Starting phenix.real_space_refine on Wed Mar 20 19:56:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjc_24484/03_2024/7rjc_24484_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjc_24484/03_2024/7rjc_24484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjc_24484/03_2024/7rjc_24484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjc_24484/03_2024/7rjc_24484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjc_24484/03_2024/7rjc_24484_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rjc_24484/03_2024/7rjc_24484_trim_updated.pdb" } resolution = 3.3 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= 0.164 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 9471 2.51 5 N 2447 2.21 5 O 2742 1.98 5 H 13664 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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-5265/modules/chem_data/mon_lib" Total number of atoms: 28373 Number of models: 1 Model: "" Number of chains: 13 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} Modifications used: {'NH1NOTPRO': 1} 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: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 664 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 9, 'TRANS': 122} 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: "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} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.73, per 1000 atoms: 0.41 Number of scatterers: 28373 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 2742 8.00 N 2447 7.00 C 9471 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: 23.00 Conformation dependent library (CDL) restraints added in 3.5 seconds 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3578 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 8 sheets defined 51.5% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... 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 helix chain 'E' and resid 83 through 86 No H-bonds generated for 'chain 'E' and resid 83 through 86' Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' 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 sheet with id= A, 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= B, 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= C, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= D, 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= E, 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) Processing sheet with id= F, first strand: chain 'E' and resid 102 through 106 removed outlier: 3.502A pdb=" N LYS E 102 " --> pdb=" O HIS E 117 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE E 106 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG E 116 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 150 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 173 through 175 Processing sheet with id= H, first strand: chain 'E' and resid 203 through 205 removed outlier: 3.761A pdb=" N ASP E 203 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU E 208 " --> pdb=" O THR E 205 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.35 Time building geometry restraints manager: 23.80 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: 6289 1.41 - 1.70: 8708 1.70 - 1.98: 72 1.98 - 2.27: 15 Bond restraints: 28739 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 28734 not shown) Histogram of bond angle deviations from ideal: 86.62 - 104.91: 303 104.91 - 123.20: 48504 123.20 - 141.48: 2772 141.48 - 159.77: 0 159.77 - 178.05: 6 Bond angle restraints: 51585 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 86.62 17.71 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 88.19 16.14 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 89.76 -14.10 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 51580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 13328 35.28 - 70.56: 313 70.56 - 105.84: 35 105.84 - 141.12: 1 141.12 - 176.40: 1 Dihedral angle restraints: 13678 sinusoidal: 7048 harmonic: 6630 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 -139.00 16.40 0 2.50e+00 1.60e-01 4.30e+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 13675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2155 0.102 - 0.205: 109 0.205 - 0.307: 17 0.307 - 0.409: 2 0.409 - 0.512: 