Starting phenix.real_space_refine on Tue Sep 24 07:11:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/09_2024/6h3c_0132.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/09_2024/6h3c_0132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/09_2024/6h3c_0132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/09_2024/6h3c_0132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/09_2024/6h3c_0132.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3c_0132/09_2024/6h3c_0132.cif" } resolution = 3.9 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= 0.003 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 136 5.16 5 C 15942 2.51 5 N 4334 2.21 5 O 4708 1.98 5 H 24860 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 49982 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4134 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 5, 'TRANS': 249} Chain: "B" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4122 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 2 Chain: "C" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6077 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 354} Chain: "D" Number of atoms: 3761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3761 Classifications: {'peptide': 237} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 220} Chain: "F" Number of atoms: 4134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4134 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 5, 'TRANS': 249} Chain: "G" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4122 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 2 Chain: "H" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6077 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 354} Chain: "I" Number of atoms: 3761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3761 Classifications: {'peptide': 237} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 220} Chain: "E" Number of atoms: 6893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6893 Classifications: {'peptide': 440} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 417} Chain breaks: 1 Chain: "J" Number of atoms: 6893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6893 Classifications: {'peptide': 440} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 417} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 17.47, per 1000 atoms: 0.35 Number of scatterers: 49982 At special positions: 0 Unit cell: (165.98, 181.46, 149.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 136 16.00 O 4708 8.00 N 4334 7.00 C 15942 6.00 H 24860 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 - 3.00 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: 9.76 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 122 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 124 " pdb=" ZN G 401 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 122 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 124 " 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5980 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 24 sheets defined 45.7% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 removed outlier: 3.504A pdb=" N ASN A 19 " --> pdb=" O PHE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.543A pdb=" N ARG A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 182 through 192 removed outlier: 3.526A pdb=" N LYS A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 203 through 255 removed outlier: 3.613A pdb=" N ARG A 207 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 93 through 112 Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 234 through 252 removed outlier: 3.521A pdb=" N CYS B 240 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 279 Processing helix chain 'B' and resid 279 through 316 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 14 through 24 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 112 through 133 removed outlier: 3.537A pdb=" N ARG C 131 " --> pdb=" O PHE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 4.017A pdb=" N THR C 144 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 154 removed outlier: 3.575A pdb=" N GLU C 153 " --> pdb=" O GLN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 231 through 234 Processing helix chain 'C' and resid 245 through 280 Proline residue: C 251 - end of helix removed outlier: 5.109A pdb=" N HIS C 255 " --> pdb=" O PRO C 251 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU C 273 " --> pdb=" O HIS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 377 Proline residue: C 371 - end of helix Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 119 through 135 Processing helix chain 'D' and resid 162 through 171 removed outlier: 3.686A pdb=" N LEU D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR D 171 " --> pdb=" O CYS D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 192 Processing helix chain 'D' and resid 229 through 238 removed outlier: 5.620A pdb=" N MET D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.604A pdb=" N GLU D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 269 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 287 through 292 Processing helix chain 'D' and resid 292 through 299 Processing helix chain 'D' and resid 307 through 311 Processing helix chain 'F' and resid 6 through 19 removed outlier: 3.503A pdb=" N ASN F 19 " --> pdb=" O PHE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 106 through 120 removed outlier: 3.544A pdb=" N ARG F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 168 Processing helix chain 'F' and resid 182 through 192 removed outlier: 3.526A pdb=" N LYS F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 196 Processing helix chain 'F' and resid 203 through 255 removed outlier: 3.614A pdb=" N ARG F 207 " --> pdb=" O MET F 203 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR F 213 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU F 216 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 27 Processing helix chain 'G' and resid 93 through 112 Processing helix chain 'G' and resid 132 through 146 Processing helix chain 'G' and resid 225 through 232 Processing helix chain 'G' and resid 234 through 252 removed outlier: 3.521A pdb=" N CYS G 240 " --> pdb=" O PRO G 236 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU G 243 " --> pdb=" O LEU G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 279 Processing helix chain 'G' and resid 279 through 316 Processing helix chain 'H' and resid 2 through 9 Processing helix chain 'H' and resid 14 through 24 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 99 through 104 Processing helix chain 'H' and resid 109 through 111 No H-bonds generated for 'chain 'H' and resid 109 through 111' Processing helix chain 'H' and resid 112 through 133 removed outlier: 3.538A pdb=" N ARG H 131 " --> pdb=" O PHE H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 147 removed outlier: 4.018A pdb=" N THR H 144 " --> pdb=" O PHE H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 154 removed outlier: 3.576A pdb=" N GLU H 153 " --> pdb=" O GLN H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 230 Processing helix chain 'H' and resid 231 through 234 Processing helix chain 'H' and resid 245 through 280 Proline residue: H 251 - end of helix removed outlier: 5.110A pdb=" N HIS H 255 " --> pdb=" O PRO H 251 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU H 273 " --> pdb=" O HIS H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 377 Proline residue: H 371 - end of helix Processing helix chain 'I' and resid 102 through 107 Processing helix chain 'I' and resid 119 through 135 Processing helix chain 'I' and resid 162 through 171 removed outlier: 3.687A pdb=" N LEU I 166 " --> pdb=" O ASP I 162 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR I 171 " --> pdb=" O CYS I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 192 Processing helix chain 'I' and resid 229 through 238 removed outlier: 5.620A pdb=" N MET I 235 " --> pdb=" O PRO I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 255 removed outlier: 3.604A pdb=" N GLU I 254 " --> pdb=" O ASN I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 269 Processing helix chain 'I' and resid 270 through 272 No H-bonds generated for 'chain 'I' and resid 270 through 272' Processing helix chain 'I' and resid 287 through 292 Processing helix chain 'I' and resid 292 through 299 Processing helix chain 'I' and resid 307 through 311 Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 32 through 48 Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 69 through 74 Processing helix chain 'E' and resid 88 through 105 removed outlier: 3.770A pdb=" N LEU E 103 " --> pdb=" O GLN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 134 Processing helix chain 'E' and resid 184 through 196 Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 234 through 240 Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 296 through 298 No H-bonds generated for 'chain 'E' and resid 296 through 298' Processing helix chain 'E' and resid 307 through 322 Processing helix chain 'E' and resid 323 through 347 Processing helix chain 'E' and resid 353 through 355 No H-bonds generated for 'chain 'E' and resid 353 through 355' Processing helix chain 'E' and resid 366 through 369 Processing helix chain 'E' and resid 371 through 381 removed outlier: 4.645A pdb=" N ARG E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 416 through 439 removed outlier: 3.585A pdb=" N ILE E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 454 removed outlier: 4.307A pdb=" N SER E 449 " --> pdb=" O GLN E 445 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU E 452 " --> pdb=" O LYS E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 473 Processing helix chain 'J' and resid 27 through 32 Processing helix chain 'J' and resid 32 through 48 Processing helix chain 'J' and resid 60 through 68 Processing helix chain 'J' and resid 69 through 74 Processing helix chain 'J' and resid 88 through 105 removed outlier: 3.770A pdb=" N LEU J 103 " --> pdb=" O GLN J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 134 Processing helix chain 'J' and resid 184 through 196 Processing helix chain 'J' and resid 212 through 223 Processing helix chain 'J' and resid 234 through 240 Processing helix chain 'J' and resid 245 through 249 Processing helix chain 'J' and resid 290 through 295 Processing helix chain 'J' and resid 296 through 298 No H-bonds generated for 'chain 'J' and resid 296 through 298' Processing helix chain 'J' and resid 307 through 322 Processing helix chain 'J' and resid 323 through 347 Processing helix chain 'J' and resid 353 through 355 No H-bonds generated for 'chain 'J' and resid 353 through 355' Processing helix chain 'J' and resid 366 through 369 Processing helix chain 'J' and resid 371 through 381 removed outlier: 4.645A pdb=" N ARG J 377 " --> pdb=" O ALA J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 412 Processing helix chain 'J' and resid 416 through 439 removed outlier: 3.585A pdb=" N ILE J 433 " --> pdb=" O GLU J 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 454 removed outlier: 4.307A pdb=" N SER J 449 " --> pdb=" O GLN J 445 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU J 452 " --> pdb=" O LYS J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 157 removed outlier: 3.536A pdb=" N GLN A 156 " --> pdb=" O ARG A 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 161 removed outlier: 6.736A pdb=" N ALA A 3 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA A 2 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE A 56 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER A 4 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ASN A 58 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A 29 " --> pdb=" O HIS A 57 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS A 59 " --> pdb=" O PHE A 27 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE A 27 " --> pdb=" O HIS A 59 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU A 25 " --> pdb=" O PRO A 61 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP A 94 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N PHE A 130 " --> pdb=" O TRP A 94 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG A 96 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE A 132 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ARG A 98 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N SER A 134 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARG B 167 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE B 157 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL B 117 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLY B 40 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY B 119 " --> pdb=" O CYS B 38 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 37 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL B 77 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE B 39 " --> pdb=" O HIS B 75 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER B 76 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 12 " --> pdb=" O HIS B 217 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL B 219 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 14 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 70 removed outlier: 3.510A pdb=" N LYS A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 36 through 41 removed outlier: 4.755A pdb=" N LEU C 40 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARG C 55 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AA6, first strand: chain 'C' and resid 286 through 288 removed outlier: 6.778A pdb=" N THR C 298 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 297 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 325 " --> pdb=" O GLN C 344 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR C 340 " --> pdb=" O SER C 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 155 through 160 removed outlier: 4.310A pdb=" N GLY D 158 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE D 144 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 143 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS D 94 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL D 216 " --> pdb=" O CYS D 98 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N TYR D 280 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL D 245 " --> pdb=" O TYR D 280 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL D 282 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR D 247 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AA9, first strand: chain 'F' and resid 154 through 157 removed outlier: 