Starting phenix.real_space_refine on Wed Feb 21 10:47:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1u_15089/02_2024/8a1u_15089_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1u_15089/02_2024/8a1u_15089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1u_15089/02_2024/8a1u_15089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1u_15089/02_2024/8a1u_15089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1u_15089/02_2024/8a1u_15089_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1u_15089/02_2024/8a1u_15089_trim_updated.pdb" } resolution = 2.86 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= 0.006 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 P 10 5.49 5 S 90 5.16 5 Na 2 4.78 5 C 9773 2.51 5 N 2431 2.21 5 O 2948 1.98 5 H 14698 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29956 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 6907 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 424} Chain: "B" Number of atoms: 6064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6064 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 14, 'TRANS': 380} Chain: "C" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 3814 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3173 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 9, 'TRANS': 192} Chain: "E" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3078 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "F" Number of atoms: 6232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6232 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 24, 'TRANS': 380} Chain: "B" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 287 Unusual residues: {' NA': 2, '3PE': 3, 'FMN': 1, 'LMT': 2, 'RBF': 1, 'UQ2': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 18 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'FAD': 1, 'FES': 1, 'NAI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18468 SG CYS D 112 67.470 82.093 58.748 1.00 62.30 S ATOM 20360 SG CYS E 26 64.820 82.419 61.324 1.00 45.30 S ATOM 17135 SG CYS D 29 68.048 84.324 64.922 1.00 49.86 S ATOM 21865 SG CYS E 120 70.928 84.246 62.438 1.00 49.97 S ATOM 24066 SG CYS F 70 51.840 65.779 37.331 1.00 25.59 S ATOM 24115 SG CYS F 76 50.749 62.207 36.894 1.00 16.87 S ATOM 24149 SG CYS F 79 55.484 60.490 38.329 1.00 17.24 S ATOM 24633 SG CYS F 111 56.705 64.001 38.884 1.00 19.42 S Time building chain proxies: 12.80, per 1000 atoms: 0.43 Number of scatterers: 29956 At special positions: 0 Unit cell: (114.57, 136.211, 132.392, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 4 26.01 S 90 16.00 P 10 15.00 Na 2 11.00 O 2948 8.00 N 2431 7.00 C 9773 6.00 H 14698 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.91 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E1001 " pdb="FE1 FES E1001 " - pdb=" SG CYS E 26 " pdb="FE1 FES E1001 " - pdb=" SG CYS D 112 " pdb="FE2 FES E1001 " - pdb=" SG CYS E 120 " pdb="FE2 FES E1001 " - pdb=" SG CYS D 29 " pdb=" FES F1502 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 79 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 70 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 76 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 111 " Number of angles added : 12 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 85 helices and 13 sheets defined 47.7% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.81 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 163 through 169 removed outlier: 3.789A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 215 through 218 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.597A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 379 through 383' Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 415 through 424 removed outlier: 3.511A pdb=" N ALA A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU A 420 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'B' and resid 24 through 34 Processing helix chain 'B' and resid 53 through 86 removed outlier: 3.696A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE B 65 " --> pdb=" O TRP B 61 " (cutoff:3.500A) Proline residue: B 66 - end of helix Processing helix chain 'B' and resid 90 through 98 Processing helix chain 'B' and resid 100 through 107 removed outlier: 3.777A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 151 Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 159 through 167 Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 204 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 277 through 289 Processing helix chain 'B' and resid 295 through 315 Processing helix chain 'B' and resid 321 through 324 Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 354 through 374 Processing helix chain 'B' and resid 382 through 409 Proline residue: B 394 - end of helix Processing helix chain 