 89 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7047 (mm-30) REVERT: L 172 MET cc_start: 0.6969 (mmt) cc_final: 0.6036 (mmt) outliers start: 48 outliers final: 37 residues processed: 276 average time/residue: 0.8695 time to fit residues: 387.4821 Evaluate side-chains 271 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 233 time to evaluate : 4.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 135 ASP Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain O residue 172 ASP Chi-restraints excluded: chain L residue 115 PHE Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 155 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 303 optimal weight: 5.9990 chunk 252 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25568 Z= 0.272 Angle : 0.520 6.431 34577 Z= 0.281 Chirality : 0.042 0.327 3903 Planarity : 0.004 0.053 4438 Dihedral : 4.765 24.163 3456 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.50 % Allowed : 8.50 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 0.50 (0.15), residues: 3148 helix: 1.64 (0.15), residues: 1162 sheet: -0.63 (0.18), residues: 739 loop : -0.17 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 158 HIS 0.005 0.001 HIS M 98 PHE 0.032 0.001 PHE O 161 TYR 0.014 0.001 TYR J 69 ARG 0.005 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 239 time to evaluate : 3.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 9 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7993 (m-30) REVERT: H 89 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7016 (mm-30) REVERT: I 179 GLU cc_start: 0.8097 (mp0) cc_final: 0.7632 (mp0) REVERT: L 145 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8164 (mm-30) outliers start: 41 outliers final: 40 residues processed: 269 average time/residue: 0.8313 time to fit residues: 360.1284 Evaluate side-chains 275 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 234 time to evaluate : 4.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 214 GLU Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 135 ASP Chi-restraints excluded: chain J residue 157 ASN Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain O residue 172 ASP Chi-restraints excluded: chain L residue 115 PHE Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 198 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 chunk 169 optimal weight: 0.0770 chunk 302 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25568 Z= 0.166 Angle : 0.490 6.194 34577 Z= 0.263 Chirality : 0.042 0.323 3903 Planarity : 0.004 0.054 4438 Dihedral : 4.603 23.446 3456 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.21 % Allowed : 8.97 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 0.71 (0.15), residues: 3148 helix: 1.81 (0.15), residues: 1164 sheet: -0.56 (0.18), residues: 741 loop : -0.02 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 260 HIS 0.005 0.001 HIS M 98 PHE 0.018 0.001 PHE O 161 TYR 0.012 0.001 TYR J 69 ARG 0.004 0.000 ARG L 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 252 time to evaluate : 3.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 89 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6989 (mm-30) REVERT: H 121 ASP cc_start: 0.7862 (m-30) cc_final: 0.7622 (m-30) REVERT: I 179 GLU cc_start: 0.8066 (mp0) cc_final: 0.7603 (mp0) outliers start: 33 outliers final: 30 residues processed: 271 average time/residue: 0.7919 time to fit residues: 345.5151 Evaluate side-chains 270 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 3.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 135 ASP Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain O residue 172 ASP Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain L residue 237 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 198 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 149 optimal weight: 0.0070 chunk 28 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25568 Z= 0.185 Angle : 0.487 6.245 34577 Z= 0.261 Chirality : 0.041 0.324 3903 Planarity : 0.004 0.052 4438 Dihedral : 4.491 22.723 3456 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.25 % Allowed : 9.38 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 0.81 (0.15), residues: 3148 helix: 1.91 (0.16), residues: 1165 sheet: -0.54 (0.18), residues: 725 loop : 0.03 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 260 HIS 0.005 0.001 HIS M 98 PHE 0.018 0.001 PHE O 161 TYR 0.016 0.001 TYR M 236 ARG 0.003 0.000 ARG L 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 249 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 9 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: H 89 GLU cc_start: 0.7238 (mm-30) cc_final: 0.7004 (mm-30) REVERT: H 121 ASP cc_start: 0.7806 (m-30) cc_final: 0.7511 (m-30) REVERT: I 179 GLU cc_start: 0.8046 (mp0) cc_final: 0.7579 (mp0) outliers start: 34 outliers final: 31 residues processed: 272 average time/residue: 0.8217 time to fit residues: 360.8641 Evaluate side-chains 275 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 243 time to evaluate : 3.