3.537A pdb=" N GLN F 156 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 160 through 161 removed outlier: 6.735A pdb=" N ALA F 3 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 2 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE F 56 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER F 4 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ASN F 58 " --> pdb=" O SER F 4 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU F 29 " --> pdb=" O HIS F 57 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS F 59 " --> pdb=" O PHE F 27 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE F 27 " --> pdb=" O HIS F 59 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU F 25 " --> pdb=" O PRO F 61 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP F 94 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE F 130 " --> pdb=" O TRP F 94 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG F 96 " --> pdb=" O PHE F 130 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE F 132 " --> pdb=" O ARG F 96 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ARG F 98 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N SER F 134 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG G 167 " --> pdb=" O PHE G 157 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE G 157 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL G 117 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLY G 40 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY G 119 " --> pdb=" O CYS G 38 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU G 37 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL G 77 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE G 39 " --> pdb=" O HIS G 75 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER G 76 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL G 12 " --> pdb=" O HIS G 217 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL G 219 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU G 14 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 69 through 70 removed outlier: 3.510A pdb=" N LYS F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 36 through 41 removed outlier: 4.754A pdb=" N LEU H 40 " --> pdb=" O ARG H 55 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ARG H 55 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 156 through 159 Processing sheet with id=AB5, first strand: chain 'H' and resid 286 through 288 removed outlier: 6.779A pdb=" N THR H 298 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU H 297 " --> pdb=" O ILE H 312 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 325 " --> pdb=" O GLN H 344 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR H 340 " --> pdb=" O SER H 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 155 through 160 removed outlier: 4.310A pdb=" N GLY I 158 " --> pdb=" O PHE I 144 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE I 144 " --> pdb=" O GLY I 158 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU I 143 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS I 94 " --> pdb=" O VAL I 210 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL I 216 " --> pdb=" O CYS I 98 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N TYR I 280 " --> pdb=" O PHE I 243 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL I 245 " --> pdb=" O TYR I 280 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL I 282 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR I 247 " --> pdb=" O VAL I 282 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 110 through 111 Processing sheet with id=AB8, first strand: chain 'E' and resid 50 through 51 removed outlier: 6.972A pdb=" N LEU E 50 " --> pdb=" O THR E 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 113 through 116 removed outlier: 6.408A pdb=" N LEU E 227 " --> pdb=" O ILE E 252 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR E 254 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA E 229 " --> pdb=" O THR E 254 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N THR E 256 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 275 through 278 Processing sheet with id=AC2, first strand: chain 'E' and resid 350 through 351 removed outlier: 4.021A pdb=" N SER E 350 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 50 through 51 removed outlier: 6.971A pdb=" N LEU J 50 " --> pdb=" O THR J 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'J' and resid 113 through 116 removed outlier: 6.408A pdb=" N LEU J 227 " --> pdb=" O ILE J 252 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR J 254 " --> pdb=" O LEU J 227 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA J 229 " --> pdb=" O THR J 254 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR J 256 " --> pdb=" O ALA J 229 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 275 through 278 Processing sheet with id=AC6, first strand: chain 'J' and resid 350 through 351 removed outlier: 4.020A pdb=" N SER J 350 " --> pdb=" O ASP J 364 " (cutoff:3.500A) 1249 hydrogen bonds defined for protein. 3507 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: 16.55 Time building geometry restraints manager: 12.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 24790 1.04 - 1.24: 4081 1.24 - 1.44: 7957 1.44 - 1.64: 13502 1.64 - 1.85: 202 Bond restraints: 50532 Sorted by residual: bond pdb=" CB HIS E 359 " pdb=" CG HIS E 359 " ideal model delta sigma weight residual 1.497 1.382 0.115 1.40e-02 5.10e+03 6.72e+01 bond pdb=" CB HIS J 359 " pdb=" CG HIS J 359 " ideal model delta sigma weight residual 1.497 1.382 0.115 1.40e-02 5.10e+03 6.72e+01 bond pdb=" CB HIS G 122 " pdb=" CG HIS G 122 " ideal model delta sigma weight residual 1.497 1.394 0.103 1.40e-02 5.10e+03 5.37e+01 bond pdb=" CB HIS B 122 " pdb=" CG HIS B 122 " ideal model delta sigma weight residual 1.497 1.395 0.102 1.40e-02 5.10e+03 5.28e+01 bond pdb=" CA PRO I 220 " pdb=" C PRO I 220 " ideal model delta sigma weight residual 1.514 1.551 -0.036 5.50e-03 3.31e+04 4.34e+01 ... (remaining 50527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 87702 3.05 - 6.10: 3148 6.10 - 9.15: 380 9.15 - 12.19: 32 12.19 - 15.24: 4 Bond angle restraints: 91266 Sorted by residual: angle pdb=" N GLU B 210 " pdb=" CA GLU B 210 " pdb=" C GLU B 210 " ideal model delta sigma weight residual 113.20 124.14 -10.94 1.21e+00 6.83e-01 8.17e+01 angle pdb=" N GLU G 210 " pdb=" CA GLU G 210 " pdb=" C GLU G 210 " ideal model delta sigma weight residual 113.20 124.12 -10.92 1.21e+00 6.83e-01 8.14e+01 angle pdb=" N SER H 42 " pdb=" CA SER H 42 " pdb=" C SER H 42 " ideal model delta sigma weight residual 111.71 121.91 -10.20 1.15e+00 7.56e-01 7.86e+01 angle pdb=" N SER C 42 " pdb=" CA SER C 42 " pdb=" C SER C 42 " ideal model delta sigma weight residual 111.71 121.90 -10.19 1.15e+00 7.56e-01 7.85e+01 angle pdb=" CA HIS I 249 " pdb=" CB HIS I 249 " pdb=" CG HIS I 249 " ideal model delta sigma weight residual 113.80 122.65 -8.85 1.00e+00 1.00e+00 7.84e+01 ... (remaining 91261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 22547 16.86 - 33.73: 903 33.73 - 50.59: 285 50.59 - 67.46: 119 67.46 - 84.32: 30 Dihedral angle restraints: 23884 sinusoidal: 13002 harmonic: 10882 Sorted by residual: dihedral pdb=" C TYR I 240 " pdb=" N TYR I 240 " pdb=" CA TYR I 240 " pdb=" CB TYR I 240 " ideal model delta harmonic