Starting phenix.real_space_refine on Tue Feb 20 16:41:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjd_24485/02_2024/7rjd_24485_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjd_24485/02_2024/7rjd_24485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjd_24485/02_2024/7rjd_24485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjd_24485/02_2024/7rjd_24485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjd_24485/02_2024/7rjd_24485_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjd_24485/02_2024/7rjd_24485_trim_updated.pdb" } resolution = 3.2 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= 0.004 sd= 0.184 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 5 7.16 5 S 44 5.16 5 C 9501 2.51 5 N 2452 2.21 5 O 2749 1.98 5 H 13664 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 282": not complete - not flipped Residue "G TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "G ASP 99": "OD1" <-> "OD2" Residue "G TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 340": "OD1" <-> "OD2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 372": "OD1" <-> "OD2" Residue "M PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28415 Number of models: 1 Model: "" Number of chains: 13 Chain: "E" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 706 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 9, 'TRANS': 127} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 209 Chain: "A" Number of atoms: 6364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6364 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 8, 'TRANS': 407} Chain: "K" Number of atoms: 6146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6146 Classifications: {'peptide': 383} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 359} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 3736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3736 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 21, 'TRANS': 222} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1978 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "F" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1399 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1148 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 639 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "B" Number of atoms: 5392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 5392 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 345} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 723 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} 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: "K" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'HEM': 2, 'U10': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-4': 1, 'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.38, per 1000 atoms: 0.47 Number of scatterers: 28415 At special positions: 0 Unit cell: (117.42, 89.61, 159.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 5 26.01 S 44 16.00 O 2749 8.00 N 2452 7.00 C 9501 6.00 H 13664 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 89 " - pdb=" SG CYS H 111 " distance=2.03 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.40 Conformation dependent library (CDL) restraints added in 3.0 seconds 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 6 sheets defined 51.2% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 120 through 128 Processing helix chain 'E' and resid 140 through 143 No H-bonds generated for 'chain 'E' and resid 140 through 143' Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 63 through 72 Processing helix chain 'A' and resid 98 through 113 removed outlier: 4.739A pdb=" N THR A 102 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 124 through 138 Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.817A pdb=" N GLU A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 173' Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 202 through 210 Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.032A pdb=" N TYR A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 280 removed outlier: 3.912A pdb=" N LYS A 280 " --> pdb=" O THR A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.537A pdb=" N LEU A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A 339 " --> pdb=" O TRP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 365 through 378 Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 397 through 407 Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.623A pdb=" N MET A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 6 No H-bonds generated for 'chain 'K' and resid 3 through 6' Processing helix chain 'K' and resid 8 through 17 Processing helix chain 'K' and resid 29 through 51 removed outlier: 3.956A pdb=" N GLY K 33 " --> pdb=" O TRP K 30 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN K 43 " --> pdb=" O LEU K 40 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER K 46 " --> pdb=" O GLN K 43 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA K 51 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 70 Processing helix chain 'K' and resid 75 through 102 removed outlier: 3.605A pdb=" N ALA K 86 " --> pdb=" O HIS K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 135 removed outlier: 5.445A