1 Chirality restraints: 2284 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 6.55e+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 3.95e+00 chirality pdb=" CA TYR E 202 " pdb=" N TYR E 202 " pdb=" C TYR E 202 " pdb=" CB TYR E 202 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 2281 not shown) Planarity restraints: 4301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 190 " 0.030 2.00e-02 2.50e+03 6.09e-02 3.71e+01 pdb=" C LYS E 190 " -0.105 2.00e-02 2.50e+03 pdb=" O LYS E 190 " 0.039 2.00e-02 2.50e+03 pdb=" N GLY E 191 " 0.036 2.00e-02 2.50e+03 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=" CB PHE K 184 " -0.014 2.00e-02 2.50e+03 2.57e-02 1.98e+01 pdb=" CG PHE K 184 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE K 184 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE K 184 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE K 184 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE K 184 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE K 184 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE K 184 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE K 184 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE K 184 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE K 184 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE K 184 " 0.004 2.00e-02 2.50e+03 ... (remaining 4298 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.73: 72 1.73 - 2.45: 16960 2.45 - 3.17: 88777 3.17 - 3.88: 118326 3.88 - 4.60: 188693 Nonbonded interactions: 412828 Sorted by model distance: nonbonded pdb=" CB THR E 157 " pdb="FE1 FES E 301 " model vdw 1.018 3.180 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="HD11 LEU D 261 " pdb=" HG3 MET M 60 " model vdw 1.488 2.440 ... (remaining 412823 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: 5.790 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: 0.000 Extract box with map and model: 5.100 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 92.140 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.100 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 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 15075 Z= 0.478 Angle : 0.819 17.708 20544 Z= 0.534 Chirality : 0.052 0.512 2284 Planarity : 0.005 0.061 2625 Dihedral : 13.582 176.404 5270 Min Nonbonded Distance : 1.018 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % Favored : 99.60 % Cbeta Deviations : 0.11 % 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: 0.13 (0.20), residues: 1887 helix: 0.54 (0.17), residues: 970 sheet: -0.73 (0.39), residues: 174 loop : -0.13 (0.24), residues: 743 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) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 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 338 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 335 time to evaluate : 2.481 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: A 31 THR cc_start: 0.8357 (t) cc_final: 0.7964 (p) REVERT: A 97 THR cc_start: 0.7310 (t) cc_final: 0.7000 (t) REVERT: A 245 ILE cc_start: 0.8469 (pt) cc_final: 0.8218 (pt) REVERT: A 256 SER cc_start: 0.8981 (m) cc_final: 0.8714 (m) REVERT: A 384 SER cc_start: 0.8481 (t) cc_final: 0.8164 (m) REVERT: A 391 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8226 (mtpt) REVERT: K 246 TYR cc_start: 0.8244 (m-80) cc_final: 0.7837 (m-80) REVERT: K 272 GLU cc_start: 0.7507 (tt0) cc_final: 0.7059 (tp30) REVERT: D 135 TYR cc_start: 0.7708 (m-80) cc_final: 0.7164 (m-80) REVERT: G 61 LYS cc_start: 0.8071 (tmmt) cc_final: 0.7804 (mptt) REVERT: G 117 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7009 (mmtt) REVERT: F 21 LYS cc_start: 0.8193 (mmtp) cc_final: 0.7895 (mttm) REVERT: H 111 CYS cc_start: 0.6638 (m) cc_final: 0.6197 (m) REVERT: H 121 CYS cc_start: 0.8289 (t) cc_final: 0.7642 (t) REVERT: I 40 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8247 (tp30) REVERT: B 18 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7360 (mptt) REVERT: B 132 LYS cc_start: 0.7891 (ttpp) cc_final: 0.7647 (ttmm) REVERT: B 152 ARG cc_start: 0.7399 (mtt180) cc_final: 0.6779 (mmm160) REVERT: B 165 THR cc_start: 0.8882 (m) cc_final: 0.8573 (t) REVERT: B 185 ILE cc_start: 0.8433 (pt) cc_final: 0.8226 (mt) REVERT: B 186 SER