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 214 GLU Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 135 ASP Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain O residue 172 ASP Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 198 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 0.9980 chunk 289 optimal weight: 2.9990 chunk 264 optimal weight: 0.8980 chunk 282 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 221 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 266 optimal weight: 0.7980 chunk 281 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25568 Z= 0.171 Angle : 0.476 6.191 34577 Z= 0.254 Chirality : 0.041 0.324 3903 Planarity : 0.004 0.053 4438 Dihedral : 4.392 22.101 3456 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.14 % Allowed : 9.49 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 0.94 (0.15), residues: 3148 helix: 2.02 (0.16), residues: 1164 sheet: -0.43 (0.18), residues: 718 loop : 0.06 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 260 HIS 0.005 0.001 HIS M 98 PHE 0.014 0.001 PHE O 161 TYR 0.012 0.001 TYR J 69 ARG 0.006 0.000 ARG L 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 251 time to evaluate : 3.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 89 GLU cc_start: 0.7244 (mm-30) cc_final: 0.7022 (mm-30) REVERT: H 121 ASP cc_start: 0.7794 (m-30) cc_final: 0.7494 (m-30) REVERT: I 179 GLU cc_start: 0.8040 (mp0) cc_final: 0.7575 (mp0) outliers start: 31 outliers final: 28 residues processed: 271 average time/residue: 0.8357 time to fit residues: 363.8613 Evaluate side-chains 271 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 243 time to evaluate : 4.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 135 ASP Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 198 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 312 optimal weight: 10.0000 chunk 287 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25568 Z= 0.283 Angle : 0.510 6.420 34577 Z= 0.274 Chirality : 0.042 0.327 3903 Planarity : 0.004 0.064 4438 Dihedral : 4.465 22.771 3456 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.25 % Allowed : 9.74 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 0.80 (0.15), residues: 3148 helix: 1.94 (0.16), residues: 1165 sheet: -0.57 (0.18), residues: 725 loop : 0.00 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 260 HIS 0.005 0.001 HIS M 98 PHE 0.015 0.001 PHE O 161 TYR 0.013 0.001 TYR J 69 ARG 0.010 0.000 ARG L 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 239 time to evaluate : 4.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 GLN cc_start: 0.7515 (tm-30) cc_final: 0.7166 (tm-30) REVERT: H 89 GLU cc_start: 0.7267 (mm-30) cc_final: 0.7023 (mm-30) REVERT: H 121 ASP cc_start: 0.7866 (m-30) cc_final: 0.7605 (m-30) REVERT: I 179 GLU cc_start: 0.8069 (mp0) cc_final: 0.7618 (mp0) REVERT: L 172 MET cc_start: 0.6694 (mmt) cc_final: 0.6121 (mmt) outliers start: 34 outliers final: 33 residues processed: 264 average time/residue: 0.8665 time to fit residues: 368.7635 Evaluate side-chains 265 residues out of total 2730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 232 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 135 ASP Chi-restraints excluded: chain J residue 157 ASN Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain O residue 172 ASP Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 198 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 1.9990 chunk 265 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 229 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.118189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.093920 restraints weight = 115631.888| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.36 r_work: 0.3210 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25568 Z= 0.173 Angle : 0.479 6.208 34577 Z= 0.255 Chirality : 0.041 0.325 3903 Planarity : 0.004 0.059 4438 Dihedral : 4.380 22.240 3456 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.06 % Allowed : 9.85 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: 0.95 (0.15), residues: 3148 helix: 2.06 (0.16), residues: 1164 sheet: -0.44 (0.18), residues: 718 loop : 0.06 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 260 HIS 0.005 0.001 HIS M 98 PHE 0.015 0.001 PHE P 44 TYR 0.013 0.001 TYR M 236 ARG 0.008 0.000 ARG L 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10170.52 seconds wall clock time: 180 minutes 45.69 seconds (10845.69 seconds total)