Starting phenix.real_space_refine on Sun Mar 24 19:04:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smq_10245/03_2024/6smq_10245_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smq_10245/03_2024/6smq_10245.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smq_10245/03_2024/6smq_10245_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smq_10245/03_2024/6smq_10245_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smq_10245/03_2024/6smq_10245_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smq_10245/03_2024/6smq_10245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smq_10245/03_2024/6smq_10245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smq_10245/03_2024/6smq_10245_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smq_10245/03_2024/6smq_10245_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 21504 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 82 5.16 5 C 14061 2.51 5 N 3702 2.21 5 O 4291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A ARG 438": "NH1" <-> "NH2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 516": "OD1" <-> "OD2" Residue "B ASP 536": "OD1" <-> "OD2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 601": "OD1" <-> "OD2" Residue "B GLU 643": "OE1" <-> "OE2" Residue "B PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 837": "OD1" <-> "OD2" Residue "B ASP 880": "OD1" <-> "OD2" Residue "B ASP 882": "OD1" <-> "OD2" Residue "B TYR 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 926": "OD1" <-> "OD2" Residue "B ASP 991": "OD1" <-> "OD2" Residue "B TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 23": "OD1" <-> "OD2" Residue "D ASP 30": "OD1" <-> "OD2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D ASP 77": "OD1" <-> "OD2" Residue "D ASP 94": "OD1" <-> "OD2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ASP 182": "OD1" <-> "OD2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D ASP 329": "OD1" <-> "OD2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 415": "OE1" <-> "OE2" Residue "D ARG 438": "NH1" <-> "NH2" Residue "D GLU 455": "OE1" <-> "OE2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E ASP 190": "OD1" <-> "OD2" Residue "E ASP 208": "OD1" <-> "OD2" Residue "E ASP 294": "OD1" <-> "OD2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E ASP 335": "OD1" <-> "OD2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 429": "OD1" <-> "OD2" Residue "E PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 601": "OD1" <-> "OD2" Residue "E ASP 613": "OD1" <-> "OD2" Residue "E GLU 643": "OE1" <-> "OE2" Residue "E PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 733": "OD1" <-> "OD2" Residue "E TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 817": "OE1" <-> "OE2" Residue "E ASP 837": "OD1" <-> "OD2" Residue "E TYR 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 924": "OE1" <-> "OE2" Residue "E PHE 946": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22136 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3843 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 460} Chain: "B" Number of atoms: 7076 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 903, 7068 Classifications: {'peptide': 903} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 871} Conformer: "B" Number of residues, atoms: 903, 7068 Classifications: {'peptide': 903} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 871} bond proxies already assigned to first conformer: 7222 Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 82 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "D" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3843 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 460} Chain: "E" Number of atoms: 7138 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 911, 7130 Classifications: {'peptide': 911} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 879} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 911, 7130 Classifications: {'peptide': 911} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 879} Chain breaks: 1 bond proxies already assigned to first conformer: 7284 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'5PL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'5PL:plan-1': 1, 'PLM:plan-1': 1, '5PL:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'C8E': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'5PL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'5PL:plan-1': 1, 'PLM:plan-1': 1, '5PL:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'C8E': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Time building chain proxies: 16.85, per 1000 atoms: 0.76 Number of scatterers: 22136 At special positions: 0 Unit cell: (134.82, 149.8, 150.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 82 16.00 O 4291 8.00 N 3702 7.00 C 14061 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.95 Conformation dependent library (CDL) restraints added in 6.2 seconds 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5136 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 23 sheets defined 19.2% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.83 Creating SS restraints... Processing helix chain 'A' and resid 38 through 54 removed outlier: 3.911A pdb=" N ASN A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 82 through 85 No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 105 through 132 removed outlier: 3.685A pdb=" N TYR A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 166 removed outlier: 3.660A pdb=" N LEU A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 249 through 258 removed outlier: 4.266A pdb=" N MET A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.602A pdb=" N LEU A 330 " --> pdb=" O TRP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 381 through 394 removed outlier: 4.060A pdb=" N LEU A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 412 removed outlier: 4.147A pdb=" N ALA A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 431 Processing helix chain 'A' and resid 438 through 444 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 189 through 194 removed outlier: 3.940A pdb=" N THR B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 262 through 271 Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.976A