cc_start: 0.8335 (t) cc_final: 0.7930 (m) REVERT: B 327 LYS cc_start: 0.8230 (tppp) cc_final: 0.7631 (ttmt) outliers start: 3 outliers final: 2 residues processed: 337 average time/residue: 0.6465 time to fit residues: 309.1739 Evaluate side-chains 245 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 243 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 88 MET 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: 0.1980 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN ** M 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15075 Z= 0.215 Angle : 0.544 12.915 20544 Z= 0.275 Chirality : 0.039 0.151 2284 Planarity : 0.004 0.053 2625 Dihedral : 8.171 178.823 2089 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.54 % Allowed : 6.51 % Favored : 92.95 % 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: 1887 helix: 0.74 (0.17), residues: 970 sheet: -0.58 (0.40), residues: 159 loop : 0.00 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 142 HIS 0.008 0.001 HIS K 96 PHE 0.013 0.001 PHE I 30 TYR 0.015 0.001 TYR K 378 ARG 0.008 0.000 ARG M 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 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 258 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 250 time to evaluate : 2.337 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: A 31 THR cc_start: 0.8411 (t) cc_final: 0.8033 (p) REVERT: A 97 THR cc_start: 0.7406 (t) cc_final: 0.7034 (t) REVERT: A 117 ASP cc_start: 0.7193 (m-30) cc_final: 0.6984 (t0) REVERT: A 245 ILE cc_start: 0.8462 (pt) cc_final: 0.8224 (pt) REVERT: A 384 SER cc_start: 0.8494 (t) cc_final: 0.8139 (m) REVERT: A 391 LYS cc_start: 0.8588 (ttmm) cc_final: 0.8219 (mtpt) REVERT: K 246 TYR cc_start: 0.8234 (m-80) cc_final: 0.7867 (m-80) REVERT: K 272 GLU cc_start: 0.7521 (tt0) cc_final: 0.7159 (mm-30) REVERT: D 135 TYR cc_start: 0.7906 (m-80) cc_final: 0.7359 (m-80) REVERT: G 4 SER cc_start: 0.7967 (m) cc_final: 0.7594 (p) REVERT: G 61 LYS cc_start: 0.8043 (tmmt) cc_final: 0.7781 (mptt) REVERT: G 117 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7050 (mmtt) REVERT: F 21 LYS cc_start: 0.8223 (mmtp) cc_final: 0.7928 (mttm) REVERT: H 111 CYS cc_start: 0.6599 (m) cc_final: 0.6310 (m) REVERT: I 40 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8290 (tp30) REVERT: B 18 LYS cc_start: 0.7886 (mtmm) cc_final: 0.7332 (mptt) REVERT: B 132 LYS cc_start: 0.7897 (ttpp) cc_final: 0.7640 (ttmm) REVERT: B 152 ARG cc_start: 0.7397 (mtt180) cc_final: 0.6722 (mmm160) REVERT: B 168 LYS cc_start: 0.7646 (mtmm) cc_final: 0.7260 (mtmm) REVERT: B 186 SER cc_start: 0.8405 (t) cc_final: 0.8058 (m) REVERT: B 327 LYS cc_start: 0.8299 (tppp) cc_final: 0.7766 (ttmt) REVERT: M 60 MET cc_start: 0.7258 (ttp) cc_final: 0.6990 (ttm) outliers start: 8 outliers final: 6 residues processed: 253 average time/residue: 0.6249 time to fit residues: 229.9158 Evaluate side-chains 229 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 223 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain E residue 88 MET 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: 0.9980 chunk 141 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 57 ASN ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 15075 Z= 0.359 Angle : 0.576 10.665 20544 Z= 0.301 Chirality : 0.041 0.176 2284 Planarity : 0.004 0.051 2625 Dihedral : 7.861 179.830 2087 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.68 % Allowed : 6.65 % Favored : 91.67 % 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: 0.28 (0.20), residues: 1887 helix: 0.71 (0.17), residues: 961 sheet: -0.71 (0.41), residues: 152 loop : -0.12 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 142 HIS 0.007 0.001 HIS H 104 PHE 0.016 0.001 PHE K 278 TYR 0.020 0.002 TYR H 107 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 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 278 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 253 time to evaluate : 2.342 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: A 245 ILE cc_start: 0.8537 (pt) cc_final: 0.8319 (pt) REVERT: A 384 SER cc_start: 0.8610 (t) cc_final: 0.8254 (m) REVERT: K 17 LEU cc_start: 0.8433 (mt) cc_final: 0.8199 (mt) REVERT: K 246 TYR cc_start: 0.8238 (m-80) cc_final: 0.7751 (m-80) REVERT: K 272 GLU cc_start: 0.7176 (tt0) cc_final: 0.6765 (mm-30) REVERT: D 135 TYR cc_start: 0.8213 (m-80) cc_final: 0.7692 (m-80) REVERT: G 4 SER cc_start: 0.8250 (m) cc_final: 0.7998 (p) REVERT: G 60 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8468 (mt) REVERT: G 61 LYS cc_start: 0.7810 (tmmt) cc_final: 0.7440 (mptt) REVERT: G 97 GLU cc_start: 0.8357 (tp30) cc_final: 0.7989 (tp30) REVERT: G 117 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7063 (mmtt) REVERT: F 11 MET cc_start: 0.8275 (ttp) cc_final: 0.7912 (ttp) REVERT: F 21 LYS cc_start: 0.8316 (mmtp) cc_final: 0.8028 (mttm) REVERT: F 73 ARG cc_start: 0.7091 (tmt170) cc_final: 0.6730 (mtt-85) REVERT: H 84 HIS cc_start: 0.8432 (t70) cc_final: 0.7939 (t-90) REVERT: H 111 CYS cc_start: 0.6534 (m) cc_final: 0.6243 (m) REVERT: I 40 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8404 (tm-30) REVERT: B 132 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7727 (ttmm) REVERT: B 152 ARG cc_start: 0.7593 (mtt180) cc_final: 0.6724 (mmm160) REVERT: B 168 LYS cc_start: 0.7708 (mtmm) cc_final: 0.7307 (mtmm) REVERT: B 186 SER cc_start: 0.8798 (t) cc_final: 0.8230 (m) REVERT: B 327 LYS cc_start: 0.8323 (tppp) cc_final: 0.7841 (ttpt) REVERT: M 60 MET cc_start: 0.8079 (ttp) cc_final: 0.7661 (ttt) outliers start: 25 outliers final: 21 residues processed: 264 average time/residue: 0.6392 time to fit residues: 243.3193 Evaluate side-chains 255 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 233 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN K 177 GLN D 59 HIS D 237 ASN I 41 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15075 Z= 0.289 Angle : 0.535 10.253 20544 Z= 0.276 Chirality : 0.039 0.149 2284 Planarity : 0.004 0.093 2625 Dihedral : 7.676 179.924 2087 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.14 % Allowed : 9.07 % Favored : 89.79 % 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: 0.46 (0.20), residues: 1887 helix: 0.92 (0.17), residues: 950 sheet: -0.64 (0.40), residues: 163 loop : -0.10 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 142 HIS 0.008 0.001 HIS D 244 PHE 0.013 0.001 PHE A 327 TYR 0.020 0.001 TYR H 107 ARG 0.004 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 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 251 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 234 time to evaluate : 2.445 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: A 31 THR cc_start: 0.8474 (t) cc_final: 0.8140 (p) REVERT: A 384 SER cc_start: 0.8626 (t) cc_final: 0.8268 (m) REVERT: K 17 LEU cc_start: 0.8461 (mt) cc_final: 0.8223 (mt) REVERT: K 246 TYR cc_start: 0.8223 (m-80) cc_final: 0.7752 (m-80) REVERT: K 272 GLU cc_start: 0.7262 (tt0) cc_final: 0.6826 (mm-30) REVERT: D 111 GLU cc_start: 0.6465 (mp0) cc_final: 0.6247 (mp0) REVERT: D 135 TYR cc_start: 0.8239 (m-80) cc_final: 0.7749 (m-80) REVERT: G 4 SER cc_start: 0.8242 (m) cc_final: 0.8026 (p) REVERT: G 60 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8486 (mt) REVERT: G 61 LYS cc_start: 0.7772 (tmmt) cc_final: 0.7413 (mptt) REVERT: G 97 GLU cc_start: 0.8360 (tp30) cc_final: 0.8019 (tp30) REVERT: G 117 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7117 (mmtt) REVERT: F 11 MET cc_start: 0.8174 (ttp) cc_final: 0.7799 (ttp) REVERT: F 21 LYS cc_start: 0.8315 (mmtp) cc_final: 0.8039 (mttm) REVERT: F 73 ARG cc_start: 0.7045 (tmt170) cc_final: 0.6705 (mtt-85) REVERT: H 111 CYS cc_start: 0.6518 (m) cc_final: 0.6216 (m) REVERT: I 40 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8424 (tm-30) REVERT: B 132 LYS cc_start: 0.7991 (ttpp) cc_final: 0.7682 (ttpt) REVERT: B 152 ARG cc_start: 0.7617 (mtt180) cc_final: 0.6703 (mmm160) REVERT: B 168 LYS cc_start: 0.7721 (mtmm) cc_final: 0.7301 (mtmm) REVERT: B 186 SER cc_start: 0.8779 (t) cc_final: 0.8210 (m) REVERT: B 327 LYS cc_start: 0.8321 (tppp) cc_final: 0.7832 (ttpt) REVERT: M 60 MET cc_start: 0.8092 (ttp) cc_final: 0.7772 (ttm) outliers start: 17 outliers final: 12 residues processed: 241 average time/residue: 0.6150 time to fit residues: 213.6165 Evaluate side-chains 240 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 227 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 15075 Z= 0.323 Angle : 0.541 9.671 20544 Z= 0.278 Chirality : 0.040 0.150 