sigma weight residual -122.60 -112.33 -10.27 0 2.50e+00 1.60e-01 1.69e+01 dihedral pdb=" C TYR D 240 " pdb=" N TYR D 240 " pdb=" CA TYR D 240 " pdb=" CB TYR D 240 " ideal model delta harmonic sigma weight residual -122.60 -112.35 -10.25 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" N PHE C 73 " pdb=" C PHE C 73 " pdb=" CA PHE C 73 " pdb=" CB PHE C 73 " ideal model delta harmonic sigma weight residual 122.80 132.23 -9.43 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 23881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2801 0.104 - 0.209: 868 0.209 - 0.313: 159 0.313 - 0.418: 10 0.418 - 0.522: 4 Chirality restraints: 3842 Sorted by residual: chirality pdb=" CA PHE C 73 " pdb=" N PHE C 73 " pdb=" C PHE C 73 " pdb=" CB PHE C 73 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" CA PHE H 73 " pdb=" N PHE H 73 " pdb=" C PHE H 73 " pdb=" CB PHE H 73 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" CA SER I 102 " pdb=" N SER I 102 " pdb=" C SER I 102 " pdb=" CB SER I 102 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 ... (remaining 3839 not shown) Planarity restraints: 7496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 316 " 0.041 2.00e-02 2.50e+03 8.34e-02 6.95e+01 pdb=" C GLU G 316 " -0.144 2.00e-02 2.50e+03 pdb=" O GLU G 316 " 0.052 2.00e-02 2.50e+03 pdb=" OXT GLU G 316 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 316 " -0.041 2.00e-02 2.50e+03 8.32e-02 6.92e+01 pdb=" C GLU B 316 " 0.144 2.00e-02 2.50e+03 pdb=" O GLU B 316 " -0.052 2.00e-02 2.50e+03 pdb=" OXT GLU B 316 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 240 " -0.093 2.00e-02 2.50e+03 4.09e-02 5.02e+01 pdb=" CG TYR I 240 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR I 240 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR I 240 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR I 240 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR I 240 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR I 240 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 240 " -0.076 2.00e-02 2.50e+03 pdb=" HD1 TYR I 240 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR I 240 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR I 240 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR I 240 " 0.003 2.00e-02 2.50e+03 ... (remaining 7493 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1983 2.15 - 2.77: 99431 2.77 - 3.38: 145524 3.38 - 3.99: 191440 3.99 - 4.60: 300410 Nonbonded interactions: 738788 Sorted by model distance: nonbonded pdb=" H ARG H 224 " pdb=" H ILE H 225 " model vdw 1.542 2.100 nonbonded pdb=" H ARG C 224 " pdb=" H ILE C 225 " model vdw 1.542 2.100 nonbonded pdb=" H GLY E 393 " pdb=" H ASP E 394 " model vdw 1.577 2.100 nonbonded pdb=" H GLY J 393 " pdb=" H ASP J 394 " model vdw 1.578 2.100 nonbonded pdb=" H THR G 163 " pdb=" H LYS G 164 " model vdw 1.636 2.100 ... (remaining 738783 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.690 Extract box with map and model: 1.440 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 95.060 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.160 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 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 : 0.020 0.142 25672 Z= 1.323 Angle : 1.861 15.244 34764 Z= 1.261 Chirality : 0.100 0.522 3842 Planarity : 0.009 0.083 4526 Dihedral : 10.539 84.319 9598 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.33 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -0.37 (0.15), residues: 3114 helix: 0.10 (0.14), residues: 1244 sheet: 0.31 (0.24), residues: 456 loop : -0.63 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.008 TRP G 130 HIS 0.013 0.003 HIS D 292 PHE 0.050 0.007 PHE C 369 TYR 0.092 0.009 TYR I 240 ARG 0.009 0.001 ARG F 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 720 time to evaluate : 2.904 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: 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: 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: 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: 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: 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: 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: A 128 LEU cc_start: 0.8654 (tp) cc_final: 0.8232 (tp) REVERT: A 173 TYR cc_start: 0.8450 (m-80) cc_final: 0.7873 (m-80) REVERT: A 205 ASP cc_start: 0.7605 (p0) cc_final: 0.7176 (p0) REVERT: B 85 LYS cc_start: 0.7893 (mttm) cc_final: 0.6928 (tmtt) REVERT: B 97 LEU cc_start: 0.8922 (mt) cc_final: 0.8649 (tt) REVERT: B 161 LYS cc_start: 0.8837 (pttt) cc_final: 0.8314 (mttt) REVERT: B 243 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8052 (mm-30) REVERT: C 1 MET cc_start: 0.4558 (ttm) cc_final: 0.3841 (ttp) REVERT: C 111 GLU cc_start: 0.6939 (pm20) cc_final: 0.6477 (tm-30) REVERT: C 216 TYR cc_start: 0.7390 (m-80) cc_final: 0.6975 (t80) REVERT: C 302 MET cc_start: -0.1096 (ttm) cc_final: -0.1609 (ttp) REVERT: D 105 MET cc_start: 0.3706 (mmm) cc_final: 0.3279 (mmt) REVERT: D 135 LYS cc_start: 0.2158 (mttm) cc_final: 0.1910 (tppt) REVERT: D 186 LEU cc_start: 0.6483 (tp) cc_final: 0.6035 (mm) REVERT: F 128 LEU cc_start: 0.8627 (tp) cc_final: 0.8223 (tp) REVERT: F 173 TYR cc_start: 0.8475 (m-80) cc_final: 0.7914 (m-80) REVERT: F 205 ASP cc_start: 0.7569 (p0) cc_final: 0.7147 (p0) REVERT: G 85 LYS cc_start: 0.7858 (mttm) cc_final: 0.6949 (tmtt) REVERT: G 97 LEU cc_start: 0.8916 (mt) cc_final: 0.8644 (tt) REVERT: G 161 LYS cc_start: 0.8777 (pttt) cc_final: 0.8324 (mttt) REVERT: G 243 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8060 (mm-30) REVERT: H 1 MET cc_start: 0.4518 (ttm) cc_final: 0.3815 (ttp) REVERT: H 111 GLU cc_start: 0.6842 (pm20) cc_final: 0.6455 (tm-30) REVERT: H 216 TYR cc_start: 0.7353 (m-80) cc_final: 0.6945 (t80) REVERT: H 302 MET cc_start: -0.1144 (ttm) cc_final: -0.1630 (ttp) REVERT: I 105 MET cc_start: 0.3567 (mmm) cc_final: 0.3183 (mmt) REVERT: I 135 LYS cc_start: 0.2208 (mttm) cc_final: 0.1977 (tppt) REVERT: I 186 LEU cc_start: 0.6512 (tp) cc_final: 0.6064 (mm) REVERT: E 443 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8464 (mmmm) REVERT: J 443 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8453 (mmmm) REVERT: J 447 PHE cc_start: 0.6082 (p90) cc_final: 0.5607 (p90) outliers start: 0 outliers final: 0 residues processed: 720 average time/residue: 0.7889 time to fit residues: 882.8505 Evaluate side-chains 433 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 0.8980 chunk 234 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 147 optimal weight: 0.7980 chunk 180 optimal weight: 20.0000 chunk 281 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25672 Z= 0.269 Angle : 0.779 8.217 34764 Z= 0.430 Chirality : 0.046 0.205 3842 Planarity : 0.006 0.063 4526 Dihedral : 6.084 82.061 3424 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.14 % Favored : 94.48 % Rotamer: Outliers : 1.33 % Allowed : 9.26 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3114 helix: 0.51 (0.14), residues: 1244 sheet: -0.14 (0.23), residues: 468 loop : -1.04 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 36 HIS 0.008 0.002 HIS I 249 PHE 0.030 0.002 PHE A 148 TYR 0.029 0.002 TYR D 240 ARG 0.010 0.001 ARG E 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 481 time to evaluate : 2.952 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: 