pdb=" N ASN B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 303 No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 321 through 325 Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 446 through 452 removed outlier: 3.555A pdb=" N LYS B 451 " --> pdb=" O PRO B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 714 No H-bonds generated for 'chain 'B' and resid 712 through 714' Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 850 through 852 No H-bonds generated for 'chain 'B' and resid 850 through 852' Processing helix chain 'B' and resid 895 through 897 No H-bonds generated for 'chain 'B' and resid 895 through 897' Processing helix chain 'B' and resid 912 through 915 removed outlier: 3.636A pdb=" N LEU B 915 " --> pdb=" O LYS B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 912 through 915' Processing helix chain 'B' and resid 938 through 940 No H-bonds generated for 'chain 'B' and resid 938 through 940' Processing helix chain 'D' and resid 38 through 55 removed outlier: 4.012A pdb=" N ASN D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 66 No H-bonds generated for 'chain 'D' and resid 63 through 66' Processing helix chain 'D' and resid 82 through 85 No H-bonds generated for 'chain 'D' and resid 82 through 85' Processing helix chain 'D' and resid 105 through 132 Processing helix chain 'D' and resid 139 through 167 removed outlier: 4.176A pdb=" N ARG D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.541A pdb=" N ALA D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 removed outlier: 3.963A pdb=" N ALA D 253 " --> pdb=" O TYR D 249 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 325 through 330 Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 361 through 363 No H-bonds generated for 'chain 'D' and resid 361 through 363' Processing helix chain 'D' and resid 381 through 394 Processing helix chain 'D' and resid 398 through 400 No H-bonds generated for 'chain 'D' and resid 398 through 400' Processing helix chain 'D' and resid 402 through 411 Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'D' and resid 438 through 444 removed outlier: 3.922A pdb=" N VAL D 443 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 480 No H-bonds generated for 'chain 'D' and resid 478 through 480' Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 139 through 142 Processing helix chain 'E' and resid 189 through 194 removed outlier: 4.093A pdb=" N THR E 194 " --> pdb=" O ASP E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 262 through 271 Processing helix chain 'E' and resid 410 through 416 Processing helix chain 'E' and resid 446 through 452 Processing helix chain 'E' and resid 574 through 576 No H-bonds generated for 'chain 'E' and resid 574 through 576' Processing helix chain 'E' and resid 636 through 638 No H-bonds generated for 'chain 'E' and resid 636 through 638' Processing helix chain 'E' and resid 712 through 714 No H-bonds generated for 'chain 'E' and resid 712 through 714' Processing helix chain 'E' and resid 738 through 740 No H-bonds generated for 'chain 'E' and resid 738 through 740' Processing helix chain 'E' and resid 850 through 852 No H-bonds generated for 'chain 'E' and resid 850 through 852' Processing helix chain 'E' and resid 894 through 899 removed outlier: 4.223A pdb=" N THR E 899 " --> pdb=" O ARG E 896 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 914 No H-bonds generated for 'chain 'E' and resid 912 through 914' Processing helix chain 'E' and resid 960 through 962 No H-bonds generated for 'chain 'E' and resid 960 through 962' Processing sheet with id= A, first strand: chain 'A' and resid 71 through 73 Processing sheet with id= B, first strand: chain 'A' and resid 308 through 311 Processing sheet with id= C, first strand: chain 'A' and resid 342 through 346 removed outlier: 6.100A pdb=" N GLY A 351 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 122 through 125 removed outlier: 6.891A pdb=" N GLN B 227 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET B 203 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE B 225 " --> pdb=" O MET B 203 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL B 205 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 223 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 179 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE B 226 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 181 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR B 228 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 149 through 152 Processing sheet with id= F, first strand: chain 'B' and resid 329 through 339 removed outlier: 3.554A pdb=" N TYR B 245 " --> pdb=" O ALA B1011 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP B 882 " --> pdb=" O LYS B 950 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 952 " --> pdb=" O ASP B 880 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP B 880 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU B 954 " --> pdb=" O SER B 878 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER B 878 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY B 867 " --> pdb=" O ASN B 778 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 775 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N SER B 751 " --> pdb=" O THR B 787 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR B 628 " --> pdb=" O THR B 658 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLY B 660 " --> pdb=" O TRP B 626 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N TRP B 626 " --> pdb=" O GLY B 660 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLY B 507 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 526 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER B 457 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG B 396 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 465 " --> pdb=" O ASN B 388 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 383 " --> pdb=" O ASN B 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN B 380 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 385 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ARG B 378 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ALA B 387 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU B 376 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU B 389 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASN B 374 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLY B 391 " --> pdb=" O ARG B 372 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG B 372 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 393 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER B 370 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ASN B 395 " --> pdb=" O ARG B 368 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ARG B 368 " --> pdb=" O ASN B 395 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ARG B 397 " --> pdb=" O PHE B 366 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE B 366 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 370 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR B 347 " --> pdb=" O GLY B 340 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 354 through 357 Processing sheet with id= H, first strand: chain 'B' and resid 673 through 675 Processing sheet with id= I, first strand: chain 'B' and resid 731 through 734 Processing sheet with id= J, first strand: chain 'B' and resid 795 through 798 removed outlier: 3.509A pdb=" N LEU B 798 " --> pdb=" O THR B 803 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR B 803 " --> pdb=" O LEU B 798 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 890 through 892 Processing sheet with id= L, first strand: chain 'B' and resid 946 through 949 removed outlier: 4.336A pdb=" N LEU B 982 " --> pdb=" O LEU B 949 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 812 through 815 removed outlier: 5.833A pdb=" N LYS B 858 " --> pdb=" O PHE B 813 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N MET B 815 " --> pdb=" O ILE B 856 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE B 856 " --> pdb=" O MET B 815 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 818 through 821 removed outlier: 7.060A pdb=" N LEU B 829 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 71 through 73 Processing sheet with id= P, first strand: chain 'D' and resid 308 through 311 Processing sheet with id= Q, first strand: chain 'E' and resid 122 through 125 removed outlier: 7.196A pdb=" N GLN E 227 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N MET E 203 " --> pdb=" O PHE E 225 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE E 225 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL E 205 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL E 223 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU E 179 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE E 226 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE E 181 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N THR E 228 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 149 through 152 Processing sheet with id= S, first strand: chain 'E' and resid 329 through 339 removed outlier: 3.713A pdb=" N SER E 244 " --> pdb=" O GLN E 333 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE E 241 " --> pdb=" O LEU E1015 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE E 886 " --> pdb=" O PHE E 946 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP E 882 " --> pdb=" O LYS E 950 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU E 952 " --> pdb=" O ASP E 880 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASP E 880 " --> pdb=" O LEU E 952 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU E 954 " --> pdb=" O SER E 878 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER E 878 " --> pdb=" O LEU E 954 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA E 881 " --> pdb=" O LEU E 870 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR E 885 " --> pdb=" O GLY E 866 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY E 867 " --> pdb=" O ASN E 778 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR E 628 " --> pdb=" O THR E 658 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLY E 660 " --> pdb=" O TRP E 626 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N TRP E 626 " --> pdb=" O GLY E 660 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N GLY E 507 " --> pdb=" O GLY E 559 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER E 457 " --> pdb=" O ARG E 396 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG E 396 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR E 347 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY E 340 " --> pdb=" O TYR E 347 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 673 through 675 Processing sheet with id= U, first strand: chain 'E' and resid 890 through 892 Processing sheet with id= V, first strand: chain 'E' and resid 812 through 815 removed outlier: 6.153A pdb=" N LYS E 858 " --> pdb=" O PHE E 813 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N MET E 815 " --> pdb=" O ILE E 856 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE E 856 " --> pdb=" O MET E 815 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 818 through 822 removed outlier: 6.850A pdb=" N LEU E 829 " --> pdb=" O ALA E 819 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE E 821 " --> pdb=" O LYS E 827 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS E 827 " --> pdb=" O ILE E 821 " (cutoff:3.500A) 817 hydrogen bonds defined for protein. 2347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.20 Time building geometry restraints manager: 7.