2284 Planarity : 0.004 0.053 2625 Dihedral : 7.656 179.573 2087 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.81 % Allowed : 8.73 % Favored : 89.46 % 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: 0.45 (0.20), residues: 1887 helix: 0.98 (0.17), residues: 949 sheet: -0.59 (0.40), residues: 163 loop : -0.22 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 114 HIS 0.005 0.001 HIS D 244 PHE 0.016 0.001 PHE K 89 TYR 0.012 0.001 TYR K 358 ARG 0.008 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 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 269 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 242 time to evaluate : 2.151 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: A 97 THR cc_start: 0.7564 (t) cc_final: 0.7196 (t) REVERT: A 361 GLU cc_start: 0.7235 (tt0) cc_final: 0.6944 (tt0) REVERT: A 384 SER cc_start: 0.8645 (t) cc_final: 0.8299 (m) REVERT: K 17 LEU cc_start: 0.8468 (mt) cc_final: 0.8237 (mt) REVERT: K 107 LYS cc_start: 0.7750 (mtpp) cc_final: 0.7524 (mmmm) REVERT: K 246 TYR cc_start: 0.8203 (m-80) cc_final: 0.7738 (m-80) REVERT: K 272 GLU cc_start: 0.7247 (tt0) cc_final: 0.6863 (mm-30) REVERT: D 111 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6310 (mp0) REVERT: D 135 TYR cc_start: 0.8220 (m-80) cc_final: 0.7752 (m-80) REVERT: G 30 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7203 (mt0) REVERT: G 56 MET cc_start: 0.7912 (mmm) cc_final: 0.7604 (mmm) REVERT: G 60 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8486 (mt) REVERT: G 61 LYS cc_start: 0.7790 (tmmt) cc_final: 0.7425 (mptt) REVERT: G 97 GLU cc_start: 0.8401 (tp30) cc_final: 0.8073 (tp30) REVERT: G 117 LYS cc_start: 0.8401 (ttmt) cc_final: 0.7130 (mmtt) REVERT: F 11 MET cc_start: 0.8112 (ttp) cc_final: 0.7752 (ttp) REVERT: F 21 LYS cc_start: 0.8301 (mmtp) cc_final: 0.8043 (mttm) REVERT: F 73 ARG cc_start: 0.7057 (tmt170) cc_final: 0.6691 (mtt-85) REVERT: H 84 HIS cc_start: 0.8670 (t70) cc_final: 0.8298 (t-90) REVERT: H 111 CYS cc_start: 0.6491 (m) cc_final: 0.6185 (m) REVERT: I 40 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8488 (tm-30) REVERT: B 132 LYS cc_start: 0.7978 (ttpp) cc_final: 0.7652 (ttpt) REVERT: B 152 ARG cc_start: 0.7583 (mtt180) cc_final: 0.6675 (mmm160) REVERT: B 168 LYS cc_start: 0.7765 (mtmm) cc_final: 0.7347 (mtmm) REVERT: B 186 SER cc_start: 0.8710 (t) cc_final: 0.8171 (m) REVERT: B 327 LYS cc_start: 0.8304 (tppp) cc_final: 0.7768 (ttpt) REVERT: M 60 MET cc_start: 0.8352 (ttp) cc_final: 0.8101 (ttm) outliers start: 27 outliers final: 20 residues processed: 252 average time/residue: 0.6234 time to fit residues: 228.1974 Evaluate side-chains 257 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 234 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 180 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15075 Z= 0.232 Angle : 0.509 8.721 20544 Z= 0.258 Chirality : 0.038 0.150 2284 Planarity : 0.004 0.052 2625 Dihedral : 7.513 179.155 2087 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.48 % Allowed : 10.07 % Favored : 88.45 % 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: 0.70 (0.20), residues: 1887 helix: 1.19 (0.17), residues: 951 sheet: -0.65 (0.40), residues: 168 loop : -0.06 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 142 HIS 0.004 0.001 HIS D 244 PHE 0.016 0.001 PHE K 89 TYR 0.014 0.001 TYR H 107 ARG 0.009 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 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 257 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 235 time to evaluate : 2.237 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: A 361 GLU cc_start: 0.7226 (tt0) cc_final: 0.6926 (tt0) REVERT: A 384 SER cc_start: 0.8631 (t) cc_final: 0.8292 (m) REVERT: K 17 LEU cc_start: 0.8435 (mt) cc_final: 0.8198 (mt) REVERT: K 246 TYR cc_start: 0.8222 (m-80) cc_final: 0.7775 (m-80) REVERT: K 272 GLU cc_start: 0.7228 (tt0) cc_final: 0.6729 (mm-30) REVERT: K 283 ARG cc_start: 0.7945 (mtm180) cc_final: 0.7599 (mtm-85) REVERT: D 111 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6296 (mp0) REVERT: D 135 TYR cc_start: 0.8231 (m-80) cc_final: 0.7781 (m-80) REVERT: G 30 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7181 (mt0) REVERT: G 60 