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: 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: 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: 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: 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: 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: A 96 ARG cc_start: 0.8586 (ttt90) cc_final: 0.8255 (ttm-80) REVERT: A 131 SER cc_start: 0.8959 (t) cc_final: 0.8457 (m) REVERT: A 173 TYR cc_start: 0.8288 (m-80) cc_final: 0.7868 (m-80) REVERT: B 85 LYS cc_start: 0.7623 (mttm) cc_final: 0.6731 (tmtt) REVERT: B 97 LEU cc_start: 0.8898 (mt) cc_final: 0.8680 (tt) REVERT: B 161 LYS cc_start: 0.8835 (pttt) cc_final: 0.8375 (mttt) REVERT: B 304 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6356 (tm-30) REVERT: B 309 MET cc_start: 0.7903 (tpp) cc_final: 0.7632 (tpp) REVERT: C 216 TYR cc_start: 0.7490 (m-80) cc_final: 0.7225 (t80) REVERT: C 302 MET cc_start: -0.0532 (ttm) cc_final: -0.1223 (ttp) REVERT: C 349 TYR cc_start: 0.4499 (p90) cc_final: 0.2440 (t80) REVERT: C 358 MET cc_start: 0.2477 (tmm) cc_final: 0.1865 (tmm) REVERT: D 105 MET cc_start: 0.3169 (mmm) cc_final: 0.2895 (mmt) REVERT: D 186 LEU cc_start: 0.6470 (tp) cc_final: 0.6053 (mm) REVERT: F 96 ARG cc_start: 0.8555 (ttt90) cc_final: 0.8244 (ttm-80) REVERT: F 131 SER cc_start: 0.9023 (t) cc_final: 0.8564 (m) REVERT: F 205 ASP cc_start: 0.7309 (p0) cc_final: 0.6888 (p0) REVERT: G 85 LYS cc_start: 0.7622 (mttm) cc_final: 0.6734 (tmtt) REVERT: G 97 LEU cc_start: 0.8872 (mt) cc_final: 0.8664 (tt) REVERT: G 161 LYS cc_start: 0.8786 (pttt) cc_final: 0.8391 (mttt) REVERT: G 304 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6344 (tm-30) REVERT: G 309 MET cc_start: 0.7921 (tpp) cc_final: 0.7639 (tpp) REVERT: H 216 TYR cc_start: 0.7469 (m-80) cc_final: 0.7171 (t80) REVERT: H 302 MET cc_start: -0.0465 (ttm) cc_final: -0.1268 (ttp) REVERT: H 349 TYR cc_start: 0.4627 (p90) cc_final: 0.2521 (t80) REVERT: I 105 MET cc_start: 0.3171 (mmm) cc_final: 0.2709 (mmt) REVERT: I 186 LEU cc_start: 0.6455 (tp) cc_final: 0.6027 (mm) REVERT: E 95 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7652 (tm-30) REVERT: E 221 ASP cc_start: 0.6629 (m-30) cc_final: 0.6334 (m-30) REVERT: E 230 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6623 (m-30) REVERT: E 443 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8459 (mmmm) REVERT: J 51 GLU cc_start: 0.6338 (mt-10) cc_final: 0.5974 (mt-10) REVERT: J 95 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7614 (tm-30) REVERT: J 230 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6558 (m-30) REVERT: J 443 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8490 (mmmm) outliers start: 37 outliers final: 31 residues processed: 503 average time/residue: 0.7444 time to fit residues: 606.5667 Evaluate side-chains 445 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 412 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain J residue 261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 chunk 304 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 226 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 177 GLN B 244 GLN ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS F 155 ASN ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 HIS G 177 GLN G 244 GLN ** G 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 25672 Z= 0.435 Angle : 0.755 7.392 34764 Z= 0.420 Chirality : 0.045 0.212 3842 Planarity : 0.006 0.059 4526 Dihedral : 6.070 84.802 3424 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.36 % Favored : 93.32 % Rotamer: Outliers : 2.20 % Allowed : 10.67 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -0.96 (0.14), residues: 3114 helix: 0.30 (0.14), residues: 1270 sheet: -0.71 (0.23), residues: 466 loop : -1.46 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 113 HIS 0.013 0.002 HIS H 227 PHE 0.022 0.002 PHE D 243 TYR 0.026 0.002 TYR E 174 ARG 0.007 0.001 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 400 time to evaluate : 2.917 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: 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: 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: 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: 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: symmetry clash REVERT: A 173 TYR cc_start: 0.8657 (m-80) cc_final: 0.8292 (m-80) REVERT: B 85 LYS cc_start: 0.7759 (mttm) cc_final: 0.6753 (tmtt) REVERT: B 88 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.6420 (t0) REVERT: B 97 LEU cc_start: 0.8913 (mt) cc_final: 0.8701 (tt) REVERT: B 160 ASP cc_start: 0.6427 (t0) cc_final: 0.5812 (t0) REVERT: B 161 LYS cc_start: 0.8815 (pttt) cc_final: 0.8387 (mttm) REVERT: B 309 MET cc_start: 0.7917 (tpp) cc_final: 0.7664 (tpp) REVERT: C 236 HIS cc_start: 0.6117 (t70) cc_final: 0.5879 (t70) REVERT: C 302 MET cc_start: -0.0343 (ttm) cc_final: -0.1162 (ttp) REVERT: D 105 MET cc_start: 0.3800 (mmm) cc_final: 0.3508 (mmt) REVERT: D 186 LEU cc_start: 0.6461 (tp) cc_final: 0.6064 (mm) REVERT: F 131 SER cc_start: 0.8898 (t) cc_final: 0.8304 (p) REVERT: F 173 TYR cc_start: 0.8636 (m-80) cc_final: 0.7762 (m-80) REVERT: F 205 ASP cc_start: 0.7608 (p0) cc_final: 0.7266 (p0) REVERT: G 85 LYS cc_start: 0.7775 (mttm) cc_final: 0.6789 (tmtt) REVERT: G 88 ASP cc_start: 0.6833 (OUTLIER) cc_final: 0.6410 (t0) REVERT: G 97 LEU cc_start: 0.8897 (mt) cc_final: 0.8694 (tt) REVERT: G 160 ASP cc_start: 0.6660 (t0) cc_final: 0.6108 (t0) REVERT: G 161 LYS cc_start: 0.8762 (pttt) cc_final: 0.8413 (mttt) REVERT: G 243 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8004 (mm-30) REVERT: G 309 MET cc_start: 0.7935 (tpp) cc_final: 0.7732 (tpp) REVERT: H 236 HIS cc_start: 0.6135 (t70) cc_final: 0.5902 (t70) REVERT: H 302 MET cc_start: -0.0413 (ttm) cc_final: -0.1258 (ttp) REVERT: H 349 TYR cc_start: 0.4219 (p90) cc_final: 0.2462 (t80) REVERT: I 105 MET cc_start: 0.3752 (mmm) cc_final: 0.3459 (mmt) REVERT: I 186 LEU cc_start: 0.6436 (tp) cc_final: 0.5998 (mm) REVERT: E 230 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: E 443 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8480 (mmmm) REVERT: E 447 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.5145 (p90) REVERT: J 187 GLN cc_start: 0.7387 (mt0) cc_final: 0.7002 (mp10) REVERT: J 230 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: J 443 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8478 (mmmm) REVERT: J 447 PHE cc_start: 0.6101 (OUTLIER) cc_final: 0.5375 (p90) outliers start: 61 outliers final: 40 residues processed: 443 average time/residue: 0.6615 time to fit residues: 471.1977 Evaluate side-chains 389 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 343 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 240 CYS Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 70 CYS Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 447 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 3.9990 chunk 212 optimal weight: 30.0000 chunk 146 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 189 optimal weight: 30.0000 chunk 283 optimal weight: 1.9990 chunk 299 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 268 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 HIS ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 HIS ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 GLN ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN H 100 GLN ** I 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 ASN J 389 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25672 Z= 0.208 Angle : 0.632 7.359 34764 Z= 0.343 Chirality : 0.042 0.175 3842 Planarity : 0.005 0.056 4526 Dihedral : 5.840 79.167 3424 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.91 % Favored : 93.71 % Rotamer: Outliers : 2.31 % Allowed : 11.03 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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 (0.14), residues: 3114 helix: 0.55 (0.14), residues: 1274 sheet: -0.70 (0.24), residues: 448 loop : -1.49 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 261 HIS 0.008 0.001 HIS H 227 PHE 0.017 0.002 PHE F 148 TYR 0.020 0.002 TYR D 240 ARG 0.004 0.000 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 382 time to evaluate : 2.943 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: 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: 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: 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: 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: A 131 SER cc_start: 0.8820 (t) cc_final: 0.8176 (p) REVERT: A 173 TYR cc_start: 0.8528 (m-80) cc_final: 0.8217 (m-80) REVERT: B 85 LYS cc_start: 0.7631 (mttm) cc_final: 0.6750 (tmtt) REVERT: B 88 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.6237 (t0) REVERT: B 97 LEU cc_start: 0.8886 (mt) cc_final: 0.8669 (tt) REVERT: B 160 ASP cc_start: 0.6719 (t0) cc_final: 0.6482 (t0) REVERT: B 161 LYS cc_start: 0.8731 (pttt) cc_final: 0.8398 (mttt) REVERT: B 309 MET cc_start: 0.7903 (tpp) cc_final: 0.7674 (tpp) REVERT: C 216 TYR cc_start: 0.7617 (m-80) cc_final: 0.7126 (m-10) REVERT: C 302 MET cc_start: -0.0282 (ttm) cc_final: -0.1096 (ttp) REVERT: D 186 LEU cc_start: 0.6408 (tp) cc_final: 0.5960 (mm) REVERT: F 96 ARG cc_start: 0.8503 (ttt90) cc_final: 0.8236 (ttm-80) REVERT: F 131 SER cc_start: 0.8895 (t) cc_final: 0.8312 (p) REVERT: F 173 TYR cc_start: 0.8515 (m-80) cc_final: 0.7649 (m-80) REVERT: G 88 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.6259 (t0) REVERT: G 97 LEU cc_start: 0.8894 (mt) cc_final: 0.8687 (tt) REVERT: G 161 LYS cc_start: 0.8689 (pttt) cc_final: 0.8439 (mttt) REVERT: G 243 GLU cc_start: 0.8807 (mm-30) cc_final: 0.7981 (mm-30) REVERT: H 216 TYR cc_start: 0.7575 (m-80) cc_final: 0.7134 (m-10) REVERT: H 302 MET cc_start: -0.0401 (ttm) cc_final: -0.1224 (ttp) REVERT: I 186 LEU cc_start: 0.6402 (tp) cc_final: 0.5973 (mm) REVERT: E 42 GLU cc_start: 0.7590 (tp30) cc_final: 0.6798 (tp30) REVERT: E 230 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7253 (m-30) REVERT: E 443 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8468 (mmmm) REVERT: J 42 GLU cc_start: 0.7587 (tp30) cc_final: 0.6804 (tp30) REVERT: J 230 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7323 (m-30) REVERT: J 443 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8438 (mmmm) outliers start: 64 outliers final: 46 residues processed: 426 average time/residue: 0.6534 time to fit residues: 446.8702 Evaluate side-chains 402 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 352 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 240 CYS Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 255 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 447 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 268 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 HIS ** G 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25672 Z= 0.242 Angle : 0.620 7.806 34764 Z= 0.336 Chirality : 0.041 0.171 3842 Planarity : 0.005 0.057 4526 Dihedral : 5.709 74.086 3424 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.68 % Favored : 92.94 % Rotamer: Outliers : 2.24 % Allowed : 11.39 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -0.83 (0.14), residues: 3114 helix: 0.62 (0.14), residues: 1268 sheet: -0.74 (0.23), residues: 484 loop : -1.60 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 261 HIS 0.008 0.001 HIS B 25 PHE 0.014 0.001 PHE I 131 TYR 0.018 0.002 TYR D 240 ARG 0.006 0.000 ARG G 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 354 time to evaluate : 2.956 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: 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: 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: 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: 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: A 131 SER cc_start: 0.8777 (t) cc_final: 0.8152 (p) REVERT: A 173 TYR cc_start: 0.8607 (m-80) cc_final: 0.8327 (m-80) REVERT: B 85 LYS cc_start: 0.7640 (mttm) cc_final: 0.6763 (tmtt) REVERT: B 88 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.6354 (t0) REVERT: B 97 LEU cc_start: 0.8911 (mt) cc_final: 0.8700 (tt) REVERT: B 160 ASP cc_start: 0.6791 (t0) cc_final: 0.6449 (t0) REVERT: B 161 LYS cc_start: 0.8694 (pttt) cc_final: 0.8376 (mttt) REVERT: C 13 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6896 (ttm) REVERT: C 302 MET cc_start: -0.0228 (ttm) cc_final: -0.1038 (ttp) REVERT: D 186 LEU cc_start: 0.6370 (tp) cc_final: 0.5943 (mm) REVERT: F 128 LEU cc_start: 0.8661 (tp) cc_final: 0.8437 (tp) REVERT: F 131 SER cc_start: 0.8823 (t) cc_final: 0.8233 (p) REVERT: F 173 TYR cc_start: 0.8602 (m-80) cc_final: 0.7823 (m-80) REVERT: G 88 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.6329 (t0) REVERT: G 97 LEU cc_start: 0.8901 (mt) cc_final: 0.8699 (tt) REVERT: G 161 LYS cc_start: 0.8612 (pttt) cc_final: 0.8409 (mttt) REVERT: G 243 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8031 (mm-30) REVERT: G 309 MET cc_start: 0.7775 (tpp) cc_final: 0.7505 (tpp) REVERT: H 13 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6959 (ttm) REVERT: H 302 MET cc_start: -0.0362 (ttm) cc_final: -0.1157 (ttp) REVERT: I 186 LEU cc_start: 0.6418 (tp) cc_final: 0.6006 (mm) REVERT: E 443 LYS cc_start: 0.8761 (mmtt) cc_final: 0.8503 (mmmm) REVERT: J 230 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7131 (m-30) REVERT: J 443 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8443 (mmmm) outliers start: 62 outliers final: 44 residues processed: 393 average time/residue: 0.6734 time to fit residues: 431.1839 Evaluate side-chains 388 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 339 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 240 CYS Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 447 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 0.7980 chunk 269 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 chunk 73 optimal weight: 0.0000 chunk 299 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN C 100 GLN ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 293 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25672 Z= 0.240 Angle : 0.615 7.123 34764 Z= 0.332 Chirality : 0.041 0.218 3842 Planarity : 0.005 0.058 4526 Dihedral : 5.598 68.767 3424 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.78 % Favored : 92.84 % Rotamer: Outliers : 2.38 % Allowed : 11.61 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -0.82 (0.15), residues: 3114 helix: 0.70 (0.14), residues: 1270 sheet: -0.80 (0.24), residues: 444 loop : -1.64 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 261 HIS 0.017 0.001 HIS G 217 PHE 0.014 0.001 PHE I 