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3729 1.30 - 1.43: 6182 1.43 - 1.55: 12541 1.55 - 1.68: 20 1.68 - 1.81: 158 Bond restraints: 22630 Sorted by residual: bond pdb=" CB THR E 212 " pdb=" CG2 THR E 212 " ideal model delta sigma weight residual 1.521 1.420 0.101 3.30e-02 9.18e+02 9.37e+00 bond pdb=" N GLY B 276 " pdb=" CA GLY B 276 " ideal model delta sigma weight residual 1.448 1.474 -0.025 8.80e-03 1.29e+04 8.38e+00 bond pdb=" CB VAL E 464 " pdb=" CG1 VAL E 464 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.19e+00 bond pdb=" CA GLY E 574 " pdb=" C GLY E 574 " ideal model delta sigma weight residual 1.530 1.506 0.025 1.04e-02 9.25e+03 5.77e+00 bond pdb=" CB ASN B 997 " pdb=" CG ASN B 997 " ideal model delta sigma weight residual 1.516 1.575 -0.059 2.50e-02 1.60e+03 5.61e+00 ... (remaining 22625 not shown) Histogram of bond angle deviations from ideal: 96.47 - 104.22: 325 104.22 - 111.97: 10034 111.97 - 119.72: 8920 119.72 - 127.47: 11121 127.47 - 135.22: 201 Bond angle restraints: 30601 Sorted by residual: angle pdb=" CBR 5PL D 601 " pdb=" CBS 5PL D 601 " pdb=" CBT 5PL D 601 " ideal model delta sigma weight residual 131.61 109.98 21.63 3.00e+00 1.11e-01 5.20e+01 angle pdb=" CBR 5PL A 601 " pdb=" CBS 5PL A 601 " pdb=" CBT 5PL A 601 " ideal model delta sigma weight residual 131.61 110.67 20.94 3.00e+00 1.11e-01 4.87e+01 angle pdb=" C ALA E 131 " pdb=" N GLU E 132 " pdb=" CA GLU E 132 " ideal model delta sigma weight residual 121.54 132.38 -10.84 1.91e+00 2.74e-01 3.22e+01 angle pdb=" CA GLY B 276 " pdb=" C GLY B 276 " pdb=" O GLY B 276 " ideal model delta sigma weight residual 122.37 118.26 4.11 7.30e-01 1.88e+00 3.18e+01 angle pdb=" C LYS A 347 " pdb=" N LYS A 348 " pdb=" CA LYS A 348 " ideal model delta sigma weight residual 121.54 132.12 -10.58 1.91e+00 2.74e-01 3.07e+01 ... (remaining 30596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11925 17.92 - 35.84: 1210 35.84 - 53.76: 241 53.76 - 71.68: 42 71.68 - 89.59: 20 Dihedral angle restraints: 13438 sinusoidal: 5350 harmonic: 8088 Sorted by residual: dihedral pdb=" CA ASP B 601 " pdb=" C ASP B 601 " pdb=" N LYS B 602 " pdb=" CA LYS B 602 " ideal model delta harmonic sigma weight residual 180.00 126.61 53.39 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA GLU E 132 " pdb=" C GLU E 132 " pdb=" N LYS E 133 " pdb=" CA LYS E 133 " ideal model delta harmonic sigma weight residual 180.00 132.14 47.86 0 5.00e+00 4.00e-02 9.16e+01 dihedral pdb=" CA PHE E 790 " pdb=" C PHE E 790 " pdb=" N PHE E 791 " pdb=" CA PHE E 791 " ideal model delta harmonic sigma weight residual -180.00 -141.49 -38.51 0 5.00e+00 4.00e-02 5.93e+01 ... (remaining 13435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2361 0.063 - 0.126: 728 0.126 - 0.188: 126 0.188 - 0.251: 12 0.251 - 0.314: 12 Chirality restraints: 3239 Sorted by residual: chirality pdb=" CB ILE E 473 " pdb=" CA ILE E 473 " pdb=" CG1 ILE E 473 " pdb=" CG2 ILE E 473 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA PHE B 790 " pdb=" N PHE B 790 " pdb=" C PHE B 790 " pdb=" CB PHE B 790 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB VAL E 433 " pdb=" CA VAL E 433 " pdb=" CG1 VAL E 433 " pdb=" CG2 VAL E 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 3236 not shown) Planarity restraints: 3999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 329 " 0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 330 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1003 " 0.013 2.00e-02 2.50e+03 2.05e-02 8.37e+00 pdb=" CG TYR B1003 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B1003 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B1003 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR B1003 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B1003 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B1003 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B1003 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 157 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO E 158 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 158 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 158 " -0.039 5.00e-02 4.00e+02 ... (remaining 3996 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5567 2.79 - 3.32: 17065 3.32 - 3.84: 34760 3.84 - 4.37: 41730 4.37 - 4.90: 77766 Nonbonded interactions: 176888 Sorted by model distance: nonbonded pdb=" O PRO E 737 " pdb=" OG SER E 740 " model vdw 2.261 2.440 nonbonded pdb=" O SER A 294 " pdb=" OG SER A 299 " model vdw 2.267 2.440 nonbonded pdb=" O SER E 662 " pdb=" OG SER E 662 " model vdw 2.269 2.440 nonbonded pdb=" OD2 ASP E 183 " pdb=" OG1 THR E 228 " model vdw 2.270 2.440 nonbonded pdb=" OD2 ASP D 233 " pdb=" OH TYR D 263 " model vdw 2.283 2.440 ... (remaining 176883 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 'A' and (resid 20 through 501 or (resid 601 and (name CAA or name CAE or \ name CAF or name CAG or name CAK or name CAW or name CBH or name CBI or name CBL \ or name CBM or name CBN or name CBO or name CBP or name CBR or name CBS or name \ CBT or name CBU or name CBV or name CBW or name CBX or name CBY or name CBZ or \ name OCK or name OCL or name OCN or name OCO)) or (resid 602 and (name C1 or nam \ e C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name O2 )))) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 115 through 721 or resid 723 through 837 or resid 842 thro \ ugh 1017 or (resid 1101 through 1102 and (name C10 or name C11 or name C13 or na \ me C14 or name C6 or name C7 or name C8 or name O12 or name O9 )))) selection = (chain 'E' and (resid 115 through 721 or resid 723 through 1017 or (resid 1101 t \ hrough 1102 and (name C10 or name C11 or name C13 or name C14 or name C6 or name \ C7 or name C8 or name O12 or name O9 )))) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.020 Extract box with map and model: 3.470 Check model and map are aligned: 0.340 Set scattering table: 0.180 Process input model: 63.060 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.120 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.011 0.101 22630 Z= 0.677 Angle : 1.040 21.627 30601 Z= 0.559 Chirality : 0.062 0.314 3239 Planarity : 0.006 0.086 3999 Dihedral : 15.029 89.595 8302 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.41 % Favored : 92.41 % Rotamer: Outliers : 0.43 % Allowed : 8.28 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -3.34 (0.13), residues: 2781 helix: -2.89 (0.15), residues: 561 sheet: -0.76 (0.18), residues: 796 loop : -2.85 (0.13), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 874 HIS 0.019 0.003 HIS E 582 PHE 0.028 0.003 PHE B 790 TYR 0.048 0.003 TYR B1003 ARG 0.011 0.001 ARG E 515 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 329 time to evaluate : 2.319 Fit side-chains REVERT: A 101 ASP cc_start: 0.7657 (m-30) cc_final: 0.7305 (m-30) REVERT: A 403 LYS cc_start: 0.8784 (tmtt) cc_final: 0.8559 (tttp) REVERT: A 494 GLN cc_start: 0.8870 (pt0) cc_final: 0.8647 (pt0) REVERT: B 140 ASP cc_start: 0.8706 (t0) cc_final: 0.8463 (t0) REVERT: B 417 MET cc_start: 0.8964 (mmm) cc_final: 