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8504 (mt) REVERT: G 61 LYS cc_start: 0.7787 (tmmt) cc_final: 0.7416 (mptt) REVERT: G 117 LYS cc_start: 0.8359 (ttmt) cc_final: 0.7019 (mmtt) REVERT: F 11 MET cc_start: 0.8131 (ttp) cc_final: 0.7748 (ttp) REVERT: F 21 LYS cc_start: 0.8300 (mmtp) cc_final: 0.8045 (mttm) REVERT: F 73 ARG cc_start: 0.7054 (tmt170) cc_final: 0.6676 (mtt-85) REVERT: H 111 CYS cc_start: 0.6453 (m) cc_final: 0.6152 (m) REVERT: B 18 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7057 (mptt) REVERT: B 132 LYS cc_start: 0.7957 (ttpp) cc_final: 0.7630 (ttpt) REVERT: B 152 ARG cc_start: 0.7676 (mtt180) cc_final: 0.6576 (mmm160) REVERT: B 168 LYS cc_start: 0.7683 (mtmm) cc_final: 0.7256 (mtmm) REVERT: B 186 SER cc_start: 0.8718 (t) cc_final: 0.8174 (m) REVERT: B 327 LYS cc_start: 0.8302 (tppp) cc_final: 0.7767 (ttpt) REVERT: M 60 MET cc_start: 0.8281 (ttp) cc_final: 0.8078 (ttm) outliers start: 22 outliers final: 15 residues processed: 245 average time/residue: 0.6225 time to fit residues: 218.8129 Evaluate side-chains 245 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 227 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 180 optimal weight: 20.0000 chunk 112 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15075 Z= 0.329 Angle : 0.539 9.587 20544 Z= 0.276 Chirality : 0.040 0.160 2284 Planarity : 0.004 0.050 2625 Dihedral : 7.586 179.690 2087 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.68 % Allowed : 10.28 % Favored : 88.05 % 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: 0.56 (0.20), residues: 1887 helix: 1.09 (0.17), residues: 956 sheet: -0.73 (0.40), residues: 170 loop : -0.14 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 114 HIS 0.006 0.001 HIS D 244 PHE 0.021 0.001 PHE K 89 TYR 0.011 0.001 TYR K 358 ARG 0.012 0.001 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 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 257 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 232 time to evaluate : 2.341 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: A 97 THR cc_start: 0.7592 (t) cc_final: 0.7235 (t) REVERT: A 361 GLU cc_start: 0.7255 (tt0) cc_final: 0.6941 (tt0) REVERT: A 384 SER cc_start: 0.8651 (t) cc_final: 0.8314 (m) REVERT: K 17 LEU cc_start: 0.8472 (mt) cc_final: 0.8249 (mt) REVERT: K 246 TYR cc_start: 0.8235 (m-80) cc_final: 0.7803 (m-80) REVERT: K 272 GLU cc_start: 0.7239 (tt0) cc_final: 0.6792 (mm-30) REVERT: K 283 ARG cc_start: 0.7985 (mtm180) cc_final: 0.7666 (mtm-85) REVERT: D 111 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6225 (mp0) REVERT: D 135 TYR cc_start: 0.8211 (m-80) cc_final: 0.7789 (m-80) REVERT: G 30 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7204 (mt0) REVERT: G 60 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8485 (mt) REVERT: G 61 LYS cc_start: 0.7859 (tmmt) cc_final: 0.7497 (mptt) REVERT: G 117 LYS cc_start: 0.8424 (ttmt) cc_final: 0.7052 (mmtt) REVERT: F 11 MET cc_start: 0.8159 (ttp) cc_final: 0.7789 (ttp) REVERT: F 21 LYS cc_start: 0.8310 (mmtp) cc_final: 0.8064 (mttm) REVERT: F 73 ARG cc_start: 0.7068 (tmt170) cc_final: 0.6708 (mtt-85) REVERT: B 54 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7252 (t80) REVERT: B 132 LYS cc_start: 0.8018 (ttpp) cc_final: 0.7673 (ttpt) REVERT: B 152 ARG cc_start: 0.7692 (mtt180) cc_final: 0.6591 (mmm160) REVERT: B 168 LYS cc_start: 0.7722 (mtmm) cc_final: 0.7272 (mtmm) REVERT: B 186 SER cc_start: 0.8713 (t) cc_final: 0.8180 (m) REVERT: B 327 LYS cc_start: 0.8322 (tppp) cc_final: 0.7763 (ttpt) REVERT: B 366 ASP cc_start: 0.8505 (t0) cc_final: 0.8049 (t0) outliers start: 25 outliers final: 17 residues processed: 246 average time/residue: 0.6163 time to fit residues: 218.4771 Evaluate side-chains 252 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 231 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15075 Z= 0.240 Angle : 0.522 11.274 20544 Z= 0.265 Chirality : 0.039 0.158 2284 Planarity : 0.004 0.054 2625 Dihedral : 7.479 179.054 2087 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.48 % Allowed : 11.15 % Favored : 87.37 % 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: 0.67 (0.20), residues: 1887 helix: 1.17 (0.17), residues: 957 sheet: -0.79 (0.39), residues: 171 loop : -0.04 