'C' and resid 8 through 53 removed outlier: 4.591A pdb=" N ASP C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.793A pdb=" N TRP C 189 " --> pdb=" O TRP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 245 through 253 removed outlier: 3.597A pdb=" N ASP C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.941A pdb=" N THR D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 61 Processing helix chain 'D' and resid 71 through 92 Processing helix chain 'D' and resid 95 through 110 removed outlier: 6.144A pdb=" N VAL D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE D 109 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'D' and resid 122 through 124 No H-bonds generated for 'chain 'D' and resid 122 through 124' Processing helix chain 'D' and resid 127 through 157 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 179 through 182 Processing helix chain 'D' and resid 184 through 201 removed outlier: 3.609A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 17 through 20 No H-bonds generated for 'chain 'E' and resid 17 through 20' Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 35 through 62 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 76 through 101 removed outlier: 5.039A pdb=" N PHE E 80 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE E 81 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU E 98 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE E 101 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 113 through 116 No H-bonds generated for 'chain 'E' and resid 113 through 116' Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'E' and resid 136 through 166 removed outlier: 3.651A pdb=" N LYS E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 4.408A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHE E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 29 Processing helix chain 'F' and resid 55 through 62 Processing helix chain 'F' and resid 92 through 96 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 125 through 129 Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 186 through 194 removed outlier: 4.181A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 235 through 237 No H-bonds generated for 'chain 'F' and resid 235 through 237' Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 282 through 296 Proline residue: F 287 - end of helix Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 320 through 329 Processing helix chain 'F' and resid 344 through 346 No H-bonds generated for 'chain 'F' and resid 344 through 346' Processing helix chain 'F' and resid 355 through 362 Processing helix chain 'F' and resid 370 through 372 No H-bonds generated for 'chain 'F' and resid 370 through 372' Processing helix chain 'F' and resid 381 through 393 Processing helix chain 'F' and resid 398 through 400 No H-bonds generated for 'chain 'F' and resid 398 through 400' Processing sheet with id= A, first strand: chain 'A' and resid 0 through 4 removed outlier: 6.265A pdb=" N VAL A 189 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N HIS A 209 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 191 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N PHE A 211 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS A 193 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLY A 213 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP A 237 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N THR A 152 " --> pdb=" O TRP A 237 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE A 239 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.106A pdb=" N GLU A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL A 76 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.255A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 273 through 278 removed outlier: 3.569A pdb=" N VAL A 325 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 71 through 77 removed outlier: 14.188A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.398A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 169 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU C 165 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= G, first strand: chain 'C' and resid 204 through 206 Processing sheet with id= H, first strand: chain 'F' and resid 46 through 49 removed outlier: 7.193A pdb=" N MET F 119 " --> pdb=" O SER F 38 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU F 122 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE F 83 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 133 through 136 Processing sheet with id= J, first strand: chain 'F' and resid 147 through 152 Processing sheet with id= K, first strand: chain 'F' and resid 167 through 172 Processing sheet with id= L, first strand: chain 'F' and resid 175 through 178 Processing sheet with id= M, first strand: chain 'F' and resid 374 through 378 removed outlier: 3.551A pdb=" N TYR F 309 " --> pdb=" O HIS F 336 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1773 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: 11.58 Time building geometry restraints manager: 25.