0.8492 (mmt) REVERT: B 436 MET cc_start: 0.8463 (mtm) cc_final: 0.8183 (mtp) REVERT: B 573 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8508 (t) REVERT: B 776 SER cc_start: 0.8918 (p) cc_final: 0.8701 (t) REVERT: B 788 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8646 (tttm) REVERT: B 854 THR cc_start: 0.8615 (m) cc_final: 0.8095 (p) REVERT: D 22 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8638 (pp) REVERT: D 398 THR cc_start: 0.8327 (t) cc_final: 0.7965 (m) REVERT: E 232 LYS cc_start: 0.7965 (ptmm) cc_final: 0.7554 (mmtp) REVERT: E 1013 ILE cc_start: 0.9263 (tp) cc_final: 0.9054 (tp) outliers start: 10 outliers final: 6 residues processed: 336 average time/residue: 0.3467 time to fit residues: 177.8214 Evaluate side-chains 266 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 258 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 516 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 217 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 GLN B 150 GLN B 374 ASN B 463 ASN B 469 GLN B 638 ASN B 702 GLN B 713 ASN B 748 ASN B 754 ASN B 782 ASN B 894 ASN B 932 GLN B 935 GLN B 951 ASN B1005 ASN D 86 ASN D 449 ASN D 457 GLN D 490 GLN E 103 GLN E 269 GLN E 278 ASN E 463 ASN E 469 GLN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 ASN E 748 ASN E 754 ASN E 800 ASN E 828 GLN E 932 GLN E 980 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22630 Z= 0.213 Angle : 0.570 10.899 30601 Z= 0.303 Chirality : 0.043 0.165 3239 Planarity : 0.004 0.065 3999 Dihedral : 8.011 75.660 3202 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.43 % Favored : 94.46 % Rotamer: Outliers : 1.76 % Allowed : 11.58 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.25 (0.14), residues: 2781 helix: -1.31 (0.20), residues: 580 sheet: -0.30 (0.18), residues: 795 loop : -2.34 (0.14), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 697 HIS 0.006 0.001 HIS E 582 PHE 0.020 0.001 PHE B 712 TYR 0.019 0.001 TYR B 514 ARG 0.004 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 299 time to evaluate : 2.419 Fit side-chains REVERT: A 94 ASP cc_start: 0.7552 (t0) cc_final: 0.7018 (p0) REVERT: A 101 ASP cc_start: 0.7348 (m-30) cc_final: 0.7097 (m-30) REVERT: A 164 MET cc_start: 0.8518 (mmm) cc_final: 0.8175 (mmm) REVERT: A 421 MET cc_start: 0.8547 (tpp) cc_final: 0.8245 (tpt) REVERT: B 140 ASP cc_start: 0.8666 (t0) cc_final: 0.8447 (t0) REVERT: B 417 MET cc_start: 0.8842 (mmm) cc_final: 0.8465 (mmt) REVERT: B 436 MET cc_start: 0.8437 (mtm) cc_final: 0.7956 (mtp) REVERT: B 707 LEU cc_start: 0.8394 (tt) cc_final: 0.8118 (tp) REVERT: B 783 ARG cc_start: 0.8469 (tpt170) cc_final: 0.8255 (tpt-90) REVERT: B 788 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8618 (tttm) REVERT: D 22 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8451 (pp) REVERT: D 336 PHE cc_start: 0.8527 (m-80) cc_final: 0.8242 (m-80) REVERT: D 449 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7625 (t0) REVERT: E 232 LYS cc_start: 0.7936 (ptmm) cc_final: 0.7489 (mmtp) REVERT: E 713 ASN cc_start: 0.8269 (t0) cc_final: 0.7915 (t0) REVERT: E 922 ASN cc_start: 0.7587 (t0) cc_final: 0.6427 (p0) REVERT: E 1013 ILE cc_start: 0.8866 (tp) cc_final: 0.8657 (tt) outliers start: 41 outliers final: 29 residues processed: 323 average time/residue: 0.3291 time to fit residues: 167.6754 Evaluate side-chains 296 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 265 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 878 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 982 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 252 optimal weight: 8.9990 chunk 273 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 202 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 GLN B 894 ASN B 932 GLN D 449 ASN D 450 ASN D 490 GLN E 198 ASN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 997 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22630 Z= 0.175 Angle : 0.538 10.531 30601 Z= 0.285 Chirality : 0.042 0.162 3239 Planarity : 0.004 0.053 3999 Dihedral : 7.379 74.372 3198 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.47 % Favored : 94.46 % Rotamer: Outliers : 2.19 % Allowed : 13.64 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.64 (0.15), residues: 2781 helix: -0.45 (0.22), residues: 575 sheet: 0.01 (0.18), residues: 800 loop : -2.08 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 697 HIS 0.004 0.001 HIS B 939 PHE 0.017 0.001 PHE B 712 TYR 0.017 0.001 TYR B 514 ARG 0.006 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 299 time to evaluate : 2.422 Fit side-chains REVERT: A 94 ASP cc_start: 0.7484 (t0) cc_final: 0.7030 (p0) REVERT: A 214 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8403 (m) REVERT: A 421 MET cc_start: 0.8588 (tpp) cc_final: 0.8305 (tpt) REVERT: B 140 ASP cc_start: 0.8619 (t0) cc_final: 0.8381 (t0) REVERT: B 308 LYS cc_start: 0.8775 (mptt) cc_final: 0.8339 (mtpp) REVERT: B 407 MET cc_start: 0.7705 (mmm) cc_final: 0.7423 (tpp) REVERT: B 417 MET cc_start: 0.8780 (mmm) cc_final: 0.8483 (mmt) REVERT: B 436 MET cc_start: 0.8430 (mtm) cc_final: 0.7937 (mtp) REVERT: B 547 GLU cc_start: 0.7489 (tt0) cc_final: 0.7260 (tt0) REVERT: B 638 ASN cc_start: 0.8667 (m-40) cc_final: 0.7957 (t0) REVERT: D 22 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8477 (pp) REVERT: D 334 GLU cc_start: 0.7371 (pm20) cc_final: 0.7156 (pm20) REVERT: D 336 PHE cc_start: 0.8431 (m-80) cc_final: 0.8014 (m-80) REVERT: D 449 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.8000 (t0) REVERT: E 232 LYS cc_start: 0.8026 (ptmm) cc_final: 0.7553 (mmtp) REVERT: E 283 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8270 (tttt) REVERT: E 922 ASN cc_start: 0.7595 (t0) cc_final: 0.6488 (p0) REVERT: E 1013 ILE cc_start: 0.8846 (tp) cc_final: 0.8646 (tt) outliers start: 51 outliers final: 33 residues processed: 324 average time/residue: 0.3196 time to fit residues: 163.2803 Evaluate side-chains 306 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 270 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 746 TYR Chi-restraints excluded: chain E residue 962 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 268 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 240 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B 