pdb=" N MET K 112 " --> pdb=" O PRO K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 153 removed outlier: 4.073A pdb=" N ALA K 153 " --> pdb=" O ASN K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 166 removed outlier: 3.502A pdb=" N ILE K 161 " --> pdb=" O GLY K 158 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL K 162 " --> pdb=" O ASN K 159 " (cutoff:3.500A) Proline residue: K 163 - end of helix removed outlier: 3.511A pdb=" N TRP K 166 " --> pdb=" O PRO K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 204 Proline residue: K 187 - end of helix removed outlier: 4.144A pdb=" N HIS K 204 " --> pdb=" O ALA K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 244 Processing helix chain 'K' and resid 254 through 257 Processing helix chain 'K' and resid 273 through 284 Proline residue: K 277 - end of helix Processing helix chain 'K' and resid 288 through 308 removed outlier: 5.110A pdb=" N LEU K 302 " --> pdb=" O ALA K 298 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU K 303 " --> pdb=" O ILE K 299 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) Proline residue: K 306 - end of helix Processing helix chain 'K' and resid 320 through 341 removed outlier: 3.762A pdb=" N GLN K 341 " --> pdb=" O GLY K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 382 removed outlier: 4.149A pdb=" N GLN K 350 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR K 363 " --> pdb=" O TYR K 359 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL K 367 " --> pdb=" O TYR K 363 " (cutoff:3.500A) Proline residue: K 368 - end of helix Processing helix chain 'D' and resid 45 through 48 No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 103 through 111 Processing helix chain 'D' and resid 143 through 150 Processing helix chain 'D' and resid 169 through 176 Processing helix chain 'D' and resid 225 through 240 Processing helix chain 'D' and resid 244 through 277 Proline residue: D 275 - end of helix Processing helix chain 'G' and resid 5 through 16 Processing helix chain 'G' and resid 19 through 35 Proline residue: G 27 - end of helix Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 54 through 62 Processing helix chain 'G' and resid 65 through 84 Processing helix chain 'G' and resid 104 through 121 Processing helix chain 'F' and resid 41 through 81 removed outlier: 3.646A pdb=" N VAL F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR F 49 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N TYR F 59 " --> pdb=" O ASN F 55 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) Proline residue: F 63 - end of helix Processing helix chain 'F' and resid 87 through 92 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 77 through 98 Proline residue: H 81 - end of helix Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 112 through 132 removed outlier: 3.890A pdb=" N CYS H 125 " --> pdb=" O CYS H 121 " (cutoff:3.500A) Proline residue: H 128 - end of helix removed outlier: 4.686A pdb=" N PHE H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN H 132 " --> pdb=" O PRO H 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 41 removed outlier: 3.712A pdb=" N PHE I 24 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU I 39 " --> pdb=" O ASN I 35 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU I 40 " --> pdb=" O LYS I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 54 removed outlier: 5.344A pdb=" N GLY I 52 " --> pdb=" O LYS I 48 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE I 54 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 64 through 74 removed outlier: 3.741A pdb=" N ARG B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 109 removed outlier: 3.946A pdb=" N LEU B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Proline residue: B 99 - end of helix removed outlier: 4.283A pdb=" N VAL B 102 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 124 through 135 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 169 through 176 Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 194 through 203 Processing helix chain 'B' and resid 205 through 208 Processing helix chain 'B' and resid 248 through 261 removed outlier: 4.462A pdb=" N GLY B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B 254 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 258 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 259 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 300 through 314 removed outlier: 3.692A pdb=" N GLN B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 336 removed outlier: 4.666A pdb=" N LYS B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'M' and resid 48 through 78 removed outlier: 3.705A pdb=" N SER M 78 " --> pdb=" O ALA M 74 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 173 through 175 Processing sheet with id= B, first strand: chain 'A' and resid 23 through 25 removed outlier: 3.689A pdb=" N GLY A 198 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 45 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.262A pdb=" N ILE A 415 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= E, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.735A pdb=" N LYS B 18 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 233 removed outlier: 6.411A pdb=" N TYR B 359 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL B 232 " --> pdb=" O TYR B 359 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA B 361 " --> pdb=" O VAL B 232 " (cutoff:3.500A) 687 hydrogen bonds defined for protein. 