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.11: 14685 1.11 - 1.39: 5896 1.39 - 1.66: 9375 1.66 - 1.93: 151 1.93 - 2.21: 8 Bond restraints: 30115 Sorted by residual: bond pdb=" C4 RBF B 502 " pdb=" C4A RBF B 502 " ideal model delta sigma weight residual 1.481 1.406 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C4 FAD F1501 " pdb=" C4X FAD F1501 " ideal model delta sigma weight residual 1.481 1.408 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C2 UQ2 B 507 " pdb=" C3 UQ2 B 507 " ideal model delta sigma weight residual 1.339 1.408 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 UQ2 B 507 " pdb=" C6 UQ2 B 507 " ideal model delta sigma weight residual 1.485 1.420 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C3 UQ2 B 507 " pdb=" C4 UQ2 B 507 " ideal model delta sigma weight residual 1.486 1.426 0.060 2.00e-02 2.50e+03 9.01e+00 ... (remaining 30110 not shown) Histogram of bond angle deviations from ideal: 75.49 - 87.55: 4 87.55 - 99.62: 1 99.62 - 111.68: 34407 111.68 - 123.74: 17661 123.74 - 135.80: 2269 Bond angle restraints: 54342 Sorted by residual: angle pdb=" C2 LMT B 503 " pdb=" C3 LMT B 503 " pdb=" C4 LMT B 503 " ideal model delta sigma weight residual 117.09 107.50 9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C2 LMT B 505 " pdb=" C3 LMT B 505 " pdb=" C4 LMT B 505 " ideal model delta sigma weight residual 117.09 107.72 9.37 3.00e+00 1.11e-01 9.75e+00 angle pdb=" C2 LMT D 302 " pdb=" C3 LMT D 302 " pdb=" C4 LMT D 302 " ideal model delta sigma weight residual 117.09 107.76 9.33 3.00e+00 1.11e-01 9.67e+00 angle pdb=" C10 LMT B 505 " pdb=" C9 LMT B 505 " pdb=" C8 LMT B 505 " ideal model delta sigma weight residual 116.03 107.48 8.55 3.00e+00 1.11e-01 8.12e+00 angle pdb=" C10 LMT B 503 " pdb=" C9 LMT B 503 " pdb=" C8 LMT B 503 " ideal model delta sigma weight residual 116.03 107.76 8.27 3.00e+00 1.11e-01 7.60e+00 ... (remaining 54337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.66: 13798 34.66 - 69.32: 543 69.32 - 103.99: 52 103.99 - 138.65: 11 138.65 - 173.31: 2 Dihedral angle restraints: 14406 sinusoidal: 7991 harmonic: 6415 Sorted by residual: dihedral pdb=" C10 FMN C1000 " pdb=" C1' FMN C1000 " pdb=" N10 FMN C1000 " pdb=" C2' FMN C1000 " ideal model delta sinusoidal sigma weight residual -102.41 70.90 -173.31 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C10 FMN B 501 " pdb=" C1' FMN B 501 " pdb=" N10 FMN B 501 " pdb=" C2' FMN B 501 " ideal model delta sinusoidal sigma weight residual 257.59 91.73 165.86 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" O5' FAD F1501 " pdb=" O3P FAD F1501 " pdb=" P FAD F1501 " pdb=" PA FAD F1501 " ideal model delta sinusoidal sigma weight residual 298.23 171.58 126.65 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 14403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1909 0.045 - 0.091: 303 0.091 - 0.136: 123 0.136 - 0.181: 3 0.181 - 0.226: 11 Chirality restraints: 2349 Sorted by residual: chirality pdb=" C4' LMT D 302 " pdb=" C3' LMT D 302 " pdb=" C5' LMT D 302 " pdb=" O1B LMT D 302 " both_signs ideal model delta sigma weight residual False -2.55 -2.78 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C4' LMT B 505 " pdb=" C3' LMT B 505 " pdb=" C5' LMT B 505 " pdb=" O1B LMT B 505 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C4' LMT B 503 " pdb=" C3' LMT B 503 " pdb=" C5' LMT B 503 " pdb=" O1B LMT B 503 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2346 not shown) Planarity restraints: 4395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ2 B 507 " 0.004 2.00e-02 2.50e+03 3.27e-02 3.20e+01 pdb=" C2 UQ2 B 507 " 0.020 2.00e-02 2.50e+03 pdb=" C3 UQ2 B 507 " -0.019 2.00e-02 2.50e+03 pdb=" C4 UQ2 B 507 " -0.000 2.00e-02 2.50e+03 pdb=" C5 UQ2 B 507 " 0.022 2.00e-02 2.50e+03 pdb=" C6 UQ2 B 507 " -0.009 2.00e-02 2.50e+03 pdb=" C7 UQ2 B 507 " -0.057 2.00e-02 2.50e+03 pdb=" CM5 UQ2 B 507 " 0.049 2.00e-02 2.50e+03 pdb=" O1 UQ2 B 507 " -0.003 2.00e-02 2.50e+03 pdb=" O2 UQ2 B 507 " 0.052 2.00e-02 2.50e+03 pdb=" O3 UQ2 B 507 " -0.055 2.00e-02 2.50e+03 pdb=" O4 UQ2 B 507 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 128 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO D 129 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 129 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 129 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 206 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO F 207 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO F 207 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 