Starting phenix.real_space_refine on Wed Mar 20 10:22:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3j_25660/03_2024/7t3j_25660.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3j_25660/03_2024/7t3j_25660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3j_25660/03_2024/7t3j_25660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3j_25660/03_2024/7t3j_25660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3j_25660/03_2024/7t3j_25660.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3j_25660/03_2024/7t3j_25660.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 33 5.16 5 C 16843 2.51 5 N 4913 2.21 5 O 5227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 34": "OE1" <-> "OE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "G GLU 302": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "H TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "K GLU 173": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27076 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 196 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "K" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 15.48, per 1000 atoms: 0.57 Number of scatterers: 27076 At special positions: 0 Unit cell: (128.1, 161.7, 175.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 60 15.00 O 5227 8.00 N 4913 7.00 C 16843 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.87 Conformation dependent library (CDL) restraints added in 5.3 seconds 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6226 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 53 sheets defined 34.8% alpha, 20.6% beta 5 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 7.69 Creating SS restraints... Processing helix chain 'A' and resid 9 through 33 removed outlier: 3.944A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 49 through 58 removed outlier: 4.128A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.899A pdb=" N LYS A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 195 through 212 Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.910A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 removed outlier: 3.506A pdb=" N ILE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.519A pdb=" N ASP A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.774A pdb=" N LEU A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 397 Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.686A pdb=" N LEU A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.728A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.744A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.536A pdb=" N LEU B 118 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.902A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.597A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.899A pdb=" N GLY B 312 " --> pdb=" O PRO B 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.991A pdb=" N LEU C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 74 through 77 removed outlier: 3.528A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 77' Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.730A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 118 " --> pdb=" O ARG C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.837A pdb=" N VAL C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA C 136 " --> pdb=" O ASP C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 132 through 136' Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 150 through 163 removed outlier: 3.610A pdb=" N ALA D 154 " --> pdb=" O PHE D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.512A pdb=" N ILE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 322 through 332 removed outlier: 3.521A pdb=" N LEU D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 51 through 55 Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 208 through 223 Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.530A pdb=" N GLY E 305 " --> pdb=" O GLU E 302 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER E 306 " --> pdb=" O PRO E 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 302 through 306' Processing helix chain 'E' and resid 322 through 332 removed outlier: 3.532A pdb=" N LEU E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 55 removed outlier: 3.796A pdb=" N SER F 55 " --> pdb=" O ARG F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 208 through 223 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 92 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 322 through 332 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 322 through 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 82 through 92 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 150 through 163 Processing helix chain 'I' and resid 164 through 171 removed outlier: 6.331A pdb=" N ARG I 169 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 302 through 304 No H-bonds generated for 'chain 'I' and resid 302 through 304' Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 