1788 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: 10.22 Time building geometry restraints manager: 23.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.12: 13655 1.12 - 1.41: 6311 1.41 - 1.70: 8730 1.70 - 1.98: 72 1.98 - 2.27: 15 Bond restraints: 28783 Sorted by residual: bond pdb=" C CYS D 82 " pdb=" O CYS D 82 " ideal model delta sigma weight residual 1.237 1.076 0.161 1.17e-02 7.31e+03 1.89e+02 bond pdb=" C2D HEC D 301 " pdb=" C3D HEC D 301 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" CAB HEC D 301 " pdb=" CBB HEC D 301 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" CAC HEC D 301 " pdb=" CBC HEC D 301 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C ILE F 30 " pdb=" N SER F 31 " ideal model delta sigma weight residual 1.331 1.234 0.097 1.48e-02 4.57e+03 4.26e+01 ... (remaining 28778 not shown) Histogram of bond angle deviations from ideal: 86.61 - 104.90: 305 104.90 - 123.19: 48548 123.19 - 141.48: 2785 141.48 - 159.77: 0 159.77 - 178.05: 6 Bond angle restraints: 51644 Sorted by residual: angle pdb=" S1 FES E 301 " pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 86.61 17.72 1.20e+00 6.94e-01 2.18e+02 angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 88.18 16.15 1.14e+00 7.69e-01 2.01e+02 angle pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " pdb="FE2 FES E 301 " ideal model delta sigma weight residual 75.66 89.77 -14.11 1.14e+00 7.69e-01 1.53e+02 angle pdb="FE1 FES E 301 " pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " ideal model delta sigma weight residual 75.66 90.34 -14.68 1.20e+00 6.94e-01 1.50e+02 angle pdb=" CA CYS D 82 " pdb=" C CYS D 82 " pdb=" O CYS D 82 " ideal model delta sigma weight residual 120.55 109.72 10.83 1.06e+00 8.90e-01 1.04e+02 ... (remaining 51639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 13352 35.28 - 70.56: 313 70.56 - 105.84: 35 105.84 - 141.12: 1 141.12 - 176.40: 1 Dihedral angle restraints: 13702 sinusoidal: 7057 harmonic: 6645 Sorted by residual: dihedral pdb=" CD ARG D 282 " pdb=" NE ARG D 282 " pdb=" CZ ARG D 282 " pdb=" NH1 ARG D 282 " ideal model delta sinusoidal sigma weight residual 0.00 176.40 -176.40 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C HIS E 117 " pdb=" N HIS E 117 " pdb=" CA HIS E 117 " pdb=" CB HIS E 117 " ideal model delta harmonic sigma weight residual -122.60 -139.06 16.46 0 2.50e+00 1.60e-01 4.33e+01 dihedral pdb=" C3M U10 K 403 " pdb=" C3 U10 K 403 " pdb=" O3 U10 K 403 " pdb=" C4 U10 K 403 " ideal model delta sinusoidal sigma weight residual 244.38 105.86 138.51 1 2.00e+01 2.50e-03 4.20e+01 ... (remaining 13699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2158 0.103 - 0.206: 105 0.206 - 0.309: 21 0.309 - 0.411: 4 0.411 - 0.514: 2 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CA HIS E 117 " pdb=" N HIS E 117 " pdb=" C HIS E 117 " pdb=" CB HIS E 117 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" CA TRP E 108 " pdb=" N TRP E 108 " pdb=" C TRP E 108 " pdb=" CB TRP E 108 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CA ILE E 188 " pdb=" N ILE E 188 " pdb=" C ILE E 188 " pdb=" CB ILE E 188 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 2287 not shown) Planarity restraints: 4308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS K 96 " 0.056 2.00e-02 2.50e+03 4.00e-02 3.60e+01 pdb=" CG HIS K 96 " -0.069 2.00e-02 2.50e+03 pdb=" ND1 HIS K 96 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS K 96 " -0.053 2.00e-02 2.50e+03 pdb=" CE1 HIS K 96 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS K 96 " 0.060 2.00e-02 2.50e+03 pdb=" HD1 HIS K 96 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS K 96 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 HIS K 96 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 149 " 0.026 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C TRP E 149 " -0.087 2.00e-02 2.50e+03 pdb=" O TRP E 149 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU E 150 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 91 " 0.022 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C VAL E 91 " -0.078 2.00e-02 2.50e+03 pdb=" O VAL E 91 " 0.029 2.00e-02 2.50e+03 pdb=" N GLU E 92 " 0.028 2.00e-02 2.50e+03 ... (remaining 4305 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 110 1.80 - 2.50: 21262 2.50 - 3.20: 89498 3.20 - 3.90: 117070 3.90 - 4.60: 185104 Nonbonded interactions: 413044 Sorted by model distance: nonbonded pdb=" H LYS F 36 " pdb=" O TYR M 40 " model vdw 1.103 1.850 nonbonded pdb=" HB2 GLN A 156 " pdb=" HG3 GLN M 34 " model vdw 1.227 2.440 nonbonded pdb=" HE2 PHE I 30 " pdb="HD12 LEU M 63 " model vdw 1.335 2.270 nonbonded pdb=" CB THR E 157 " pdb="FE1 FES E 301 " model vdw 1.342 3.180 nonbonded pdb="HD11 LEU D 261 " pdb=" HG3 MET M 60 " model vdw 1.488 2.440 ... (remaining 413039 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: 1.200 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: 0.470 Extract box with map and model: 6.330 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 91.710 Find