207 " -0.018 5.00e-02 4.00e+02 ... (remaining 4392 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 1187 2.16 - 2.77: 57835 2.77 - 3.38: 87517 3.38 - 3.99: 115081 3.99 - 4.60: 178928 Nonbonded interactions: 440548 Sorted by model distance: nonbonded pdb=" O LYS E 10 " pdb=" H GLU E 15 " model vdw 1.556 1.850 nonbonded pdb=" O GLY E 175 " pdb=" HG1 THR E 179 " model vdw 1.563 1.850 nonbonded pdb=" O PHE A 351 " pdb=" HD1 HIS A 354 " model vdw 1.643 1.850 nonbonded pdb=" H GLY B 198 " pdb=" O5' RBF B 502 " model vdw 1.649 1.850 nonbonded pdb=" HH TYR B 360 " pdb=" OD1 ASN B 390 " model vdw 1.652 1.850 ... (remaining 440543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 0.510 Extract box with map and model: 3.180 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 103.090 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 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 : 0.004 0.075 15417 Z= 0.241 Angle : 0.556 9.586 20887 Z= 0.255 Chirality : 0.042 0.226 2349 Planarity : 0.003 0.037 2587 Dihedral : 17.894 173.311 5847 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.71 % Allowed : 12.90 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.90 (0.20), residues: 1886 helix: 2.50 (0.18), residues: 881 sheet: 0.11 (0.39), residues: 173 loop : 0.22 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 PHE 0.011 0.001 PHE B 213 TYR 0.013 0.001 TYR B 360 ARG 0.002 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 227 time to evaluate : 2.444 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: A 255 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8282 (mt-10) REVERT: A 292 MET cc_start: 0.7909 (mtt) cc_final: 0.7692 (mtm) REVERT: A 374 MET cc_start: 0.8788 (ttt) cc_final: 0.8501 (ttt) REVERT: A 433 GLN cc_start: 0.7974 (tp40) cc_final: 0.7690 (tp-100) REVERT: A 441 LYS cc_start: 0.7733 (tttt) cc_final: 0.7499 (ttmp) REVERT: A 445 GLU cc_start: 0.7402 (tt0) cc_final: 0.6834 (tp30) REVERT: B 154 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6541 (mm-30) REVERT: C 118 ARG cc_start: 0.7877 (ttp-170) cc_final: 0.7651 (ttp80) REVERT: C 125 TYR cc_start: 0.8926 (m-80) cc_final: 0.8645 (m-80) REVERT: D 44 MET cc_start: 0.8884 (tpt) cc_final: 0.8578 (tpt) REVERT: D 63 ARG cc_start: 0.7346 (ptt-90) cc_final: 0.7058 (ptt90) REVERT: D 124 LYS cc_start: 0.7821 (pttt) cc_final: 0.7573 (ptpp) REVERT: D 159 LYS cc_start: 0.8587 (mtmt) cc_final: 0.7999 (mtmt) REVERT: E 36 LYS cc_start: 0.6971 (ptmm) cc_final: 0.6770 (ptmm) REVERT: E 57 ASN cc_start: 0.6884 (t0) cc_final: 0.6659 (t0) REVERT: F 10 MET cc_start: 0.5992 (tpp) cc_final: 0.5779 (tpp) REVERT: F 21 VAL cc_start: 0.6815 (t) cc_final: 0.6605 (p) REVERT: F 115 VAL cc_start: 0.6905 (p) cc_final: 0.6700 (p) outliers start: 11 outliers final: 12 residues processed: 238 average time/residue: 2.5401 time to fit residues: 672.9330 Evaluate side-chains 202 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 183 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 30.0000 chunk 141 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 169 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 257 ASN E 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15417 Z= 0.288 Angle : 0.528 6.912 20887 Z= 0.265 Chirality : 0.042 0.174 2349 Planarity : 0.004 0.050 2587 Dihedral : 13.272 170.184 2534 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.81 % Allowed : 16.32 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.49 (0.20), residues: 1886 helix: 2.01 (0.18), residues: 881 sheet: 0.09 (0.39), residues: 174 loop : 0.15 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 103 HIS 0.006 0.001 HIS B 328 PHE 0.019 0.001 PHE B 392 TYR 0.012 0.001 TYR D 141 ARG 0.004 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7739 (mmp80) cc_final: 0.7354 (mmp80) REVERT: A 255 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8346 (mt-10) REVERT: A 374 MET cc_start: 0.8844 (ttt) cc_final: 0.8514 (ttt) REVERT: A 388 MET cc_start: 0.9203 (mtt) cc_final: 0.8836 (mtp) REVERT: A 433 GLN cc_start: 0.8087 (tp40) cc_final: 0.7729 (tp-100) REVERT: A 441 LYS cc_start: 0.7791 (tttt) cc_final: 0.7515 (ttmp) REVERT: A 445 GLU cc_start: 0.7480 (tt0) cc_final: 0.6867 (tp30) REVERT: B 154 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6501 (mm-30) REVERT: B 256 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8492 (mt0) REVERT: C 118 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.7502 (ttp80) REVERT: C 125 TYR cc_start: 0.8984 (m-80) cc_final: 0.8695 (m-80) REVERT: D 44 MET cc_start: 0.8946 (tpt) cc_final: 0.8669 (tpt) REVERT: D 124 LYS cc_start: 0.7696 (pttt) cc_final: 0.7472 (ptpp) REVERT: E 57 ASN cc_start: 0.6855 (t0) cc_final: 0.6577 (t0) REVERT: E 105 LEU cc_start: 0.6308 (mm) cc_final: 0.5856 (mt) outliers start: 28 outliers final: 18 