498 ASN B 748 ASN B 894 ASN E 186 GLN E 469 GLN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 22630 Z= 0.577 Angle : 0.731 11.253 30601 Z= 0.386 Chirality : 0.051 0.212 3239 Planarity : 0.005 0.136 3999 Dihedral : 8.323 73.785 3198 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.41 % Favored : 92.52 % Rotamer: Outliers : 2.70 % Allowed : 15.23 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.73 (0.15), residues: 2781 helix: -0.45 (0.22), residues: 566 sheet: -0.15 (0.18), residues: 814 loop : -2.10 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 697 HIS 0.012 0.002 HIS E 582 PHE 0.027 0.002 PHE E 791 TYR 0.028 0.002 TYR B 514 ARG 0.008 0.001 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 257 time to evaluate : 2.741 Fit side-chains REVERT: A 101 ASP cc_start: 0.7381 (m-30) cc_final: 0.6842 (m-30) REVERT: A 214 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8452 (m) REVERT: A 421 MET cc_start: 0.8689 (tpp) cc_final: 0.8388 (tpt) REVERT: B 140 ASP cc_start: 0.8716 (t0) cc_final: 0.8441 (t0) REVERT: B 238 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7537 (mtp85) REVERT: B 336 ILE cc_start: 0.8938 (mt) cc_final: 0.8636 (tp) REVERT: B 417 MET cc_start: 0.8959 (mmm) cc_final: 0.8428 (mmt) REVERT: B 436 MET cc_start: 0.8527 (mtm) cc_final: 0.8060 (mtp) REVERT: B 602 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7294 (mmtp) REVERT: B 638 ASN cc_start: 0.8792 (m-40) cc_final: 0.8001 (t0) REVERT: D 22 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8474 (pp) REVERT: D 334 GLU cc_start: 0.7349 (pm20) cc_final: 0.7116 (pm20) REVERT: D 336 PHE cc_start: 0.8485 (m-80) cc_final: 0.8161 (m-80) REVERT: E 232 LYS cc_start: 0.8047 (ptmm) cc_final: 0.7540 (mmtp) REVERT: E 283 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8176 (tttt) REVERT: E 713 ASN cc_start: 0.8278 (t0) cc_final: 0.7962 (t0) REVERT: E 1013 ILE cc_start: 0.9012 (tp) cc_final: 0.8775 (tt) outliers start: 63 outliers final: 51 residues processed: 296 average time/residue: 0.3182 time to fit residues: 150.1958 Evaluate side-chains 304 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 250 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 976 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 200 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 229 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 GLN B 748 ASN B 778 ASN B 894 ASN B 916 ASN D 449 ASN E 365 ASN E 469 GLN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22630 Z= 0.140 Angle : 0.514 10.351 30601 Z= 0.274 Chirality : 0.042 0.157 3239 Planarity : 0.003 0.048 3999 Dihedral : 7.118 74.469 3198 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 2.40 % Allowed : 16.34 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.25 (0.15), residues: 2781 helix: 0.00 (0.22), residues: 582 sheet: 0.15 (0.18), residues: 783 loop : -1.81 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 697 HIS 0.003 0.001 HIS B 939 PHE 0.019 0.001 PHE B 712 TYR 0.015 0.001 TYR B 514 ARG 0.003 0.000 ARG D 438 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 277 time to evaluate : 2.421 Fit side-chains REVERT: A 94 ASP cc_start: 0.7575 (t0) cc_final: 0.7128 (p0) REVERT: A 348 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7427 (tttm) REVERT: A 421 MET cc_start: 0.8600 (tpp) cc_final: 0.8387 (tpt) REVERT: B 308 LYS cc_start: 0.8700 (mptt) cc_final: 0.8307 (mtpp) REVERT: B 417 MET cc_start: 0.8735 (mmm) cc_final: 0.8513 (mmt) REVERT: B 436 MET cc_start: 0.8403 (mtm) cc_final: 0.7929 (mtp) REVERT: B 551 ASP cc_start: 0.7764 (p0) cc_final: 0.7545 (p0) REVERT: B 573 THR cc_start: 0.8381 (m) cc_final: 0.8178 (t) REVERT: B 602 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7052 (mmtp) REVERT: B 638 ASN cc_start: 0.8599 (m-40) cc_final: 0.7847 (t0) REVERT: D 22 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8430 (pp) REVERT: D 336 PHE cc_start: 0.8465 (m-80) cc_final: 0.8020 (m-80) REVERT: D 449 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7651 (t0) REVERT: E 232 LYS cc_start: 0.8013 (ptmm) cc_final: 0.7542 (mmtp) REVERT: E 283 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8203 (tttt) REVERT: E 692 ASN cc_start: 0.8463 (p0) cc_final: 0.8245 (p0) REVERT: E 922 ASN cc_start: 0.7751 (t0) cc_final: 0.6517 (p0) outliers start: 56 outliers final: 38 residues processed: 309 average time/residue: 0.3113 time to fit residues: 155.2246 Evaluate side-chains 308 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 267 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 746 TYR Chi-restraints excluded: chain E residue 790 PHE Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain E residue 960 ASN Chi-restraints excluded: chain E residue 962 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 20.0000 chunk 241 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B 748 ASN B 894 ASN B 932 GLN E 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.072 22630 Z= 0.654 Angle : 0.765 11.405 30601 Z= 0.404 Chirality : 0.052 0.218 3239 Planarity : 0.006 0.153 3999 Dihedral : 8.218 73.068 3198 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.77 % Favored : 92.16 % Rotamer: Outliers : 2.79 % Allowed : 16.52 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.56 (0.15), residues: 2781 helix: -0.25 (0.22), residues: 564 sheet: -0.08 (0.18), residues: 804 loop : -1.99 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 697 HIS 0.012 0.002 HIS E 582 PHE 0.031 0.002 PHE E 791 TYR 0.033 0.003 TYR E 637 ARG 0.008 0.001 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 256 time to evaluate : 2.474 Fit side-chains REVERT: A 214 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8377 (m) REVERT: A 421 MET cc_start: 0.8683 (tpp) cc_final: 0.8429 (tpt) REVERT: B 336 ILE cc_start: 0.8944 (mt) cc_final: 0.8644 (tp) REVERT: B 417 MET cc_start: 0.8995 (mmm) cc_final: 0.8471 (mmt) REVERT: B 436 MET cc_start: 0.8541 (mtm) cc_final: 0.8263 (mtp) REVERT: B 602 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7380 (mmtp) REVERT: B 638 ASN cc_start: 0.8785 (m-40) cc_final: 0.7979 (t0) REVERT: D 22 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8530 (pp) REVERT: D 51 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8794 (tp) REVERT: D 336 PHE cc_start: 0.8531 (m-80) cc_final: 0.8164 (m-80) REVERT: E 232 LYS cc_start: 0.8194 (ptmm) cc_final: 0.7567 (mmtp) REVERT: E 283 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8163 (tttt) REVERT: E 613 ASP cc_start: 0.8539 (t70) cc_final: 0.8156 (t70) REVERT: E 639 LYS cc_start: 0.8103 (tptp) cc_final: 0.7865 (tptp) REVERT: E 713 ASN cc_start: 0.8333 (t0) cc_final: 0.8027 (t0) outliers start: 65 outliers final: 52 residues processed: 297 average time/residue: 0.3197 time to fit residues: 150.8524 Evaluate side-chains 305 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 249 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 894 ASN Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain E residue 960 ASN Chi-restraints excluded: chain E residue 962 LEU Chi-restraints excluded: chain E residue 976 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 267 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 894 ASN B 916 ASN E 469 GLN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22630 Z= 0.265 Angle : 0.582 10.546 30601 Z= 0.310 Chirality : 0.044 0.170 3239 Planarity : 0.004 0.059 3999 Dihedral : 7.515 72.675 3198 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 2.83 % Allowed : 16.60 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.31 (0.15), residues: 2781 helix: -0.09 (0.22), residues: 586 sheet: 0.01 (0.18), residues: 806 loop : -1.78 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 697 HIS 0.006 0.001 HIS E 582 PHE 0.018 0.001 PHE B 790 TYR 0.020 0.001 TYR B 514 ARG 0.004 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 254 time to evaluate : 2.524 Fit side-chains REVERT: A 94 ASP cc_start: 0.7641 (t0) cc_final: 0.7094 (p0) REVERT: A 214 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8421 (m) REVERT: A 286 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: A 348 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7484 (ttpt) REVERT: A 421 MET cc_start: 0.8615 (tpp) cc_final: 0.8353 (tpt) REVERT: B 308 LYS cc_start: 0.8711 (mptt) cc_final: 0.8319 (mtpp) REVERT: B 417 MET cc_start: 0.8864 (mmm) cc_final: 0.8481 (mmt) REVERT: B 436 MET cc_start: 0.8457 (mtm) cc_final: 0.7994 (mtp) REVERT: B 602 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7234 (mmtp) REVERT: B 604 MET cc_start: 0.7823 (ttp) cc_final: 0.7358 (ttp) REVERT: B 638 ASN cc_start: 0.8675 (m-40) cc_final: 0.7931 (t0) REVERT: D 22 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8417 (pp) REVERT: D 336 PHE cc_start: 0.8505 (m-80) cc_final: 0.8077 (m-80) REVERT: E 232 LYS cc_start: 0.8073 (ptmm) cc_final: 0.7577 (mmtp) REVERT: E 283 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8359 (tttt) outliers start: 66 outliers final: 52 residues processed: 294 average time/residue: 0.3116 time to fit residues: 147.5780 Evaluate side-chains 311 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 255 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 926 ASP Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 695 LEU Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 790 PHE Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain E residue 960 ASN Chi-restraints excluded: chain E residue 962 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 132 optimal weight: 0.0060 chunk 24 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 894 ASN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22630 Z= 0.259 Angle : 0.573 10.810 30601 Z= 0.304 Chirality : 0.044 0.171 3239 Planarity : 0.004 0.058 3999 Dihedral : 7.348 72.462 3198 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.19 % Favored : 93.77 % Rotamer: Outliers : 2.70 % Allowed : 17.16 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.18 (0.16), residues: 2781 helix: 0.06 (0.22), residues: 585 sheet: 0.11 (0.18), residues: 797 loop : -1.73 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 697 HIS 0.006 0.001 HIS E 582 PHE 0.020 0.001 PHE B 790 TYR 0.020 0.001 TYR B 514 ARG 0.004 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 260 time to evaluate : 2.411 Fit side-chains REVERT: A 94 ASP cc_start: 0.7617 (t0) cc_final: 0.7106 (p0) REVERT: A 214 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8421 (m) REVERT: A 348 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7439 (ttpt) REVERT: A 421 MET cc_start: 0.8645 (tpp) cc_final: 0.8417 (tpt) REVERT: B 417 MET cc_start: 0.8859 (mmm) cc_final: 0.8481 (mmt) REVERT: B 436 MET cc_start: 0.8457 (mtm) cc_final: 0.8000 (mtp) REVERT: B 602 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7180 (mmtp) REVERT: B 604 MET cc_start: 0.7768 (ttp) cc_final: 0.7294 (ttp) REVERT: B 638 ASN cc_start: 0.8641 (m-40) cc_final: 0.7931 (t0) REVERT: B 790 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8638 (p90) REVERT: D 22 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8515 (pp) REVERT: D 336 PHE cc_start: 0.8504 (m-80) cc_final: 0.8068 (m-80) REVERT: E 232 LYS cc_start: 0.8076 (ptmm) cc_final: 0.7580 (mmtp) REVERT: E 282 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8717 (tp-100) REVERT: E 283 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8327 (tttt) REVERT: E 922 ASN cc_start: 0.7712 (t0) cc_final: 0.6638 (p0) outliers start: 63 outliers final: 54 residues processed: 297 average time/residue: 0.3120 time to fit residues: 149.2773 Evaluate side-chains 314 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 256 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 790 PHE Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 926 ASP Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 695 LEU Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 790 PHE Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain E residue 960 ASN Chi-restraints excluded: chain E residue 962 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 5.9990 chunk 256 optimal weight: 0.4980 chunk 234 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 196 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 GLN B 894 ASN B 916 ASN B 932 GLN D 449 ASN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22630 Z= 0.242 Angle : 0.560 10.543 30601 Z= 0.298 Chirality : 0.043 0.169 3239 Planarity : 0.004 0.053 3999 Dihedral : 7.069 72.878 3196 