NCS groups from input model: 0.580 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5709 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.212 15119 Z= 0.476 Angle : 0.839 17.723 20603 Z= 0.545 Chirality : 0.054 0.514 2290 Planarity : 0.005 0.050 2632 Dihedral : 13.566 176.404 5283 Min Nonbonded Distance : 1.342 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.55 % Favored : 95.03 % Rotamer: Outliers : 0.27 % Allowed : 0.40 % Favored : 99.33 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.20), residues: 1892 helix: 0.53 (0.17), residues: 970 sheet: -0.85 (0.38), residues: 174 loop : -0.17 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 142 HIS 0.037 0.001 HIS K 96 PHE 0.068 0.002 PHE K 184 TYR 0.023 0.002 TYR K 132 ARG 0.008 0.001 ARG D 282 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 363 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 359 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 THR cc_start: 0.8714 (p) cc_final: 0.8430 (t) REVERT: A 185 LYS cc_start: 0.7333 (tttp) cc_final: 0.7037 (ttpp) REVERT: A 405 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6730 (mttt) REVERT: A 406 SER cc_start: 0.8114 (t) cc_final: 0.7912 (p) REVERT: A 411 ARG cc_start: 0.7726 (mmm-85) cc_final: 0.6688 (mmt-90) REVERT: A 433 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6565 (mm-30) REVERT: K 299 ILE cc_start: 0.7823 (mt) cc_final: 0.7611 (mt) REVERT: D 80 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7254 (mm-30) REVERT: D 194 ASN cc_start: 0.5114 (m-40) cc_final: 0.4245 (t0) REVERT: D 230 LYS cc_start: 0.5994 (ttpt) cc_final: 0.5584 (tttp) REVERT: F 52 ARG cc_start: 0.5231 (mtm180) cc_final: 0.4103 (mtp85) REVERT: I 40 GLU cc_start: 0.7022 (tm-30) cc_final: 0.5987 (mm-30) REVERT: B 362 VAL cc_start: 0.6986 (t) cc_final: 0.6538 (t) REVERT: B 364 ASP cc_start: 0.4918 (t0) cc_final: 0.4560 (t70) outliers start: 4 outliers final: 0 residues processed: 362 average time/residue: 0.6557 time to fit residues: 342.9082 Evaluate side-chains 239 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.0070 chunk 169 optimal weight: 1.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN A 381 HIS K 350 GLN B 157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15119 Z= 0.228 Angle : 0.611 22.483 20603 Z= 0.298 Chirality : 0.039 0.163 2290 Planarity : 0.004 0.062 2632 Dihedral : 7.876 179.808 2089 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.14 % Allowed : 6.76 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.20), residues: 1892 helix: 0.73 (0.17), residues: 979 sheet: -0.78 (0.38), residues: 172 loop : -0.06 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 142 HIS 0.006 0.001 HIS A 381 PHE 0.019 0.001 PHE D 75 TYR 0.019 0.002 TYR D 78 ARG 0.006 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 268 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASN cc_start: 0.7668 (t0) cc_final: 0.7377 (t0) REVERT: A 185 LYS cc_start: 0.7423 (tttp) cc_final: 0.7122 (ttpp) REVERT: A 405 LYS cc_start: 0.7198 (mmtt) cc_final: 0.6761 (mttt) REVERT: A 406 SER cc_start: 0.8295 (t) cc_final: 0.7960 (p) REVERT: K 69 MET cc_start: 0.7837 (mmm) cc_final: 0.7379 (mmm) REVERT: K 299 ILE cc_start: 0.8002 (mt) cc_final: 0.7721 (mt) REVERT: D 113 LEU cc_start: 0.7154 (mt) cc_final: 0.6784 (mt) REVERT: D 194 ASN cc_start: 0.5660 (m-40) cc_final: 0.4833 (t0) REVERT: D 231 ASP cc_start: 0.8009 (m-30) cc_final: 0.7410 (m-30) REVERT: D 265 SER cc_start: 0.8159 (OUTLIER) cc_final: 0.7828 (p) REVERT: G 47 ASP cc_start: 0.8148 (m-30) cc_final: 0.7837 (m-30) REVERT: F 52 ARG cc_start: 0.5301 (mtm180) cc_final: 0.4195 (mtp85) REVERT: I 40 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6309 (mp0) REVERT: B 284 TYR cc_start: 0.8175 (m-80) cc_final: 0.7809 (m-80) outliers start: 17 outliers final: 12 residues processed: 274 average time/residue: 0.5630 time to fit residues: 235.7318 Evaluate side-chains 252 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 239 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 353 GLN Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 299 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 168 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 57 ASN K 84 ASN K 141 HIS ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 15119 Z= 0.411 Angle : 0.678 17.668 20603 Z= 0.342 Chirality : 0.043 0.167 2290 Planarity : 0.005 0.052 2632 Dihedral : 7.884 177.863 2089 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.94 % Allowed : 8.90 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.19), residues: 1892 helix: 0.52 (0.16), residues: 970 sheet: -0.96 (0.37), residues: 179 loop : -0.33 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 142 HIS 0.005 0.001 HIS K 82 PHE 0.017 0.002 PHE K 240 TYR 0.026 0.002 TYR K 132 ARG 0.004 0.001 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 259 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 75 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.5811 (t80) REVERT: A 110 SER cc_start: 0.6856 (t) cc_final: 0.6572 (m) REVERT: A 173 ASN cc_start: 0.7605 (t0) cc_final: 0.7229 (t0) REVERT: A 185 LYS cc_start: 0.7404 (tttp) cc_final: 0.7128 (ttpp) REVERT: A 222 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7611 (mp0) REVERT: A 405 LYS cc_start: 0.7434 (mmtt) cc_final: 0.6892 (mttt) REVERT: A 406 SER cc_start: 0.8306 (t) cc_final: 0.7972 (p) REVERT: K 353 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6965 (mt0) REVERT: K 356 THR cc_start: 0.8134 (m) cc_final: 0.7933 (m) REVERT: K 365 ILE cc_start: 0.7233 (mt) cc_final: 0.7024 (mm) REVERT: D 62 MET cc_start: 0.8663 (mtp) cc_final: 0.8451 (mtm) REVERT: D 64 GLU cc_start: 0.7398 (mp0) cc_final: 0.6754 (mp0) REVERT: D 80 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7840 (mm-30) REVERT: D 231 ASP cc_start: 0.8259 (m-30) cc_final: 0.7828 (m-30) REVERT: D 256 VAL cc_start: 0.7943 (t) cc_final: 0.7713 (m) REVERT: D 265 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.8112 (p) REVERT: G 40 GLU cc_start: 0.7480 (mp0) cc_final: 0.6996 (mm-30) REVERT: G 47 ASP cc_start: 0.8823 (m-30) cc_final: 0.8549 (m-30) REVERT: G 57 GLN cc_start: 0.7196 (tp40) cc_final: 0.6778 (mm-40) REVERT: G 86 GLN cc_start: 0.7761 (pt0) cc_final: 0.7487 (pt0) REVERT: G 88 LEU cc_start: 0.8307 (mt) cc_final: 0.8017 (mt) REVERT: G 109 GLU cc_start: 0.7382 (tp30) cc_final: 0.7125 (tp30) REVERT: F 88 GLU cc_start: 0.7214 (tp30) cc_final: 0.6844 (tp30) REVERT: I 40 GLU cc_start: 0.7556 (tm-30) cc_final: 0.6543 (mp0) REVERT: B 309 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7185 (mt0) outliers start: 29 outliers final: 14 residues processed: 274 average time/residue: 0.5413 time to fit residues: 226.9417 Evaluate side-chains 241 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 224 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 353 GLN Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 288 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS K 27 ASN ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 253 HIS F 22 GLN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15119 Z= 0.212 Angle : 0.528 13.400 20603 Z= 0.265 Chirality : 0.038 0.148 2290 Planarity : 0.004 0.034 2632 Dihedral : 7.583 179.067 2089 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.74 % Allowed : 10.51 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.20), residues: 1892 helix: 0.87 (0.17), residues: 970 sheet: -0.83 (0.39), residues: 165 loop : -0.25 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 142 HIS 0.013 0.001 HIS D 48 PHE 0.017 0.001 PHE K 90 TYR 0.014 0.001 TYR K 132 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 233 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 84 ASP cc_start: 0.7558 (t0) cc_final: 0.7294 (t0) REVERT: A 110 SER cc_start: 0.6858 (t) cc_final: 0.6592 (m) REVERT: A 173 ASN cc_start: 0.7670 (t0) cc_final: 0.7338 (t0) REVERT: A 185 LYS cc_start: 0.7401 (tttp) cc_final: 0.7110 (ttpp) REVERT: A 222 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7636 (mp0) REVERT: A 405 LYS cc_start: 0.7431 (mmtt) cc_final: 0.6887 (mttt) REVERT: A 406 SER cc_start: 0.8314 (t) cc_final: 0.8016 (p) REVERT: K 112 MET cc_start: 0.7316 (ttp) cc_final: 0.6667 (tpp) REVERT: K 353 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6942 (mt0) REVERT: D 48 HIS cc_start: 0.7132 (t-170) cc_final: 0.6918 (t-170) REVERT: D 64 GLU cc_start: 0.7493 (mp0) cc_final: 0.6937 (mp0) REVERT: D 80 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7718 (mm-30) REVERT: D 231 ASP cc_start: 0.8454 (m-30) cc_final: 0.8129 (m-30) REVERT: D 256 VAL cc_start: 0.7979 (t) cc_final: 0.7717 (m) REVERT: G 30 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7001 (mt0) REVERT: G 40 GLU cc_start: 0.7462 (mp0) cc_final: 0.6901 (mm-30) REVERT: G 47 ASP cc_start: 0.8834 (m-30) cc_final: 0.8561 (m-30) REVERT: G 57 GLN cc_start: 0.7127 (tp40) cc_final: 0.6804 (mm-40) REVERT: G 86 GLN cc_start: 0.7732 (pt0) cc_final: 0.7466 (pt0) REVERT: G 88 LEU cc_start: 0.8371 (mt) cc_final: 0.8151 (mt) REVERT: F 89 GLU cc_start: 0.6669 (tt0) cc_final: 0.6334 (tt0) REVERT: I 40 GLU cc_start: 0.7541 (tm-30) cc_final: 0.6442 (mp0) outliers start: 26 outliers final: 18 residues processed: 248 average time/residue: 0.5340 time to fit residues: 202.5719 Evaluate side-chains 240 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 220 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 353 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 288 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 2 optimal weight: 40.0000 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 350 GLN D 48 HIS F 22 GLN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15119 Z= 0.335 Angle : 0.583 15.032 20603 Z= 0.296 Chirality : 0.040 0.149 2290 Planarity : 0.004 0.040 2632 Dihedral : 7.672 178.237 2089 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.21 % Allowed : 10.91 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.20), residues: 1892 helix: 0.77 (0.17), residues: 990 sheet: -0.87 (0.40), residues: 165 loop : -0.43 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 142 HIS 0.005 0.001 HIS K 197 PHE 0.014 0.001 PHE K 90 TYR 0.017 0.002 TYR K 132 ARG 0.006 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 231 time to evaluate : 2.368 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: E 75 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.5945 (t80) REVERT: E 84 ASP cc_start: 0.7896 (t0) cc_final: 0.7624 (t0) REVERT: A 110 SER cc_start: 0.6954 (t) cc_final: 0.6675 (m) REVERT: A 132 SER cc_start: 0.7785 (t) cc_final: 0.7085 (m) REVERT: A 173 ASN cc_start: 0.7770 (t0) cc_final: 0.7417 (t0) REVERT: A 185 LYS cc_start: 0.7376 (tttp) cc_final: 0.7110 (ttpp) REVERT: A 222 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7696 (mp0) REVERT: A 341 SER cc_start: 0.8561 (m) cc_final: 0.8190 (t) REVERT: A 405 LYS cc_start: 0.7516 (mmtt) cc_final: 0.6867 (mttt) REVERT: A 406 SER cc_start: 0.8223 (t) cc_final: 0.7954 (p) REVERT: K 112 MET cc_start: 0.7563 (ttp) cc_final: 0.6875 (tpp) REVERT: K 353 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7234 (mt0) REVERT: D 64 GLU cc_start: 0.7687 (mp0) cc_final: 0.7181 (mp0) REVERT: D 231 ASP cc_start: 0.8566 (m-30) cc_final: 0.8350 (m-30) REVERT: D 256 VAL cc_start: 0.7984 (t) cc_final: 0.7619 (m) REVERT: G 30 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7161 (mt0) REVERT: G 40 GLU cc_start: 0.7564 (mp0) cc_final: 0.6964 (mm-30) REVERT: G 47 ASP cc_start: 0.8871 (m-30) cc_final: 0.8658 (m-30) REVERT: G 57 GLN cc_start: 0.7331 (tp40) cc_final: 0.6959 (mm-40) REVERT: G 86 GLN cc_start: 0.7757 (pt0) cc_final: 0.7042 (pt0) REVERT: H 111 CYS cc_start: 0.6860 (m) cc_final: 0.6359 (m) REVERT: I 40 GLU cc_start: 0.7682 (tm-30) cc_final: 0.6486 (mp0) REVERT: B 121 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7781 (mt-10) REVERT: B 186 SER cc_start: 0.8395 (t) cc_final: 0.8091 (p) outliers start: 33 outliers final: 25 residues processed: 247 average time/residue: 0.5884 time to fit residues: 220.4611 Evaluate side-chains 242 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 214 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 353 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 312 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.6819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15119 Z= 0.347 Angle : 0.573 10.763 20603 Z= 0.291 Chirality : 0.040 0.148 2290 Planarity : 0.004 0.048 2632 Dihedral : 7.638 179.651 2089 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.07 % Allowed : 12.12 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.19), residues: 1892 helix: 0.74 (0.17), residues: 979 sheet: -0.83 (0.41), residues: 162 loop : -0.60 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 142 HIS 0.004 0.001 HIS K 183 PHE 0.015 0.001 PHE K 90 TYR 0.014 0.002 TYR K 279 ARG 0.004 0.001 ARG K 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 231 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 SER cc_start: 0.7219 (t) cc_final: 0.6921 (m) REVERT: A 173 ASN cc_start: 0.7799 (t0) cc_final: 0.7443 (t0) REVERT: A 185 LYS cc_start: 0.7368 (tttp) cc_final: 0.7099 (ttpp) REVERT: A 222 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7641 (mp0) REVERT: A 341 SER cc_start: 0.8560 (m) cc_final: 0.8250 (t) REVERT: A 405 LYS cc_start: 0.7551 (mmtt) cc_final: 0.6898 (mttt) REVERT: A 406 SER cc_start: 0.8223 (t) cc_final: 0.7961 (p) REVERT: K 64 SER cc_start: 0.8161 (t) cc_final: 0.7781 (p) REVERT: K 112 MET cc_start: 0.7647 (ttp) cc_final: 0.6961 (tpp) REVERT: K 125 MET cc_start: 0.6334 (mtm) cc_final: 0.6094 (mtm) REVERT: K 296 PHE cc_start: 0.7646 (m-80) cc_final: 0.7432 (m-80) REVERT: D 64 GLU cc_start: 0.7725 (mp0) cc_final: 0.7322 (mp0) REVERT: D 112 GLU cc_start: 0.7449 (tt0) cc_final: 0.6927 (pt0) REVERT: G 30 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7275 (mt0) REVERT: G 57 GLN cc_start: 0.7415 (tp40) cc_final: 0.7210 (mm-40) REVERT: G 61 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7818 (tttt) REVERT: G 86 GLN cc_start: 0.7678 (pt0) cc_final: 0.7201 (pt0) REVERT: F 36 LYS cc_start: 0.6481 (mttm) cc_final: 0.6181 (mttp) REVERT: F 89 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6734 (tt0) REVERT: H 114 GLU cc_start: 0.7833 (mp0) cc_final: 0.6770 (mp0) REVERT: I 40 GLU cc_start: 0.7851 (tm-30) cc_final: 0.6803 (mp0) REVERT: B 186 SER cc_start: 0.8439 (t) cc_final: 0.8129 (p) outliers start: 31 outliers final: 24 residues processed: 254 average time/residue: 0.5374 time to fit residues: 206.1864 Evaluate side-chains 243 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 217 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 312 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 180 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15119 Z= 0.219 Angle : 0.517 10.796 20603 Z= 0.260 Chirality : 0.038 0.148 2290 Planarity : 0.004 0.047 2632 Dihedral : 7.493 179.500 2089 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.01 % Allowed : 12.32 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.20), residues: 1892 helix: 0.99 (0.17), residues: 978 sheet: -0.78 (0.41), residues: 162 loop : -0.42 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 142 HIS 0.005 0.001 HIS H 104 PHE 0.013 0.001 PHE A 327 TYR 0.012 0.001 TYR K 358 ARG 0.002 0.000 ARG K 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 223 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 75 PHE cc_start: 0.6532 (OUTLIER) cc_final: 0.5849 (t80) REVERT: A 110 SER cc_start: 0.7166 (t) cc_final: 0.6893 (m) REVERT: A 173 ASN cc_start: 0.7814 (t0) cc_final: 0.7478 (t0) REVERT: A 185 LYS cc_start: 0.7373 (tttp) cc_final: 0.7097 (ttpp) REVERT: A 222 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7643 (mp0) REVERT: A 341 SER cc_start: 0.8553 (m) cc_final: 0.8222 (t) REVERT: A 405 LYS cc_start: 0.7535 (mmtt) cc_final: 0.6880 (mttt) REVERT: K 64 SER cc_start: 0.8147 (t) cc_final: 0.7834 (p) REVERT: K 112 MET cc_start: 0.7628 (ttp) cc_final: 0.6957 (tpp) REVERT: K 125 MET cc_start: 0.6254 (mtm) cc_final: 0.6013 (mtt) REVERT: D 112 GLU cc_start: 0.7424 (tt0) cc_final: 0.6913 (pt0) REVERT: G 30 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7189 (mt0) REVERT: G 57 GLN cc_start: 0.7437 (tp40) cc_final: 0.7226 (mm-40) REVERT: G 61 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7807 (tttt) REVERT: G 86 GLN cc_start: 0.7538 (pt0) cc_final: 0.7112 (pt0) REVERT: H 95 LYS cc_start: 0.7996 (tppp) cc_final: 0.7771 (tppp) REVERT: H 114 GLU cc_start: 0.7824 (mp0) cc_final: 0.6761 (mp0) REVERT: I 40 GLU cc_start: 0.7814 (tm-30) cc_final: 0.6681 (mm-30) REVERT: B 121 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7825 (mt-10) REVERT: B 186 SER cc_start: 0.8419 (t) cc_final: 0.8147 (p) outliers start: 30 outliers final: 23 residues processed: 240 average time/residue: 0.5392 time to fit residues: 195.1274 Evaluate side-chains 242 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 208 ASN Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 312 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.7187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15119 Z= 0.326 Angle : 0.553 12.012 20603 Z= 0.280 Chirality : 0.040 0.149 2290 Planarity : 0.004 0.057 2632 Dihedral : 7.567 179.828 2089 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.21 % Allowed : 12.45 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.20), residues: 1892 helix: 0.95 (0.17), residues: 979 sheet: -1.05 (0.39), residues: 175 loop : -0.53 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 142 HIS 0.004 0.001 HIS K 197 PHE 0.015 0.001 PHE K 90 TYR 0.014 0.002 TYR K 358 ARG 0.008 0.000 ARG K 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 228 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 75 PHE cc_start: 0.6657 (OUTLIER) cc_final: 0.6013 (t80) REVERT: A 110 SER cc_start: 0.7217 (t) cc_final: 0.6928 (m) REVERT: A 134 GLN cc_start: 0.7971 (mt0) cc_final: 0.7701 (mt0) REVERT: A 173 ASN cc_start: 0.7817 (t0) cc_final: 0.7463 (t0) REVERT: A 185 LYS cc_start: 0.7385 (tttp) cc_final: 0.7124 (ttpp) REVERT: A 222 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7640 (mp0) REVERT: A 341 SER cc_start: 0.8552 (m) cc_final: 0.8238 (t) REVERT: A 405 LYS cc_start: 0.7543 (mmtt) cc_final: 0.6889 (mttt) REVERT: K 64 SER cc_start: 0.8189 (t) cc_final: 0.7813 (p) REVERT: K 112 MET cc_start: 0.7646 (ttp) cc_final: 0.6938 (tpp) REVERT: K 125 MET cc_start: 0.6357 (mtm) cc_final: 0.6121 (mtm) REVERT: D 48 HIS cc_start: 0.7848 (t70) cc_final: 0.7503 (m-70) REVERT: D 112 GLU cc_start: 0.7442 (tt0) cc_final: 0.6937 (pt0) REVERT: D 151 GLN cc_start: 0.8306 (mt0) cc_final: 0.7946 (mm-40) REVERT: G 30 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7263 (mt0) REVERT: G 57 GLN cc_start: 0.7596 (tp40) cc_final: 0.7261 (mm-40) REVERT: G 61 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7802 (tttt) REVERT: G 86 GLN cc_start: 0.7530 (pt0) cc_final: 0.7278 (pt0) REVERT: H 95 LYS cc_start: 0.7996 (tppp) cc_final: 0.7780 (tppp) REVERT: H 104 HIS cc_start: 0.8547 (OUTLIER) cc_final: 0.8222 (m-70) REVERT: H 114 GLU cc_start: 0.8021 (mp0) cc_final: 0.6891 (mp0) REVERT: I 40 GLU cc_start: 0.7936 (tm-30) cc_final: 0.6900 (mp0) REVERT: B 148 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: B 186 SER cc_start: 0.8430 (t) cc_final: 0.8140 (p) REVERT: B 366 ASP cc_start: 0.8574 (t0) cc_final: 0.8354 (t0) REVERT: M 70 SER cc_start: 0.7436 (t) cc_final: 0.7198 (m) outliers start: 33 outliers final: 26 residues processed: 248 average time/residue: 0.5434 time to fit residues: 205.6629 Evaluate side-chains 252 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 222 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 104 HIS Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 312 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.7280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15119 Z= 0.234 Angle : 0.514 10.448 20603 Z= 0.259 Chirality : 0.038 0.148 2290 Planarity : 0.004 0.048 2632 Dihedral : 7.434 179.026 2089 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.28 % Allowed : 12.72 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.20), residues: 1892 helix: 1.08 (0.17), residues: 972 sheet: -1.01 (0.39), residues: 177 loop : -0.41 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 142 HIS 0.004 0.001 HIS K 183 PHE 0.013 0.001 PHE A 327 TYR 0.012 0.001 TYR K 358 ARG 0.006 0.000 ARG K 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 216 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 75 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.5888 (t80) REVERT: A 110 SER cc_start: 0.7203 (t) cc_final: 0.6914 (m) REVERT: A 142 PRO cc_start: 0.8107 (Cg_exo) cc_final: 0.7785 (Cg_endo) REVERT: A 173 ASN cc_start: 0.7795 (t0) cc_final: 0.7438 (t0) REVERT: A 185 LYS cc_start: 0.7376 (tttp) cc_final: 0.7108 (ttpp) REVERT: A 222 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7669 (mp0) REVERT: A 341 SER cc_start: 0.8564 (m) cc_final: 0.8248 (t) REVERT: A 405 LYS