47 through 70 removed outlier: 3.522A pdb=" N PHE J 55 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 136 Processing helix chain 'J' and resid 140 through 147 removed outlier: 3.754A pdb=" N ILE J 143 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 147 " --> pdb=" O THR J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 152 removed outlier: 3.537A pdb=" N VAL J 151 " --> pdb=" O PRO J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 169 Processing helix chain 'J' and resid 180 through 189 Processing helix chain 'J' and resid 191 through 200 Processing helix chain 'J' and resid 211 through 222 Processing helix chain 'K' and resid 47 through 70 removed outlier: 4.666A pdb=" N ASP K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ILE K 58 " --> pdb=" O GLU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 136 Processing helix chain 'K' and resid 142 through 147 removed outlier: 3.872A pdb=" N LEU K 146 " --> pdb=" O TRP K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 168 Processing helix chain 'K' and resid 180 through 189 Processing helix chain 'K' and resid 191 through 200 removed outlier: 3.567A pdb=" N PHE K 195 " --> pdb=" O SER K 191 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR K 198 " --> pdb=" O ASN K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 5.658A pdb=" N GLY B 285 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLY B 287 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 240 removed outlier: 4.221A pdb=" N PHE B 81 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 267 removed outlier: 5.780A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 61 removed outlier: 3.891A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE B 61 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER B 108 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 68 removed outlier: 4.821A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 220 through 222 removed outlier: 4.696A pdb=" N ASN B 220 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB3, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AB6, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.880A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 177 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP D 196 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL D 179 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG D 194 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 181 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA D 192 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS D 183 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AB9, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AC1, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.771A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC3, first strand: chain 'D' and resid 306 through 307 removed outlier: 3.575A pdb=" N LYS D 312 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.806A pdb=" N PHE E 355 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.829A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL E 179 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG E 194 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'E' and resid 63 through 70 removed outlier: 4.513A pdb=" N ALA E 101 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC9, first strand: chain 'F' and resid 31 through 32 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.911A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL F 177 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP F 196 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL F 179 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG F 194 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD3, first strand: chain 'F' and resid 64 through 70 Processing sheet with id=AD4, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD5, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.672A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 31 through 33 Processing sheet with id=AD7, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.899A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD9, first strand: chain 'G' and resid 63 through 70 removed outlier: 4.377A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 285 through 287 Processing sheet with id=AE2, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.983A pdb=" N PHE H 355 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 188 through 196 removed outlier: 6.472A pdb=" N HIS H 183 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA H 192 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE H 181 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG H 194 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL H 179 " --> pdb=" O ARG H 194 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASP H 196 " --> pdb=" O VAL H 177 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL H 177 " --> pdb=" O ASP H 196 