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.54 % Favored : 94.42 % Rotamer: Outliers : 2.53 % Allowed : 17.25 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2781 helix: 0.17 (0.23), residues: 586 sheet: 0.15 (0.18), residues: 807 loop : -1.68 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 697 HIS 0.006 0.001 HIS E 582 PHE 0.019 0.001 PHE B 790 TYR 0.019 0.001 TYR B 514 ARG 0.006 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 268 time to evaluate : 2.374 Fit side-chains REVERT: A 94 ASP cc_start: 0.7532 (t0) cc_final: 0.7091 (p0) REVERT: A 214 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8424 (m) REVERT: A 348 LYS cc_start: 0.7671 (mtpt) cc_final: 0.7282 (ttpt) REVERT: A 421 MET cc_start: 0.8587 (tpp) cc_final: 0.8376 (tpt) REVERT: B 336 ILE cc_start: 0.8957 (mt) cc_final: 0.8654 (tt) REVERT: B 417 MET cc_start: 0.8839 (mmm) cc_final: 0.8479 (mmt) REVERT: B 436 MET cc_start: 0.8462 (mtm) cc_final: 0.8004 (mtp) REVERT: B 547 GLU cc_start: 0.7540 (tt0) cc_final: 0.7305 (tt0) REVERT: B 602 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7032 (mmtm) REVERT: B 638 ASN cc_start: 0.8594 (m-40) cc_final: 0.7921 (t0) REVERT: B 790 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8523 (p90) REVERT: D 22 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8460 (pp) REVERT: D 336 PHE cc_start: 0.8497 (m-80) cc_final: 0.7992 (m-80) REVERT: D 449 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7604 (t0) REVERT: E 232 LYS cc_start: 0.8047 (ptmm) cc_final: 0.7568 (mmtp) REVERT: E 282 GLN cc_start: 0.8990 (tp-100) cc_final: 0.8747 (tp40) REVERT: E 283 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8412 (tttt) REVERT: E 692 ASN cc_start: 0.8651 (p0) cc_final: 0.8360 (p0) outliers start: 59 outliers final: 50 residues processed: 303 average time/residue: 0.3118 time to fit residues: 151.7168 Evaluate side-chains 319 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 264 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 790 PHE Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 695 LEU Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 790 PHE Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain E residue 960 ASN Chi-restraints excluded: chain E residue 962 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 0.0870 chunk 264 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 276 optimal weight: 0.0980 chunk 254 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 894 ASN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22630 Z= 0.134 Angle : 0.526 10.722 30601 Z= 0.281 Chirality : 0.042 0.164 3239 Planarity : 0.003 0.047 3999 Dihedral : 6.827 72.800 3196 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 1.93 % Allowed : 18.10 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.92 (0.16), residues: 2781 helix: 0.34 (0.23), residues: 583 sheet: 0.32 (0.18), residues: 781 loop : -1.60 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 161 HIS 0.003 0.001 HIS E 582 PHE 0.018 0.001 PHE B 712 TYR 0.048 0.001 TYR E 637 ARG 0.005 0.000 ARG B 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 271 time to evaluate : 2.602 Fit side-chains REVERT: A 94 ASP cc_start: 0.7512 (t0) cc_final: 0.7088 (p0) REVERT: A 348 LYS cc_start: 0.7607 (mtpt) cc_final: 0.7226 (ttpt) REVERT: A 421 MET cc_start: 0.8549 (tpp) cc_final: 0.8094 (tpt) REVERT: B 336 ILE cc_start: 0.8952 (mt) cc_final: 0.8641 (tt) REVERT: B 417 MET cc_start: 0.8794 (mmm) cc_final: 0.8477 (mmt) REVERT: B 436 MET cc_start: 0.8421 (mtm) cc_final: 0.7966 (mtp) REVERT: B 547 GLU cc_start: 0.7415 (tt0) cc_final: 0.7198 (tt0) REVERT: B 638 ASN cc_start: 0.8558 (m-40) cc_final: 0.7933 (t0) REVERT: B 790 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8442 (p90) REVERT: D 22 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8436 (pp) REVERT: D 336 PHE cc_start: 0.8507 (m-80) cc_final: 0.7999 (m-80) REVERT: D 421 MET cc_start: 0.7385 (tpt) cc_final: 0.6979 (tpp) REVERT: E 232 LYS cc_start: 0.8010 (ptmm) cc_final: 0.7560 (mmtp) REVERT: E 282 GLN cc_start: 0.8992 (tp-100) cc_final: 0.8761 (tp40) REVERT: E 283 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8408 (tttt) REVERT: E 417 MET cc_start: 0.8564 (tpp) cc_final: 0.8348 (mmt) REVERT: E 692 ASN cc_start: 0.8554 (p0) cc_final: 0.8320 (p0) outliers start: 45 outliers final: 38 residues processed: 297 average time/residue: 0.3122 time to fit residues: 148.5808 Evaluate side-chains 303 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 263 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 790 PHE Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 516 ASP Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 712 PHE Chi-restraints excluded: chain E residue 790 PHE Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 960 ASN Chi-restraints excluded: chain E residue 962 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 3.9990 chunk 234 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 32 optimal weight: 0.0670 chunk 61 optimal weight: 0.9980 chunk 220 optimal weight: 0.7980 chunk 92 optimal weight: 0.0060 chunk 226 optimal weight: 0.0970 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 overall best weight: 0.2532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN B 145 GLN B 469 GLN B 622 ASN B 894 ASN B1014 GLN D 449 ASN ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.123136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.097911 restraints weight = 30211.407| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.25 r_work: 0.2718 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22630 Z= 0.109 Angle : 0.481 10.070 30601 Z= 0.256 Chirality : 0.040 0.156 3239 Planarity : 0.003 0.042 3999 Dihedral : 5.869 71.000 3196 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.29 % Allowed : 18.62 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.66 (0.16), residues: 2781 helix: 0.76 (0.23), residues: 575 sheet: 0.41 (0.18), residues: 799 loop : -1.50 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 161 HIS 0.008 0.001 HIS D 451 PHE 0.016 0.001 PHE B 712 TYR 0.017 0.001 TYR E 637 ARG 0.008 0.000 ARG B 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4650.59 seconds wall clock time: 84 minutes 35.03 seconds (5075.03 seconds total)