cc_start: 0.7528 (mmtt) cc_final: 0.6834 (mttt) REVERT: K 64 SER cc_start: 0.8205 (t) cc_final: 0.7872 (m) REVERT: K 112 MET cc_start: 0.7602 (ttp) cc_final: 0.6878 (tpp) REVERT: K 125 MET cc_start: 0.6203 (mtm) cc_final: 0.5951 (mtm) REVERT: K 375 ASN cc_start: 0.7980 (m-40) cc_final: 0.7464 (m-40) REVERT: D 48 HIS cc_start: 0.7792 (t70) cc_final: 0.7303 (m-70) REVERT: D 151 GLN cc_start: 0.8309 (mt0) cc_final: 0.7946 (mm-40) REVERT: G 30 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7578 (mt0) REVERT: G 61 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7783 (tttt) REVERT: G 86 GLN cc_start: 0.7520 (pt0) cc_final: 0.7299 (pt0) REVERT: G 98 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6266 (mt-10) REVERT: H 95 LYS cc_start: 0.7986 (tppp) cc_final: 0.7766 (tppp) REVERT: H 114 GLU cc_start: 0.8082 (mp0) cc_final: 0.7011 (mp0) REVERT: I 40 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7653 (tp30) REVERT: B 148 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: B 186 SER cc_start: 0.8404 (t) cc_final: 0.8152 (p) REVERT: B 366 ASP cc_start: 0.8572 (t0) cc_final: 0.8332 (t0) REVERT: M 70 SER cc_start: 0.7456 (t) cc_final: 0.7213 (m) outliers start: 34 outliers final: 28 residues processed: 238 average time/residue: 0.5145 time to fit residues: 186.9623 Evaluate side-chains 247 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 215 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 208 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 312 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.7426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15119 Z= 0.312 Angle : 0.549 11.734 20603 Z= 0.278 Chirality : 0.039 0.157 2290 Planarity : 0.004 0.049 2632 Dihedral : 7.501 179.982 2089 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.48 % Allowed : 12.78 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.20), residues: 1892 helix: 0.99 (0.17), residues: 975 sheet: -1.10 (0.39), residues: 177 loop : -0.48 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 142 HIS 0.004 0.001 HIS K 197 PHE 0.015 0.001 PHE K 90 TYR 0.014 0.002 TYR K 358 ARG 0.006 0.000 ARG K 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3784 Ramachandran restraints generated. 1892 Oldfield, 0 Emsley, 1892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 230 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 75 PHE cc_start: 0.6640 (OUTLIER) cc_final: 0.5987 (t80) REVERT: A 110 SER cc_start: 0.7224 (t) cc_final: 0.6926 (m) REVERT: A 173 ASN cc_start: 0.7805 (t0) cc_final: 0.7441 (t0) REVERT: A 185 LYS cc_start: 0.7388 (tttp) cc_final: 0.7134 (ttpp) REVERT: A 222 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7695 (mp0) REVERT: A 341 SER cc_start: 0.8563 (m) cc_final: 0.8251 (t) REVERT: A 405 LYS cc_start: 0.7522 (mmtt) cc_final: 0.6838 (mttt) REVERT: K 64 SER cc_start: 0.8180 (t) cc_final: 0.7807 (p) REVERT: K 112 MET cc_start: 0.7652 (ttp) cc_final: 0.6885 (tpp) REVERT: K 125 MET cc_start: 0.6296 (mtm) cc_final: 0.6051 (mtm) REVERT: D 48 HIS cc_start: 0.7605 (t70) cc_final: 0.7054 (m-70) REVERT: D 151 GLN cc_start: 0.8308 (mt0) cc_final: 0.7919 (mm-40) REVERT: G 30 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7221 (mt0) REVERT: G 98 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6282 (mt-10) REVERT: H 95 LYS cc_start: 0.8066 (tppp) cc_final: 0.7834 (tppp) REVERT: H 109 GLU cc_start: 0.8031 (tt0) cc_final: 0.7273 (tt0) REVERT: H 114 GLU cc_start: 0.8050 (mp0) cc_final: 0.7500 (mp0) REVERT: I 40 GLU cc_start: 0.7972 (tm-30) cc_final: 0.6945 (mp0) REVERT: B 148 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7403 (tt0) REVERT: B 186 SER cc_start: 0.8408 (t) cc_final: 0.8137 (p) REVERT: B 366 ASP cc_start: 0.8580 (t0) cc_final: 0.8352 (t0) REVERT: M 52 PHE cc_start: 0.8203 (t80) cc_final: 0.7847 (t80) REVERT: M 70 SER cc_start: 0.7321 (t) cc_final: 0.7080 (m) outliers start: 37 outliers final: 31 residues processed: 255 average time/residue: 0.5334 time to fit residues: 207.8531 Evaluate side-chains 260 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 225 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 208 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 312 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN H 97 GLN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.125431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.105418 restraints weight = 50286.411| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.44 r_work: 0.2961 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.7644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15119 Z= 0.379 Angle : 0.578 11.829 20603 Z= 0.297 Chirality : 0.041 0.155 2290 Planarity : 0.004 0.051 2632 Dihedral : 7.624 179.095 2089 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.54 % Allowed : 12.99 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.20), residues: 1892 helix: 0.86 (0.17), residues: 974 sheet: -1.18 (0.39), residues: 174 loop : -0.61 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 142 HIS 0.004 0.001 HIS K 82 PHE 0.016 0.001 PHE K 90 TYR 0.015 0.002 TYR K 132 ARG 0.005 0.000 ARG K 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6490.20 seconds wall clock time: 116 minutes 4.90 seconds (6964.90 seconds total)