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.823A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.823A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS H 261 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR H 97 " --> pdb=" O LYS H 261 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS H 263 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU H 265 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ALA H 101 " --> pdb=" O LEU H 265 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AE7, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.944A pdb=" N VAL H 307 " --> pdb=" O LYS H 312 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.698A pdb=" N GLY I 353 " --> pdb=" O PHE I 33 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.523A pdb=" N ARG I 117 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL I 177 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP I 196 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL I 179 " --> pdb=" O ARG I 194 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG I 194 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE I 181 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA I 192 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS I 183 " --> pdb=" O ALA I 190 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.523A pdb=" N ARG I 117 " --> pdb=" O ASP I 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.945A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 243 through 244 removed outlier: 4.575A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR J 12 " --> pdb=" O TYR J 31 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR J 31 " --> pdb=" O THR J 12 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA J 14 " --> pdb=" O THR J 29 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR J 29 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG J 16 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN J 27 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N HIS J 26 " --> pdb=" O THR J 41 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR J 41 " --> pdb=" O HIS J 26 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP J 28 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE J 39 " --> pdb=" O TRP J 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU J 30 " --> pdb=" O MET J 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF5, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.524A pdb=" N VAL I 307 " --> pdb=" O LYS I 312 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'J' and resid 85 through 91 removed outlier: 3.603A pdb=" N ASP J 73 " --> pdb=" O VAL J 91 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU J 119 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER J 99 " --> pdb=" O GLY J 120 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 4 through 6 removed outlier: 6.198A pdb=" N HIS K 26 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR K 41 " --> pdb=" O HIS K 26 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TRP K 28 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE K 39 " --> pdb=" O TRP K 28 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU K 30 " --> pdb=" O MET K 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 85 through 90 removed outlier: 5.362A pdb=" N LEU K 119 " --> pdb=" O THR K 113 " (cutoff:3.500A) 1123 hydrogen bonds defined for protein. 3072 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 8.75 Time building geometry restraints manager: 10.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7141 1.33 - 1.45: 5339 1.45 - 1.57: 15125 1.57 - 1.69: 120 1.69 - 1.81: 52 Bond restraints: 27777 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.39e+00 bond pdb=" CB ARG A 302 " pdb=" CG ARG A 302 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.83e+00 bond pdb=" CA LYS A 71 " pdb=" C LYS A 71 " ideal model delta sigma weight residual 1.524 1.544 -0.020 1.26e-02 6.30e+03 2.62e+00 bond pdb=" CB GLN K 27 " pdb=" CG GLN K 27 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.61e+00 bond pdb=" C HIS C 93 " pdb=" N PRO C 94 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.61e+00 ... (remaining 27772 not shown) Histogram of bond angle deviations from ideal: 94.00 - 102.12: 80 102.12 - 110.23: 6294 110.23 - 118.35: 15358 118.35 - 126.47: 15633 126.47 - 134.59: 680 Bond angle restraints: 38045 Sorted by residual: angle pdb=" C LYS G 77 " pdb=" N THR G 78 " pdb=" CA THR G 78 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" CB MET K 1 " pdb=" CG MET K 1 " pdb=" SD MET K 1 " ideal model delta sigma weight residual 112.70 124.91 -12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C PRO B 205 " pdb=" N GLU B 206 " pdb=" CA GLU B 206 " ideal model delta sigma weight residual 121.54 128.86 -7.32 1.91e+00 2.74e-01 1.47e+01 angle pdb=" N PRO D 246 " pdb=" CD PRO D 246 " pdb=" CG PRO D 246 " ideal model delta sigma weight residual 103.20 97.50 5.70 1.50e+00 4.44e-01 