residues processed: 215 average time/residue: 2.5422 time to fit residues: 609.5816 Evaluate side-chains 208 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 189 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 285 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 HIS E 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15417 Z= 0.340 Angle : 0.567 8.151 20887 Z= 0.287 Chirality : 0.044 0.260 2349 Planarity : 0.005 0.067 2587 Dihedral : 11.878 169.727 2530 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.84 % Allowed : 16.52 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.19), residues: 1886 helix: 1.53 (0.18), residues: 875 sheet: 0.03 (0.39), residues: 172 loop : -0.11 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 103 HIS 0.006 0.001 HIS B 46 PHE 0.020 0.002 PHE F 11 TYR 0.016 0.002 TYR F 179 ARG 0.004 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 189 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8302 (mt-10) REVERT: A 339 MET cc_start: 0.8259 (mmm) cc_final: 0.7986 (mmt) REVERT: A 374 MET cc_start: 0.8862 (ttt) cc_final: 0.8559 (ttt) REVERT: A 388 MET cc_start: 0.9346 (mtt) cc_final: 0.8930 (mtt) REVERT: A 415 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: A 416 GLU cc_start: 0.8300 (pt0) cc_final: 0.7844 (pt0) REVERT: A 441 LYS cc_start: 0.7824 (tttt) cc_final: 0.7559 (ttmp) REVERT: A 445 GLU cc_start: 0.7520 (tt0) cc_final: 0.6846 (tp30) REVERT: B 154 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6439 (tp30) REVERT: B 256 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8453 (mt0) REVERT: C 118 ARG cc_start: 0.7857 (ttp-170) cc_final: 0.7578 (ttp80) REVERT: D 124 LYS cc_start: 0.7763 (pttt) cc_final: 0.7502 (ptpp) REVERT: E 57 ASN cc_start: 0.6830 (t0) cc_final: 0.6570 (t0) REVERT: E 105 LEU cc_start: 0.6279 (mm) cc_final: 0.5866 (mt) REVERT: F 105 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6161 (mt-10) REVERT: F 366 ASP cc_start: 0.5733 (OUTLIER) cc_final: 0.5230 (m-30) outliers start: 44 outliers final: 25 residues processed: 220 average time/residue: 2.4253 time to fit residues: 597.2605 Evaluate side-chains 210 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 366 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 20.0000 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 ASN F 362 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15417 Z= 0.309 Angle : 0.540 7.157 20887 Z= 0.276 Chirality : 0.043 0.285 2349 Planarity : 0.005 0.060 2587 Dihedral : 11.487 171.364 2529 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.71 % Allowed : 17.81 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1886 helix: 1.41 (0.18), residues: 874 sheet: -0.06 (0.38), residues: 170 loop : -0.19 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 103 HIS 0.006 0.001 HIS B 328 PHE 0.018 0.002 PHE B 392 TYR 0.013 0.002 TYR F 179 ARG 0.004 0.001 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 185 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.9039 (pt0) REVERT: A 339 MET cc_start: 0.8265 (mmm) cc_final: 0.7995 (mmt) REVERT: A 374 MET cc_start: 0.8854 (ttt) cc_final: 0.8540 (ttt) REVERT: A 388 MET cc_start: 0.9356 (mtt) cc_final: 0.8991 (mtt) REVERT: A 415 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: A 416 GLU cc_start: 0.8281 (pt0) cc_final: 0.7830 (pt0) REVERT: A 441 LYS cc_start: 0.7824 (tttt) cc_final: 0.7562 (ttmp) REVERT: A 445 GLU cc_start: 0.7506 (tt0) cc_final: 0.6832 (tp30) REVERT: B 154 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6474 (tp30) REVERT: B 256 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8423 (mt0) REVERT: C 118 ARG cc_start: 0.7861 (ttp-170) cc_final: 0.7592 (ttp80) REVERT: C 125 TYR cc_start: 0.8997 (m-80) cc_final: 0.8677 (m-80) REVERT: C 149 MET cc_start: 0.9285 (mtp) cc_final: 0.8941 (mtp) REVERT: D 124 LYS cc_start: 0.7796 (pttt) cc_final: 0.7537 (ptpp) REVERT: E 105 LEU cc_start: 0.6272 (mm) cc_final: 0.5869 (mt) REVERT: F 21 VAL cc_start: 0.7097 (OUTLIER) cc_final: 0.6869 (p) REVERT: F 105 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6203 (mt-10) REVERT: F 366 ASP cc_start: 0.5731 (OUTLIER) cc_final: 0.5232 (m-30) outliers start: 42 outliers final: 30 residues processed: 216 average time/residue: 2.4458 time to fit residues: 590.9081 Evaluate side-chains 220 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 366 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 ASN E 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15417 Z= 0.328 Angle : 0.549 5.604 20887 Z= 0.281 Chirality : 0.043 0.292 2349 Planarity : 0.005 0.067 2587 Dihedral : 11.390 172.004 2529 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.97 % Allowed : 17.81 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.65 (0.19), residues: 1886 helix: 1.28 (0.18), residues: 874 sheet: -0.12 (0.38), residues: 170 loop : -0.27 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 103 HIS 0.007 0.001 HIS B 328 PHE 0.020 0.002 PHE B 392 TYR 0.020 0.002 TYR F 179 ARG 0.004 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 186 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.9022 (pt0) REVERT: A 186 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8404 (m) REVERT: A 339 MET cc_start: 0.8273 (mmm) cc_final: 0.8013 (mmt) REVERT: A 374 MET cc_start: 0.8894 (ttt) cc_final: 0.8687 (ttt) REVERT: A 388 MET cc_start: 0.9304 (mtt) cc_final: 0.8924 (mtt) REVERT: A 415 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: A 416 GLU cc_start: 0.8251 (pt0) cc_final: 0.7796 (pt0) REVERT: A 441 LYS cc_start: 0.7822 (tttt) cc_final: 0.7564 (ttmp) REVERT: A 445 GLU cc_start: 0.7663 (tt0) cc_final: 0.6915 (tp30) REVERT: B 154 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6477 (tp30) REVERT: B 256 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8406 (mt0) REVERT: C 118 ARG cc_start: 0.7902 (ttp-170) cc_final: 0.7643 (ttp80) REVERT: C 149 MET cc_start: 0.9234 (mtp) cc_final: 0.8864 (mtp) REVERT: D 124 LYS cc_start: 0.7827 (pttt) cc_final: 0.7563 (ptpp) REVERT: D 145 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7495 (mp) REVERT: E 105 LEU cc_start: 0.6255 (mm) cc_final: 0.5872 (mt) REVERT: F 21 VAL cc_start: 0.7140 (OUTLIER) cc_final: 0.6912 (p) REVERT: F 105 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6182 (mt-10) REVERT: F 366 ASP cc_start: 0.5799 (OUTLIER) cc_final: 0.5297 (m-30) outliers start: 46 outliers final: 32 residues processed: 219 average time/residue: 2.4436 time to fit residues: 599.0974 Evaluate side-chains 221 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 366 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 180 optimal weight: 20.0000 chunk 150 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15417 Z= 0.225 Angle : 0.503 5.907 20887 Z= 0.257 Chirality : 0.041 0.287 2349 Planarity : 0.004 0.059 2587 Dihedral : 11.072 171.996 2529 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.45 % Allowed : 18.39 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.79 (0.19), residues: 1886 helix: 1.42 (0.18), residues: 874 sheet: -0.04 (0.38), residues: 170 loop : -0.23 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.006 0.001 HIS B 328 PHE 0.015 0.001 PHE B 392 TYR 0.019 0.001 TYR F 179 ARG 0.006 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 186 time to evaluate : 2.250 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: A 339 MET cc_start: 0.8270 (mmm) cc_final: 0.8014 (mmt) REVERT: A 374 MET cc_start: 0.8830 (ttt) cc_final: 0.8513 (ttt) REVERT: A 388 MET cc_start: 0.9301 (mtt) cc_final: 0.8931 (mtt) REVERT: A 415 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: A 416 GLU cc_start: 0.8232 (pt0) cc_final: 0.7767 (pt0) REVERT: A 441 LYS cc_start: 0.7810 (tttt) cc_final: 0.7552 (ttmp) REVERT: A 445 GLU cc_start: 0.7655 (tt0) cc_final: 0.6918 (tp30) REVERT: B 256 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8391 (mt0) REVERT: C 118 ARG cc_start: 0.7905 (ttp-170) cc_final: 0.7648 (ttp80) REVERT: C 125 TYR cc_start: 0.8967 (m-80) cc_final: 0.8679 (m-80) REVERT: C 149 MET cc_start: 0.9261 (mtp) cc_final: 0.8907 (mtp) REVERT: C 156 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: D 124 LYS cc_start: 0.7786 (pttt) cc_final: 0.7565 (ptpp) REVERT: E 17 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7998 (mmp) REVERT: E 105 LEU cc_start: 0.6245 (mm) cc_final: 0.5843 (mt) REVERT: F 21 VAL cc_start: 0.7057 (OUTLIER) cc_final: 0.6846 (p) REVERT: F 105 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6187 (mt-10) REVERT: F 366 ASP cc_start: 0.5774 (OUTLIER) cc_final: 0.5261 (m-30) outliers start: 38 outliers final: 28 residues processed: 211 average time/residue: 2.4558 time to fit residues: 579.9513 Evaluate side-chains 219 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 366 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 103 optimal weight: 0.2980 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15417 Z= 0.223 Angle : 0.499 5.839 20887 Z= 0.254 Chirality : 0.041 0.270 2349 Planarity : 0.004 0.061 2587 Dihedral : 10.897 172.061 2529 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.45 % Allowed : 18.71 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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 (0.19), residues: 1886 helix: 1.47 (0.18), residues: 873 sheet: -0.07 (0.38), residues: 170 loop : -0.22 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.006 0.001 HIS B 328 PHE 0.016 0.001 PHE D 104 TYR 0.023 0.001 TYR F 179 ARG 0.007 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.9314 (OUTLIER) cc_final: 0.9034 (pt0) REVERT: A 339 MET cc_start: 0.8230 (mmm) cc_final: 0.7971 (mmt) REVERT: A 374 MET cc_start: 0.8824 (ttt) cc_final: 0.8417 (ttt) REVERT: A 388 MET cc_start: 0.9298 (mtt) cc_final: 0.8956 (mtt) REVERT: A 415 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: A 416 GLU cc_start: 0.8218 (pt0) cc_final: 0.7759 (pt0) REVERT: A 441 LYS cc_start: 0.7812 (tttt) cc_final: 0.7554 (ttmp) REVERT: A 445 GLU cc_start: 0.7656 (tt0) cc_final: 0.6904 (tp30) REVERT: B 154 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6533 (tp30) REVERT: B 256 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8386 (mt0) REVERT: B 406 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7989 (mtpt) REVERT: C 125 TYR cc_start: 0.8969 (m-80) cc_final: 0.8682 (m-80) REVERT: C 149 MET cc_start: 0.9269 (mtp) cc_final: 0.8965 (mtp) REVERT: C 156 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: D 124 LYS cc_start: 0.7770 (pttt) cc_final: 0.7549 (ptpp) REVERT: D 145 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.7522 (mp) REVERT: E 105 LEU cc_start: 0.6245 (mm) cc_final: 0.5845 (mt) REVERT: F 21 VAL cc_start: 0.7059 (t) cc_final: 0.6850 (p) REVERT: F 105 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6258 (mt-10) REVERT: F 366 ASP cc_start: 0.5774 (OUTLIER) cc_final: 0.5234 (m-30) outliers start: 38 outliers final: 26 residues processed: 212 average time/residue: 2.5469 time to fit residues: 609.5520 Evaluate side-chains 213 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 366 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15417 Z= 0.275 Angle : 0.524 7.282 20887 Z= 0.268 Chirality : 0.042 0.266 2349 Planarity : 0.004 0.067 2587 Dihedral : 10.908 172.144 2525 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.65 % Allowed : 18.58 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.73 (0.19), residues: 1886 helix: 1.39 (0.18), residues: 873 sheet: -0.07 (0.38), residues: 169 loop : -0.29 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.006 0.001 HIS B 328 PHE 0.018 0.001 PHE B 392 TYR 0.025 0.001 TYR F 179 ARG 0.007 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.9319 (OUTLIER) cc_final: 0.9040 (pt0) REVERT: A 186 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8408 (m) REVERT: A 339 MET cc_start: 0.8238 (mmm) cc_final: 0.7984 (mmt) REVERT: A 374 MET cc_start: 0.8842 (ttt) cc_final: 0.8536 (ttt) REVERT: A 388 MET cc_start: 0.9299 (mtt) cc_final: 0.8935 (mtt) REVERT: A 415 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: A 416 GLU cc_start: 0.8219 (pt0) cc_final: 0.7773 (pt0) REVERT: A 441 LYS cc_start: 0.7820 (tttt) cc_final: 0.7563 (ttmp) REVERT: A 445 GLU cc_start: 0.7664 (tt0) cc_final: 0.6906 (tp30) REVERT: B 154 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6534 (tp30) REVERT: B 256 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8450 (mt0) REVERT: B 406 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7996 (mtpt) REVERT: C 125 TYR cc_start: 0.8974 (m-80) cc_final: 0.8682 (m-80) REVERT: C 149 MET cc_start: 0.9234 (mtp) cc_final: 0.8895 (mtp) REVERT: C 156 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: D 124 LYS cc_start: 0.7785 (pttt) cc_final: 0.7565 (ptpp) REVERT: D 145 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7492 (mp) REVERT: E 105 LEU cc_start: 0.6175 (mm) cc_final: 0.5795 (mt) REVERT: F 21 VAL cc_start: 0.7106 (OUTLIER) cc_final: 0.6895 (p) REVERT: F 105 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6211 (mt-10) REVERT: F 366 ASP cc_start: 0.5776 (OUTLIER) cc_final: 0.5257 (m-30) outliers start: 41 outliers final: 30 residues processed: 212 average time/residue: 2.5338 time to fit residues: 601.6327 Evaluate side-chains 220 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 366 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 157 optimal weight: 30.0000 chunk 167 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 110 optimal weight: 0.4980 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 153 HIS E 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15417 Z= 0.237 Angle : 0.513 9.013 20887 Z= 0.261 Chirality : 0.041 0.265 2349 Planarity : 0.004 0.066 2587 Dihedral : 10.831 172.079 2525 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.77 % Allowed : 18.65 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.75 (0.19), residues: 1886 helix: 1.40 (0.18), residues: 879 sheet: -0.04 (0.38), residues: 169 loop : -0.29 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.006 0.001 HIS B 328 PHE 0.016 0.001 PHE D 104 TYR 0.027 0.001 TYR F 179 ARG 0.006 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 185 time to evaluate : 2.361 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: A 186 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8403 (m) REVERT: A 339 MET cc_start: 0.8214 (mmm) cc_final: 0.7964 (mmt) REVERT: A 374 MET cc_start: 0.8842 (ttt) cc_final: 0.8536 (ttt) REVERT: A 388 MET cc_start: 0.9299 (mtt) cc_final: 0.8928 (mtt) REVERT: A 415 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: A 416 GLU cc_start: 0.8212 (pt0) cc_final: 0.7770 (pt0) REVERT: A 441 LYS cc_start: 0.7814 (tttt) cc_final: 0.7558 (ttmp) REVERT: A 445 GLU cc_start: 0.7660 (tt0) cc_final: 0.6906 (tp30) REVERT: B 154 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6647 (mm-30) REVERT: B 256 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8431 (mt0) REVERT: B 406 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7993 (mtpt) REVERT: C 125 TYR cc_start: 0.8971 (m-80) cc_final: 0.8682 (m-80) REVERT: C 149 MET cc_start: 0.9236 (mtp) cc_final: 0.8894 (mtp) REVERT: C 156 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: D 124 LYS cc_start: 0.7770 (pttt) cc_final: 0.7550 (ptpp) REVERT: D 145 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7529 (mp) REVERT: E 105 LEU cc_start: 0.6138 (mm) cc_final: 0.5748 (mt) REVERT: F 21 VAL cc_start: 0.7102 (t) cc_final: 0.6892 (p) REVERT: F 105 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6304 (mt-10) REVERT: F 366 ASP cc_start: 0.5773 (OUTLIER) cc_final: 0.5246 (m-30) outliers start: 43 outliers final: 32 residues processed: 218 average time/residue: 2.4374 time to fit residues: 595.1664 Evaluate side-chains 223 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 366 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 117 optimal weight: 0.0970 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15417 Z= 0.362 Angle : 0.572 10.532 20887 Z= 0.293 Chirality : 0.044 0.265 2349 Planarity : 0.005 0.077 2587 Dihedral : 11.113 172.416 2525 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.90 % Allowed : 18.52 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.19), residues: 1886 helix: 1.19 (0.18), residues: 878 sheet: -0.21 (0.37), residues: 169 loop : -0.43 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 103 HIS 0.007 0.001 HIS B 46 PHE 0.038 0.002 PHE F 182 TYR 0.044 0.002 TYR F 179 ARG 0.005 0.001 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 183 time to evaluate : 2.094 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: A 186 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8390 (m) REVERT: A 339 MET cc_start: 0.8248 (mmm) cc_final: 0.7996 (mmt) REVERT: A 374 MET cc_start: 0.8901 (ttt) cc_final: 0.8609 (ttt) REVERT: A 388 MET cc_start: 0.9298 (mtt) cc_final: 0.8948 (mtt) REVERT: A 416 GLU cc_start: 0.8216 (pt0) cc_final: 0.7783 (pt0) REVERT: A 441 LYS cc_start: 0.7827 (tttt) cc_final: 0.7567 (ttmp) REVERT: A 445 GLU cc_start: 0.7586 (tt0) cc_final: 0.6836 (tp30) REVERT: B 154 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6628 (mm-30) REVERT: B 256 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8430 (mt0) REVERT: B 406 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8016 (mtpt) REVERT: C 125 TYR cc_start: 0.8980 (m-80) cc_final: 0.8690 (m-80) REVERT: C 149 MET cc_start: 0.9200 (mtp) cc_final: 0.8908 (mtp) REVERT: C 156 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.6612 (mp0) REVERT: D 124 LYS cc_start: 0.7769 (pttt) cc_final: 0.7555 (ptpp) REVERT: D 145 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7512 (mp) REVERT: D 205 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7027 (mt0) REVERT: E 105 LEU cc_start: 0.6284 (mm) cc_final: 0.5881 (mt) REVERT: F 21 VAL cc_start: 0.7163 (OUTLIER) cc_final: 0.6935 (p) REVERT: F 105 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6285 (mt-10) REVERT: F 209 ILE cc_start: 0.5932 (tp) cc_final: 0.5732 (tt) REVERT: F 366 ASP cc_start: 0.5796 (OUTLIER) cc_final: 0.5319 (m-30) outliers start: 45 outliers final: 31 residues processed: 214 average time/residue: 2.4808 time to fit residues: 595.8177 Evaluate side-chains 222 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 182 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 366 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.160653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.110888 restraints weight = 45898.330| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.54 r_work: 0.2901 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15417 Z= 0.195 Angle : 0.499 8.382 20887 Z= 0.254 Chirality : 0.041 0.266 2349 Planarity : 0.004 0.066 2587 Dihedral : 10.798 172.099 2525 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.26 % Allowed : 19.23 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.77 (0.19), residues: 1886 helix: 1.44 (0.18), residues: 873 sheet: -0.06 (0.38), residues: 167 loop : -0.28 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.006 0.001 HIS B 328 PHE 0.016 0.001 PHE F 182 TYR 0.030 0.001 TYR F 179 ARG 0.008 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10162.89 seconds wall clock time: 179 minutes 31.97 seconds (10771.97 seconds total)