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 142 HIS 0.004 0.001 HIS H 84 PHE 0.020 0.001 PHE K 89 TYR 0.020 0.001 TYR K 378 ARG 0.010 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 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 252 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 230 time to evaluate : 2.229 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: A 361 GLU cc_start: 0.7252 (tt0) cc_final: 0.6938 (tt0) REVERT: K 17 LEU cc_start: 0.8450 (mt) cc_final: 0.8232 (mt) REVERT: K 246 TYR cc_start: 0.8221 (m-80) cc_final: 0.7789 (m-80) REVERT: K 272 GLU cc_start: 0.7233 (tt0) cc_final: 0.6754 (mm-30) REVERT: K 283 ARG cc_start: 0.7970 (mtm180) cc_final: 0.7649 (mtm-85) REVERT: D 47 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7415 (mm-30) REVERT: D 111 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.6128 (mp0) REVERT: D 135 TYR cc_start: 0.8211 (m-80) cc_final: 0.7786 (m-80) REVERT: G 30 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7201 (mt0) REVERT: G 60 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8494 (mt) REVERT: G 61 LYS cc_start: 0.7855 (tmmt) cc_final: 0.7497 (mptt) REVERT: G 117 LYS cc_start: 0.8375 (ttmt) cc_final: 0.6920 (mmtt) REVERT: F 11 MET cc_start: 0.8125 (ttp) cc_final: 0.7752 (ttp) REVERT: F 21 LYS cc_start: 0.8309 (mmtp) cc_final: 0.8072 (mttm) REVERT: F 73 ARG cc_start: 0.7045 (tmt170) cc_final: 0.6677 (mtt-85) REVERT: B 18 LYS cc_start: 0.7885 (mtmm) cc_final: 0.7043 (mptt) REVERT: B 132 LYS cc_start: 0.8000 (ttpp) cc_final: 0.7654 (ttpt) REVERT: B 152 ARG cc_start: 0.7663 (mtt180) cc_final: 0.6585 (mmm160) REVERT: B 168 LYS cc_start: 0.7722 (mtmm) cc_final: 0.7276 (mtmm) REVERT: B 186 SER cc_start: 0.8712 (t) cc_final: 0.8177 (m) REVERT: B 327 LYS cc_start: 0.8315 (tppp) cc_final: 0.7763 (ttpt) REVERT: B 366 ASP cc_start: 0.8500 (t0) cc_final: 0.7968 (t0) outliers start: 22 outliers final: 17 residues processed: 242 average time/residue: 0.6651 time to fit residues: 231.5582 Evaluate side-chains 250 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 230 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 167 optimal weight: 0.4980 chunk 101 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15075 Z= 0.300 Angle : 0.546 13.884 20544 Z= 0.278 Chirality : 0.039 0.150 2284 Planarity : 0.004 0.058 2625 Dihedral : 7.512 179.611 2087 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.75 % Allowed : 11.01 % Favored : 87.24 % 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: 0.58 (0.20), residues: 1887 helix: 1.08 (0.17), residues: 959 sheet: -0.79 (0.39), residues: 172 loop : -0.10 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 114 HIS 0.005 0.001 HIS K 197 PHE 0.024 0.001 PHE K 89 TYR 0.015 0.001 TYR K 378 ARG 0.010 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 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 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 236 time to evaluate : 2.415 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 361 GLU cc_start: 0.7276 (tt0) cc_final: 0.6964 (tt0) REVERT: K 17 LEU cc_start: 0.8451 (mt) cc_final: 0.8237 (mt) REVERT: K 246 TYR cc_start: 0.8238 (m-80) cc_final: 0.7769 (m-80) REVERT: K 272 GLU cc_start: 0.7243 (tt0) cc_final: 0.6805 (mm-30) REVERT: K 283 ARG cc_start: 0.8008 (mtm180) cc_final: 0.7694 (mtm-85) REVERT: D 47 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7488 (mm-30) REVERT: D 111 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6141 (mp0) REVERT: D 135 TYR cc_start: 0.8207 (m-80) cc_final: 0.7808 (m-80) REVERT: G 30 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7234 (mt0) REVERT: G 60 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8473 (mt) REVERT: G 61 LYS cc_start: 0.7859 (tmmt) cc_final: 0.7502 (mptt) REVERT: G 97 GLU cc_start: 0.8213 (tp30) cc_final: 0.7956 (tp30) REVERT: G 117 LYS cc_start: 0.8467 (ttmt) cc_final: 0.7035 (mmtt) REVERT: F 11 MET cc_start: 0.8144 (ttp) cc_final: 0.7777 (ttp) REVERT: F 21 LYS cc_start: 0.8309 (mmtp) cc_final: 0.8077 (mttm) REVERT: F 73 ARG cc_start: 0.7000 (tmt170) cc_final: 0.6712 (mtt-85) REVERT: B 132 LYS cc_start: 0.8026 (ttpp) cc_final: 0.7672 (ttpt) REVERT: B 152 ARG cc_start: 0.7688 (mtt180) cc_final: 0.6606 (mmm160) REVERT: B 168 