131 TYR 0.020 0.002 TYR J 174 ARG 0.005 0.000 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 347 time to evaluate : 2.900 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 SER cc_start: 0.8714 (t) cc_final: 0.8080 (p) REVERT: A 173 TYR cc_start: 0.8669 (m-80) cc_final: 0.8374 (m-80) REVERT: B 88 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6450 (t0) REVERT: B 160 ASP cc_start: 0.6745 (t0) cc_final: 0.6391 (t0) REVERT: B 161 LYS cc_start: 0.8750 (pttt) cc_final: 0.8404 (mttt) REVERT: B 309 MET cc_start: 0.7797 (tpp) cc_final: 0.7487 (tpp) REVERT: C 13 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.7107 (ttm) REVERT: C 302 MET cc_start: -0.0171 (ttm) cc_final: -0.0994 (ttp) REVERT: D 186 LEU cc_start: 0.6389 (tp) cc_final: 0.5968 (mm) REVERT: F 173 TYR cc_start: 0.8671 (m-80) cc_final: 0.7907 (m-80) REVERT: G 88 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6363 (t0) REVERT: G 97 LEU cc_start: 0.8912 (mt) cc_final: 0.8705 (tt) REVERT: G 161 LYS cc_start: 0.8617 (pttt) cc_final: 0.8391 (mttt) REVERT: G 243 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8059 (mm-30) REVERT: H 13 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7204 (ttm) REVERT: H 302 MET cc_start: -0.0297 (ttm) cc_final: -0.1114 (ttp) REVERT: I 186 LEU cc_start: 0.6437 (tp) cc_final: 0.6020 (mm) REVERT: E 443 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8462 (mmmt) REVERT: E 477 MET cc_start: 0.8080 (mtp) cc_final: 0.7784 (mtp) REVERT: J 193 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7830 (mtm110) REVERT: J 230 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7095 (m-30) REVERT: J 443 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8454 (mmmm) outliers start: 66 outliers final: 49 residues processed: 391 average time/residue: 0.6845 time to fit residues: 434.1609 Evaluate side-chains 390 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 335 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 217 HIS Chi-restraints excluded: chain G residue 240 CYS Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 193 ARG Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 447 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 219 optimal weight: 30.0000 chunk 169 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 HIS ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 25672 Z= 0.359 Angle : 0.663 7.307 34764 Z= 0.360 Chirality : 0.043 0.208 3842 Planarity : 0.005 0.063 4526 Dihedral : 5.640 61.131 3424 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.48 % Favored : 92.13 % Rotamer: Outliers : 2.56 % Allowed : 11.93 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -1.09 (0.14), residues: 3114 helix: 0.59 (0.14), residues: 1266 sheet: -1.11 (0.24), residues: 450 loop : -1.83 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 113 HIS 0.019 0.002 HIS G 217 PHE 0.016 0.002 PHE B 19 TYR 0.028 0.002 TYR E 174 ARG 0.006 0.001 ARG G 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 330 time to evaluate : 3.012 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: 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: 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: 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: B 88 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6776 (t0) REVERT: B 160 ASP cc_start: 0.6906 (t0) cc_final: 0.6475 (t0) REVERT: B 161 LYS cc_start: 0.8780 (pttt) cc_final: 0.8407 (mttt) REVERT: B 309 MET cc_start: 0.7835 (tpp) cc_final: 0.7531 (tpp) REVERT: C 13 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7316 (ttm) REVERT: C 302 MET cc_start: -0.0152 (ttm) cc_final: -0.1003 (ttp) REVERT: D 186 LEU cc_start: 0.6463 (tp) cc_final: 0.6043 (mm) REVERT: G 88 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6812 (t0) REVERT: G 161 LYS cc_start: 0.8595 (pttt) cc_final: 0.8354 (mttt) REVERT: H 13 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7292 (ttm) REVERT: H 216 TYR cc_start: 0.7493 (m-80) cc_final: 0.7182 (m-80) REVERT: H 302 MET cc_start: -0.0126 (ttm) cc_final: -0.0968 (ttp) REVERT: I 186 LEU cc_start: 0.6459 (tp) cc_final: 0.5997 (mm) REVERT: E 193 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7803 (mtm110) REVERT: E 443 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8480 (mmmt) REVERT: E 477 MET cc_start: 0.8167 (mtp) cc_final: 0.7870 (mtp) REVERT: J 193 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7855 (mtm110) REVERT: J 230 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: J 443 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8496 (mmmt) outliers start: 71 outliers final: 55 residues processed: 380 average time/residue: 0.6762 time to fit residues: 412.6681 Evaluate side-chains 367 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 305 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 213 TYR Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 240 CYS Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 47 CYS Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 193 ARG Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 447 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 0.1980 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 189 optimal weight: 30.0000 chunk 203 optimal weight: 20.0000 chunk 147 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25672 Z= 0.194 Angle : 0.600 9.332 34764 Z= 0.318 Chirality : 0.041 0.162 3842 Planarity : 0.005 0.064 4526 Dihedral : 5.440 56.440 3424 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.68 % Favored : 92.94 % Rotamer: Outliers : 2.16 % Allowed : 12.62 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -0.84 (0.15), residues: 3114 helix: 0.87 (0.14), residues: 1270 sheet: -0.94 (0.24), residues: 450 loop : -1.79 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 36 HIS 0.014 0.001 HIS G 25 PHE 0.011 0.001 PHE D 131 TYR 0.014 0.002 TYR A 213 ARG 0.005 0.000 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 336 time to evaluate : 2.956 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: 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: 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: 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: A 131 SER cc_start: 0.8684 (t) cc_final: 0.8036 (p) REVERT: A 173 TYR cc_start: 0.8751 (m-80) cc_final: 0.8444 (m-80) REVERT: B 88 ASP cc_start: 0.6838 (OUTLIER) cc_final: 0.6492 (t0) REVERT: B 160 ASP cc_start: 0.6848 (t0) cc_final: 0.6597 (t0) REVERT: B 161 LYS cc_start: 0.8695 (pttt) cc_final: 0.8318 (mttt) REVERT: B 309 MET cc_start: 0.7680 (tpp) cc_final: 0.7359 (tpp) REVERT: C 302 MET cc_start: -0.0132 (ttm) cc_final: -0.0963 (ttp) REVERT: D 186 LEU cc_start: 0.6451 (tp) cc_final: 0.6028 (mm) REVERT: F 173 TYR cc_start: 0.8717 (m-80) cc_final: 0.7992 (m-80) REVERT: G 88 ASP cc_start: 0.6844 (OUTLIER) cc_final: 0.6477 (t0) REVERT: G 161 LYS cc_start: 0.8481 (pttt) cc_final: 0.8244 (mttt) REVERT: G 243 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8179 (mm-30) REVERT: H 216 TYR cc_start: 0.7585 (m-80) cc_final: 0.7204 (m-80) REVERT: H 302 MET cc_start: -0.0125 (ttm) cc_final: -0.0925 (ttp) REVERT: I 186 LEU cc_start: 0.6469 (tp) cc_final: 0.5993 (mm) REVERT: E 443 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8432 (mmmt) REVERT: E 477 MET cc_start: 0.8190 (mtp) cc_final: 0.7881 (mtp) REVERT: J 230 