1.44e+01 angle pdb=" CB PRO D 246 " pdb=" CG PRO D 246 " pdb=" CD PRO D 246 " ideal model delta sigma weight residual 106.10 94.00 12.10 3.20e+00 9.77e-02 1.43e+01 ... (remaining 38040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 16160 35.77 - 71.54: 512 71.54 - 107.31: 42 107.31 - 143.08: 1 143.08 - 178.85: 6 Dihedral angle restraints: 16721 sinusoidal: 7075 harmonic: 9646 Sorted by residual: dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 52.46 147.54 1 1.50e+01 4.44e-03 7.87e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 52.68 147.32 1 1.50e+01 4.44e-03 7.86e+01 dihedral pdb=" O4' C M 37 " pdb=" C1' C M 37 " pdb=" N1 C M 37 " pdb=" C2 C M 37 " ideal model delta sinusoidal sigma weight residual 232.00 53.15 178.85 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 16718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3696 0.065 - 0.131: 534 0.131 - 0.196: 40 0.196 - 0.261: 7 0.261 - 0.327: 3 Chirality restraints: 4280 Sorted by residual: chirality pdb=" CB ILE E 72 " pdb=" CA ILE E 72 " pdb=" CG1 ILE E 72 " pdb=" CG2 ILE E 72 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB ILE K 6 " pdb=" CA ILE K 6 " pdb=" CG1 ILE K 6 " pdb=" CG2 ILE K 6 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB THR E 97 " pdb=" CA THR E 97 " pdb=" OG1 THR E 97 " pdb=" CG2 THR E 97 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 4277 not shown) Planarity restraints: 4785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 82 " 0.085 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO F 83 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO F 83 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO F 83 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO A 72 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 162 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.46e+00 pdb=" N PRO C 163 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 163 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 163 " 0.042 5.00e-02 4.00e+02 ... (remaining 4782 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4988 2.77 - 3.30: 24372 3.30 - 3.84: 48736 3.84 - 4.37: 57947 4.37 - 4.90: 96063 Nonbonded interactions: 232106 Sorted by model distance: nonbonded pdb=" OE1 GLN K 27 " pdb=" OG1 THR K 41 " model vdw 2.241 2.440 nonbonded pdb=" OH TYR G 290 " pdb=" O GLY G 297 " model vdw 2.244 2.440 nonbonded pdb=" O ALA J 141 " pdb=" OG1 THR J 144 " model vdw 2.266 2.440 nonbonded pdb=" OG SER B 24 " pdb=" O PHE B 31 " model vdw 2.282 2.440 nonbonded pdb=" O VAL C 100 " pdb=" OG SER C 179 " model vdw 2.298 2.440 ... (remaining 232101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } ncs_group { reference = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.060 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 74.900 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 27777 Z= 0.237 Angle : 0.740 12.205 38045 Z= 0.396 Chirality : 0.046 0.327 4280 Planarity : 0.007 0.127 4785 Dihedral : 17.151 178.855 10495 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.58 % Allowed : 17.10 % Favored : 82.32 % 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: -1.91 (0.13), residues: 3322 helix: -1.34 (0.12), residues: 1056 sheet: 0.44 (0.23), residues: 522 loop : -1.77 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 193 HIS 0.008 0.001 HIS D 159 PHE 0.015 0.002 PHE K 212 TYR 0.045 0.002 TYR D 304 ARG 0.014 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 236 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.7735 (mpt-90) cc_final: 0.7517 (mmp-170) REVERT: G 51 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: I 203 ARG cc_start: 0.7349 (ptp-110) cc_final: 0.7057 (ttm110) REVERT: J 113 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8950 (p) REVERT: K 62 PHE cc_start: 0.8702 (t80) cc_final: 0.8476 (t80) outliers start: 15 outliers final: 4 residues processed: 245 average time/residue: 0.4028 time to fit residues: 154.2788 Evaluate side-chains 223 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 217 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain J residue 123 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 303 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN F 316 GLN F 348 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27777 Z= 0.325 Angle : 0.573 7.357 38045 Z= 0.301 Chirality : 0.041 0.210 4280 Planarity : 0.005 0.073 4785 Dihedral : 14.354 176.309 4616 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.22 % Allowed : 16.68 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3322 helix: 0.20 (0.15), residues: 1049 sheet: 0.72 (0.23), residues: 503 loop : -1.53 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 49 HIS 0.008 0.001 HIS B 42 PHE 0.016 0.002 PHE I 114 TYR 0.018 0.002 TYR F 290 ARG 0.005 0.000 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 233 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 TRP cc_start: 0.8503 (t-100) cc_final: 0.8296 (t-100) REVERT: D 216 