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7260 (mtmm) REVERT: B 186 SER cc_start: 0.8705 (t) cc_final: 0.8174 (m) REVERT: B 327 LYS cc_start: 0.8315 (tppp) cc_final: 0.7749 (ttpt) REVERT: B 366 ASP cc_start: 0.8500 (t0) cc_final: 0.8048 (t0) outliers start: 26 outliers final: 21 residues processed: 249 average time/residue: 0.6229 time to fit residues: 222.5417 Evaluate side-chains 258 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 234 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 111 CYS Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 20.0000 chunk 108 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 186 optimal weight: 0.0050 chunk 171 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 0.0970 chunk 117 optimal weight: 1.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15075 Z= 0.242 Angle : 0.529 13.062 20544 Z= 0.268 Chirality : 0.039 0.148 2284 Planarity : 0.004 0.060 2625 Dihedral : 7.420 178.990 2087 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.48 % Allowed : 11.48 % Favored : 87.04 % 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: 0.71 (0.20), residues: 1887 helix: 1.22 (0.17), residues: 955 sheet: -0.81 (0.39), residues: 171 loop : -0.04 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 142 HIS 0.006 0.001 HIS H 104 PHE 0.021 0.001 PHE K 89 TYR 0.015 0.001 TYR K 378 ARG 0.009 0.000 ARG B 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 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 257 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 235 time to evaluate : 2.132 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: A 361 GLU cc_start: 0.7274 (tt0) cc_final: 0.6972 (tt0) REVERT: K 17 LEU cc_start: 0.8428 (mt) cc_final: 0.8172 (mt) REVERT: K 246 TYR cc_start: 0.8223 (m-80) cc_final: 0.7796 (m-80) REVERT: K 272 GLU cc_start: 0.7234 (tt0) cc_final: 0.6772 (mm-30) REVERT: D 111 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6045 (mp0) REVERT: D 135 TYR cc_start: 0.8178 (m-80) cc_final: 0.7781 (m-80) REVERT: G 30 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7273 (mt0) REVERT: G 60 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8479 (mt) REVERT: G 61 LYS cc_start: 0.7855 (tmmt) cc_final: 0.7501 (mptt) REVERT: G 97 GLU cc_start: 0.8199 (tp30) cc_final: 0.7943 (tp30) REVERT: G 117 LYS cc_start: 0.8419 (ttmt) cc_final: 0.6899 (mmtt) REVERT: F 11 MET cc_start: 0.8117 (ttp) cc_final: 0.7747 (ttp) REVERT: F 21 LYS cc_start: 0.8280 (mmtp) cc_final: 0.8055 (mttm) REVERT: F 73 ARG cc_start: 0.6949 (tmt170) cc_final: 0.6684 (mtt-85) REVERT: B 132 LYS cc_start: 0.8014 (ttpp) cc_final: 0.7662 (ttpt) REVERT: B 152 ARG cc_start: 0.7698 (mtt180) cc_final: 0.6591 (mmm160) REVERT: B 168 LYS cc_start: 0.7716 (mtmm) cc_final: 0.7282 (mtmm) REVERT: B 186 SER cc_start: 0.8703 (t) cc_final: 0.8173 (m) REVERT: B 327 LYS cc_start: 0.8309 (tppp) cc_final: 0.7735 (ttpt) REVERT: B 366 ASP cc_start: 0.8499 (t0) cc_final: 0.7959 (t0) outliers start: 22 outliers final: 18 residues processed: 246 average time/residue: 0.6281 time to fit residues: 221.0200 Evaluate side-chains 253 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 111 CYS Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain E residue 88 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 148 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.124395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.106073 restraints weight = 52599.083| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.68 r_work: 0.2960 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15075 Z= 0.222 Angle : 0.516 13.780 20544 Z= 0.259 Chirality : 0.038 0.147 2284 Planarity : 0.004 0.061 2625 Dihedral : 7.323 178.807 2087 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.34 % Allowed : 11.75 % Favored : 86.90 % 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: 0.85 (0.20), residues: 1887 helix: 1.34 (0.17), residues: 954 sheet: -0.72 (0.39), residues: 172 loop : 0.01 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 142 HIS 0.003 0.001 HIS D 244 PHE 0.020 0.001 PHE K 89 TYR 0.020 0.001 TYR A 314 ARG 0.010 0.000 ARG B 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6482.05 seconds wall clock time: 115 minutes 24.46 seconds (6924.46 seconds total)