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: J 443 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8435 (mmmt) outliers start: 60 outliers final: 49 residues processed: 374 average time/residue: 0.6841 time to fit residues: 413.0829 Evaluate side-chains 368 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 316 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 213 TYR Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 106 SER Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain J residue 47 CYS Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 251 ASP Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 447 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 3.9990 chunk 286 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 278 optimal weight: 4.9990 chunk 167 optimal weight: 0.4980 chunk 121 optimal weight: 3.9990 chunk 218 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 chunk 251 optimal weight: 2.9990 chunk 263 optimal weight: 0.8980 chunk 277 optimal weight: 0.0030 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25672 Z= 0.175 Angle : 0.583 6.854 34764 Z= 0.309 Chirality : 0.041 0.193 3842 Planarity : 0.005 0.052 4526 Dihedral : 5.282 52.768 3424 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.84 % Favored : 92.84 % Rotamer: Outliers : 1.77 % Allowed : 13.34 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -0.69 (0.15), residues: 3114 helix: 1.00 (0.14), residues: 1270 sheet: -0.85 (0.24), residues: 460 loop : -1.72 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 36 HIS 0.016 0.001 HIS G 25 PHE 0.014 0.001 PHE F 148 TYR 0.014 0.001 TYR F 213 ARG 0.005 0.000 ARG G 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 333 time to evaluate : 2.964 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: 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: 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: 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: A 131 SER cc_start: 0.8687 (t) cc_final: 0.8037 (p) REVERT: A 173 TYR cc_start: 0.8666 (m-80) cc_final: 0.8438 (m-80) REVERT: B 88 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6475 (t0) REVERT: B 160 ASP cc_start: 0.6816 (t0) cc_final: 0.6614 (t0) REVERT: B 161 LYS cc_start: 0.8683 (pttt) cc_final: 0.8313 (mttt) REVERT: B 309 MET cc_start: 0.7658 (tpp) cc_final: 0.7333 (tpp) REVERT: C 302 MET cc_start: -0.0006 (ttm) cc_final: -0.0832 (ttp) REVERT: D 186 LEU cc_start: 0.6471 (tp) cc_final: 0.6007 (mm) REVERT: F 173 TYR cc_start: 0.8710 (m-80) cc_final: 0.8022 (m-80) REVERT: G 88 ASP cc_start: 0.6849 (OUTLIER) cc_final: 0.6469 (t0) REVERT: G 161 LYS cc_start: 0.8471 (pttt) cc_final: 0.8237 (mttt) REVERT: G 243 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8110 (mm-30) REVERT: G 309 MET cc_start: 0.7757 (tpp) cc_final: 0.7422 (tpp) REVERT: H 216 TYR cc_start: 0.7644 (m-80) cc_final: 0.7227 (m-80) REVERT: H 302 MET cc_start: -0.0075 (ttm) cc_final: -0.0873 (ttp) REVERT: E 443 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8371 (mmmt) REVERT: E 477 MET cc_start: 0.8156 (mtp) cc_final: 0.7848 (mtp) REVERT: J 443 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8443 (mmmt) outliers start: 49 outliers final: 40 residues processed: 367 average time/residue: 0.7117 time to fit residues: 424.4198 Evaluate side-chains 361 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 319 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 213 TYR Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 251 ASP Chi-restraints excluded: chain J residue 447 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 8.9990 chunk 294 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 308 optimal weight: 5.9990 chunk 284 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 25672 Z= 0.319 Angle : 0.627 7.488 34764 Z= 0.338 Chirality : 0.042 0.156 3842 Planarity : 0.005 0.059 4526 Dihedral : 5.374 52.737 3424 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.77 % Favored : 91.91 % Rotamer: Outliers : 1.87 % Allowed : 13.41 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -0.86 (0.15), residues: 3114 helix: 0.89 (0.14), residues: 1268 sheet: -0.99 (0.23), residues: 478 loop : -1.83 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 113 HIS 0.015 0.001 HIS G 25 PHE 0.016 0.002 PHE F 148 TYR 0.017 0.002 TYR E 174 ARG 0.005 0.001 ARG B 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 302 time to evaluate : 3.801 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: 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: 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: 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: A 1 MET cc_start: 0.6382 (tpp) cc_final: 0.6068 (tpp) REVERT: A 131 SER cc_start: 0.8728 (t) cc_final: 0.8070 (p) REVERT: B 88 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6839 (t0) REVERT: B 160 ASP cc_start: 0.6980 (t0) cc_final: 0.6639 (t0) REVERT: B 161 LYS cc_start: 0.8674 (pttt) cc_final: 0.8298 (mttt) REVERT: B 309 MET cc_start: 0.7707 (tpp) cc_final: 0.7445 (tpp) REVERT: C 302 MET cc_start: 0.0187 (ttm) cc_final: -0.0637 (ttp) REVERT: F 1 MET cc_start: 0.6404 (tpp) cc_final: 0.6098 (tpp) REVERT: G 88 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6849 (t0) REVERT: G 161 LYS cc_start: 0.8468 (pttt) cc_final: 0.8213 (mttt) REVERT: G 309 MET cc_start: 0.7814 (tpp) cc_final: 0.7491 (tpp) REVERT: H 302 MET cc_start: -0.0024 (ttm) cc_final: -0.0843 (ttp) REVERT: E 443 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8335 (mmmt) REVERT: E 477 MET cc_start: 0.8185 (mtp) cc_final: 0.7878 (mtp) REVERT: J 443 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8425 (mmmt) outliers start: 52 outliers final: 46 residues processed: 339 average time/residue: 0.6535 time to fit residues: 358.1858 Evaluate side-chains 348 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 300 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 213 TYR Chi-restraints excluded: chain F residue 224 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 151 TYR Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 47 CYS Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 447 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 246 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 252 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.177375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.137462 restraints weight = 153211.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.135295 restraints weight = 84541.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.136641 restraints weight = 64433.388| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25672 Z= 0.175 Angle : 0.576 6.932 34764 Z= 0.305 Chirality : 0.041 0.155 3842 Planarity : 0.005 0.055 4526 Dihedral : 5.253 52.336 3424 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.84 % Favored : 92.90 % Rotamer: Outliers : 1.51 % Allowed : 13.91 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: -0.67 (0.15), residues: 3114 helix: 1.06 (0.14), residues: 1276 sheet: -0.97 (0.23), residues: 500 loop : -1.73 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 94 HIS 0.017 0.001 HIS G 25 PHE 0.017 0.001 PHE E 247 TYR 0.014 0.001 TYR F 213 ARG 0.005 0.000 ARG G 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9550.02 seconds wall clock time: 163 minutes 54.99 seconds (9834.99 seconds total)