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6443 (mt-10) REVERT: G 51 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8270 (mp10) REVERT: G 87 ASP cc_start: 0.8406 (m-30) cc_final: 0.8101 (m-30) REVERT: G 94 ASN cc_start: 0.8727 (p0) cc_final: 0.8470 (p0) outliers start: 58 outliers final: 35 residues processed: 275 average time/residue: 0.4055 time to fit residues: 174.2071 Evaluate side-chains 247 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 210 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 220 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 168 optimal weight: 0.0980 chunk 94 optimal weight: 0.8980 chunk 252 optimal weight: 0.9980 chunk 206 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 328 optimal weight: 4.9990 chunk 270 optimal weight: 0.6980 chunk 301 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 243 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 348 ASN J 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27777 Z= 0.151 Angle : 0.488 6.730 38045 Z= 0.255 Chirality : 0.038 0.184 4280 Planarity : 0.004 0.060 4785 Dihedral : 14.228 177.622 4610 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.11 % Allowed : 17.14 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3322 helix: 0.88 (0.15), residues: 1068 sheet: 0.87 (0.23), residues: 506 loop : -1.37 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 159 HIS 0.013 0.001 HIS A 203 PHE 0.007 0.001 PHE I 114 TYR 0.011 0.001 TYR E 304 ARG 0.004 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 216 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7323 (tp) REVERT: B 170 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7503 (ptm-80) REVERT: F 216 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: G 51 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8111 (mp10) REVERT: G 87 ASP cc_start: 0.8379 (m-30) cc_final: 0.7862 (m-30) REVERT: G 94 ASN cc_start: 0.8684 (p0) cc_final: 0.8437 (p0) REVERT: G 351 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8778 (ttp80) REVERT: K 197 LYS cc_start: 0.8271 (mtmt) cc_final: 0.8052 (mtmm) outliers start: 55 outliers final: 24 residues processed: 255 average time/residue: 0.4137 time to fit residues: 165.5567 Evaluate side-chains 233 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 220 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 300 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 204 optimal weight: 4.9990 chunk 304 optimal weight: 0.0040 chunk 322 optimal weight: 0.9990 chunk 159 optimal weight: 0.0050 chunk 289 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 overall best weight: 0.5208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 HIS J 194 ASN K 26 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27777 Z= 0.136 Angle : 0.468 7.214 38045 Z= 0.242 Chirality : 0.038 0.182 4280 Planarity : 0.004 0.059 4785 Dihedral : 14.139 177.897 4609 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.26 % Allowed : 17.10 % Favored : 80.64 % 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: -0.08 (0.15), residues: 3322 helix: 1.37 (0.16), residues: 1061 sheet: 0.84 (0.23), residues: 523 loop : -1.30 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 159 HIS 0.010 0.001 HIS B 114 PHE 0.008 0.001 PHE K 212 TYR 0.013 0.001 TYR G 314 ARG 0.004 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 220 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LYS cc_start: 0.7836 (mttt) cc_final: 0.7623 (mtmt) REVERT: B 170 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7511 (ptm-80) REVERT: D 44 MET cc_start: 0.6685 (mpp) cc_final: 0.6431 (ptp) REVERT: E 105 SER cc_start: 0.7084 (m) cc_final: 0.6691 (t) REVERT: F 216 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: F 240 ASP cc_start: 0.7526 (p0) cc_final: 0.7036 (m-30) REVERT: G 87 ASP cc_start: 0.8301 (m-30) cc_final: 0.7864 (m-30) REVERT: G 94 ASN cc_start: 0.8621 (p0) cc_final: 0.8356 (p0) REVERT: G 351 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8764 (ttp80) REVERT: J 6 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8299 (tt) REVERT: K 197 LYS cc_start: 0.8335 (mtmt) cc_final: 0.8080 (mtmm) REVERT: K 209 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7846 (mptt) outliers start: 59 outliers final: 30 residues processed: 267 average time/residue: 0.4043 time to fit residues: 168.5002 Evaluate side-chains 242 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 209 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 220 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 268 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 164 optimal weight: 4.9990 chunk 289 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS H 163 ASN H 281 ASN H 343 HIS J 194 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27777 Z= 0.208 Angle : 0.498 9.127 38045 Z= 0.257 Chirality : 0.039 0.187 4280 Planarity : 0.004 0.058 4785 Dihedral : 14.124 176.686 4606 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.49 % Allowed : 17.37 % Favored : 80.14 % 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: -0.02 (0.15), residues: 3322 helix: 1.47 (0.16), residues: 1055 sheet: 0.85 (0.23), residues: 523 loop : -1.29 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 362 HIS 0.009 0.001 HIS A 203 PHE 0.011 0.001 PHE I 114 TYR 0.015 0.001 TYR E 304 ARG 0.005 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 230 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.7203 (mt) cc_final: 0.6872 (mt) REVERT: A 228 TRP cc_start: 0.8494 (t-100) cc_final: 0.8256 (t-100) REVERT: A 281 MET cc_start: 0.5230 (mmm) cc_final: 0.4946 (tpt) REVERT: A 366 LEU cc_start: 0.7427 (tp) cc_final: 0.7194 (tp) REVERT: A 428 ILE cc_start: 0.8503 (mm) cc_final: 0.8228 (mt) REVERT: B 170 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7571 (ptm-80) REVERT: E 105 SER cc_start: 0.7374 (m) cc_final: 0.6829 (t) REVERT: E 212 ASP cc_start: 0.7212 (m-30) cc_final: 0.6978 (m-30) REVERT: F 216 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: F 240 ASP cc_start: 0.7676 (p0) cc_final: 0.7118 (m-30) REVERT: G 87 ASP cc_start: 0.8320 (m-30) cc_final: 0.7871 (m-30) REVERT: G 94 ASN cc_start: 0.8519 (p0) cc_final: 0.8275 (p0) REVERT: J 6 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8308 (tt) REVERT: K 209 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7927 (mptt) outliers start: 65 outliers final: 46 residues processed: 280 average time/residue: 0.4437 time to fit residues: 194.7894 Evaluate side-chains 261 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 213 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 220 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 108 optimal weight: 1.9990 chunk 290 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 268 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN E 186 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS H 129 ASN H 343 HIS I 186 GLN J 26 HIS J 194 ASN K 26 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 27777 Z= 0.245 Angle : 0.528 9.442 38045 Z= 0.274 Chirality : 0.040 0.189 4280 Planarity : 0.004 0.057 4785 Dihedral : 14.153 176.217 4606 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.07 % Allowed : 17.45 % Favored : 79.49 % 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: -0.05 (0.15), residues: 3322 helix: 1.42 (0.16), residues: 1063 sheet: 0.79 (0.23), residues: 519 loop : -1.28 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 362 HIS 0.010 0.001 HIS A 203 PHE 0.011 0.001 PHE I 114 TYR 0.016 0.002 TYR E 290 ARG 0.006 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 217 time to evaluate : 2.897 Fit side-chains revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6697 (t80) REVERT: A 121 LEU cc_start: 0.7406 (mt) cc_final: 0.7103 (mt) REVERT: A 228 TRP cc_start: 0.8505 (t-100) cc_final: 0.8254 (t-100) REVERT: A 366 LEU cc_start: 0.7477 (tp) cc_final: 0.7250 (tp) REVERT: A 428 ILE cc_start: 0.8486 (mm) cc_final: 0.8238 (mt) REVERT: C 125 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6960 (mm-30) REVERT: D 44 MET cc_start: 0.6845 (mpp) cc_final: 0.6442 (ptp) REVERT: D 302 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6832 (mm-30) REVERT: E 212 ASP cc_start: 0.7223 (m-30) cc_final: 0.7018 (m-30) REVERT: F 216 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: F 240 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7556 (p0) REVERT: G 87 ASP cc_start: 0.8346 (m-30) cc_final: 0.7880 (m-30) REVERT: G 94 ASN cc_start: 0.8484 (p0) cc_final: 0.8249 (p0) REVERT: J 6 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8263 (tp) REVERT: K 209 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7987 (mptt) outliers start: 80 outliers final: 60 residues processed: 276 average time/residue: 0.4016 time to fit residues: 173.6519 Evaluate side-chains 267 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 203 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 129 ASN Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 220 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 311 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 321 optimal weight: 0.0370 chunk 201 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN E 186 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS H 129 ASN I 186 GLN J 26 HIS J 194 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27777 Z= 0.206 Angle : 0.511 9.199 38045 Z= 0.265 Chirality : 0.039 0.186 4280 Planarity : 0.004 0.058 4785 Dihedral : 14.143 176.745 4606 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.03 % Allowed : 18.02 % Favored : 78.95 % 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: 0.04 (0.15), residues: 3322 helix: 1.51 (0.16), residues: 1062 sheet: 0.90 (0.23), residues: 516 loop : -1.24 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 362 HIS 0.017 0.001 HIS K 26 PHE 0.011 0.001 PHE C 183 TYR 0.014 0.001 TYR D 304 ARG 0.005 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 210 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6677 (t80) REVERT: A 121 LEU cc_start: 0.7351 (mt) cc_final: 0.7051 (mt) REVERT: A 228 TRP cc_start: 0.8484 (t-100) cc_final: 0.8224 (t-100) REVERT: A 366 LEU cc_start: 0.7488 (tp) cc_final: 0.7259 (tp) REVERT: A 397 ARG cc_start: 0.7257 (mmm-85) cc_final: 0.7022 (mtt-85) REVERT: A 428 ILE cc_start: 0.8483 (mm) cc_final: 0.8244 (mt) REVERT: C 125 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6851 (mm-30) REVERT: D 44 MET cc_start: 0.6926 (mpp) cc_final: 0.6667 (ptp) REVERT: E 212 ASP cc_start: 0.7262 (m-30) cc_final: 0.7051 (m-30) REVERT: F 216 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: G 87 ASP cc_start: 0.8365 (m-30) cc_final: 0.7893 (m-30) REVERT: G 94 ASN cc_start: 0.8494 (p0) cc_final: 0.8273 (p0) REVERT: H 129 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7613 (m110) REVERT: J 6 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8257 (tp) outliers start: 79 outliers final: 61 residues processed: 271 average time/residue: 0.4119 time to fit residues: 172.8149 Evaluate side-chains 271 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 206 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 129 ASN Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 146 ASN Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 220 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 199 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 204 optimal weight: 3.9990 chunk 219 optimal weight: 0.0030 chunk 159 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN E 186 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS H 129 ASN I 186 GLN J 26 HIS J 194 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27777 Z= 0.249 Angle : 0.532 8.101 38045 Z= 0.275 Chirality : 0.040 0.189 4280 Planarity : 0.004 0.058 4785 Dihedral : 14.127 176.880 4606 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.11 % Allowed : 18.02 % Favored : 78.87 % 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: 0.01 (0.15), residues: 3322 helix: 1.44 (0.16), residues: 1066 sheet: 0.89 (0.23), residues: 516 loop : -1.25 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 394 HIS 0.010 0.001 HIS A 203 PHE 0.011 0.001 PHE C 183 TYR 0.016 0.002 TYR E 290 ARG 0.005 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 211 time to evaluate : 3.237 Fit side-chains revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6655 (t80) REVERT: A 121 LEU cc_start: 0.7329 (mt) cc_final: 0.7045 (mt) REVERT: A 228 TRP cc_start: 0.8489 (t-100) cc_final: 0.8243 (t-100) REVERT: A 397 ARG cc_start: 0.7202 (mmm-85) cc_final: 0.6942 (mtt-85) REVERT: C 21 MET cc_start: 0.7308 (tpp) cc_final: 0.7101 (tpp) REVERT: C 125 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6843 (mm-30) REVERT: D 44 MET cc_start: 0.6969 (mpp) cc_final: 0.6756 (ptp) REVERT: D 302 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6886 (mm-30) REVERT: E 212 ASP cc_start: 0.7122 (m-30) cc_final: 0.6807 (m-30) REVERT: F 216 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: G 87 ASP cc_start: 0.8382 (m-30) cc_final: 0.7902 (m-30) REVERT: G 94 ASN cc_start: 0.8499 (p0) cc_final: 0.8285 (p0) REVERT: J 6 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8276 (tp) REVERT: K 207 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6486 (tpm170) outliers start: 81 outliers final: 66 residues processed: 271 average time/residue: 0.4277 time to fit residues: 180.3464 Evaluate side-chains 274 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 204 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 146 ASN Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 207 ARG Chi-restraints excluded: chain K residue 220 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 292 optimal weight: 0.9990 chunk 308 optimal weight: 4.9990 chunk 281 optimal weight: 0.7980 chunk 299 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 235 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 271 optimal weight: 7.9990 chunk 283 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN E 186 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS I 186 GLN J 26 HIS J 194 ASN K 26 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27777 Z= 0.168 Angle : 0.503 8.479 38045 Z= 0.259 Chirality : 0.039 0.184 4280 Planarity : 0.004 0.058 4785 Dihedral : 14.090 178.074 4606 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.80 % Allowed : 18.29 % Favored : 78.91 % 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: 0.11 (0.15), residues: 3322 helix: 1.60 (0.16), residues: 1063 sheet: 0.97 (0.23), residues: 519 loop : -1.25 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 394 HIS 0.010 0.001 HIS A 203 PHE 0.009 0.001 PHE K 212 TYR 0.015 0.001 TYR D 304 ARG 0.006 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 209 time to evaluate : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6641 (t80) REVERT: A 121 LEU cc_start: 0.7410 (mt) cc_final: 0.7136 (mt) REVERT: A 228 TRP cc_start: 0.8504 (t-100) cc_final: 0.8245 (t-100) REVERT: A 397 ARG cc_start: 0.7360 (mmm-85) cc_final: 0.6967 (ttm-80) REVERT: C 21 MET cc_start: 0.7365 (tpp) cc_final: 0.7137 (tpp) REVERT: C 46 ASP cc_start: 0.5309 (p0) cc_final: 0.4964 (p0) REVERT: C 125 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6997 (mm-30) REVERT: D 302 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6821 (mm-30) REVERT: E 105 SER cc_start: 0.7517 (m) cc_final: 0.6947 (t) REVERT: E 212 ASP cc_start: 0.7124 (m-30) cc_final: 0.6807 (m-30) REVERT: F 216 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: G 87 ASP cc_start: 0.8364 (m-30) cc_final: 0.7892 (m-30) REVERT: G 94 ASN cc_start: 0.8487 (p0) cc_final: 0.8270 (p0) REVERT: J 6 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8241 (tp) REVERT: K 207 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6346 (tpm170) REVERT: K 209 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7946 (mptt) outliers start: 73 outliers final: 59 residues processed: 264 average time/residue: 0.4224 time to fit residues: 173.9722 Evaluate side-chains 266 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 203 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 207 ARG Chi-restraints excluded: chain K residue 220 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 196 optimal weight: 3.9990 chunk 317 optimal weight: 0.7980 chunk 193 optimal weight: 0.7980 chunk 150 optimal weight: 0.0770 chunk 220 optimal weight: 6.9990 chunk 332 optimal weight: 20.0000 chunk 306 optimal weight: 0.7980 chunk 264 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN E 186 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS I 186 GLN J 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27777 Z= 0.156 Angle : 0.498 8.585 38045 Z= 0.256 Chirality : 0.038 0.182 4280 Planarity : 0.004 0.061 4785 Dihedral : 14.065 178.407 4606 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.45 % Allowed : 18.63 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3322 helix: 1.68 (0.16), residues: 1063 sheet: 0.98 (0.23), residues: 519 loop : -1.24 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 193 HIS 0.010 0.001 HIS A 203 PHE 0.038 0.001 PHE C 15 TYR 0.016 0.001 TYR E 304 ARG 0.007 0.000 ARG E 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6644 Ramachandran restraints generated. 3322 Oldfield, 0 Emsley, 3322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 213 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6643 (t80) REVERT: A 121 LEU cc_start: 0.7436 (mt) cc_final: 0.7163 (mt) REVERT: A 228 TRP cc_start: 0.8507 (t-100) cc_final: 0.8254 (t-100) REVERT: A 397 ARG cc_start: 0.7341 (mmm-85) cc_final: 0.6948 (ttm-80) REVERT: C 21 MET cc_start: 0.7371 (tpp) cc_final: 0.7135 (tpp) REVERT: C 46 ASP cc_start: 0.5296 (p0) cc_final: 0.4942 (p0) REVERT: C 125 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7145 (mm-30) REVERT: D 302 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6742 (mm-30) REVERT: E 105 SER cc_start: 0.7472 (m) cc_final: 0.6917 (t) REVERT: E 212 ASP cc_start: 0.7122 (m-30) cc_final: 0.6808 (m-30) REVERT: F 216 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: G 87 ASP cc_start: 0.8364 (m-30) cc_final: 0.8020 (m-30) REVERT: G 94 ASN cc_start: 0.8513 (p0) cc_final: 0.8275 (p0) REVERT: J 6 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8300 (tt) REVERT: K 32 TYR cc_start: 0.7645 (t80) cc_final: 0.7287 (t80) outliers start: 64 outliers final: 55 residues processed: 260 average time/residue: 0.4080 time to fit residues: 164.5592 Evaluate side-chains 263 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 205 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 351 ARG Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 220 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 210 optimal weight: 2.9990 chunk 282 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 244 optimal weight: 0.0470 chunk 39 optimal weight: 30.0000 chunk 73 optimal weight: 0.2980 chunk 265 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 HIS I 186 GLN J 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.108470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.087638 restraints weight = 75645.508| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.21 r_work: 0.3246 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 27777 Z= 0.144 Angle : 0.496 15.482 38045 Z= 0.252 Chirality : 0.038 0.178 4280 Planarity : 0.004 0.061 4785 Dihedral : 14.033 179.417 4606 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.19 % Allowed : 18.94 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3322 helix: 1.75 (0.16), residues: 1064 sheet: 1.00 (0.23), residues: 521 loop : -1.22 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 362 HIS 0.011 0.001 HIS H 343 PHE 0.031 0.001 PHE C 15 TYR 0.016 0.001 TYR E 304 ARG 0.006 0.000 ARG E 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5576.10 seconds wall clock time: 101 minutes 35.15 seconds (6095.15 seconds total)