Starting phenix.real_space_refine on Fri Jun 13 23:30:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lsj_63357/06_2025/9lsj_63357.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lsj_63357/06_2025/9lsj_63357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lsj_63357/06_2025/9lsj_63357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lsj_63357/06_2025/9lsj_63357.map" model { file = "/net/cci-nas-00/data/ceres_data/9lsj_63357/06_2025/9lsj_63357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lsj_63357/06_2025/9lsj_63357.cif" } resolution = 3.1 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 9969 2.51 5 N 2521 2.21 5 O 2870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15438 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3206 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 418} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3206 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 418} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 5332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5332 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 638} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1722 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 7, 'TRANS': 221} Chain: "E" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1762 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 222} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'CIT': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.64, per 1000 atoms: 0.62 Number of scatterers: 15438 At special positions: 0 Unit cell: (98.7, 116.55, 189, 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 78 16.00 O 2870 8.00 N 2521 7.00 C 9969 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 677 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS E 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS E 360 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 212 " distance=2.04 Simple disulfide: pdb=" SG CYS E 295 " - pdb=" SG CYS E 369 " distance=2.03 Simple disulfide: pdb=" SG CYS E 422 " - pdb=" SG CYS E 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG G 2 " - " BMA G 3 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG C1001 " - " ASN C 52 " " NAG C1002 " - " ASN C 265 " " NAG C1003 " - " ASN C 275 " " NAG C1004 " - " ASN C 398 " " NAG F 1 " - " ASN C 291 " " NAG G 1 " - " ASN C 413 " " NAG H 1 " - " ASN C 252 " " NAG I 1 " - " ASN C 507 " Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 2.0 seconds 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3636 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 21 sheets defined 40.5% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 28 through 45 Processing helix chain 'A' and resid 50 through 70 removed outlier: 3.923A pdb=" N ALA A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.709A pdb=" N TYR A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 74 through 79' Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 115 through 130 Processing helix chain 'A' and resid 131 through 132 No H-bonds generated for 'chain 'A' and resid 131 through 132' Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 136 through 143 removed outlier: 4.488A pdb=" N GLY A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 166 removed outlier: 3.607A pdb=" N THR A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 177 Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 204 through 237 removed outlier: 3.968A pdb=" N TYR A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 289 removed outlier: 4.006A pdb=" N THR A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 removed outlier: 3.653A pdb=" N TRP A 303 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 335 Processing helix chain 'A' and resid 336 through 348 Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.772A pdb=" N ILE A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 384 Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.756A pdb=" N THR A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 415 Processing helix chain 'A' and resid 419 through 446 removed outlier: 4.422A pdb=" N GLY A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 45 Processing helix chain 'B' and resid 50 through 71 removed outlier: 3.785A pdb=" N ILE B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 79 removed outlier: 4.375A pdb=" N LYS B 77 " --> pdb=" O PRO B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 96 Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 115 through 131 removed outlier: 3.620A pdb=" N LEU B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 141 Processing helix chain 'B' and resid 143 through 167 removed outlier: 3.622A pdb=" N THR B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 204 through 237 removed outlier: 4.146A pdb=" N TYR B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 289 removed outlier: 3.630A pdb=" N THR B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 Processing helix chain 'B' and resid 318 through 335 Processing helix chain 'B' and resid 336 through 348 Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 359 through 384 removed outlier: 3.690A pdb=" N ALA B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 396 Processing helix chain 'B' and resid 403 through 414 removed outlier: 4.265A pdb=" N LEU B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 446 removed outlier: 3.654A pdb=" N GLY B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 74 removed outlier: 3.905A pdb=" N TYR C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 115 through 122 removed outlier: 4.367A pdb=" N PHE C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 removed outlier: 4.542A pdb=" N ILE C 193 " --> pdb=" O GLU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.697A pdb=" N LEU C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 274 removed outlier: 3.833A pdb=" N PHE C 268 " --> pdb=" O ASN C 265 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 269 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLY C 270 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU C 271 " --> pdb=" O PHE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 319 removed outlier: 4.050A pdb=" N LEU C 318 " --> pdb=" O SER C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 Processing helix chain 'C' and resid 449 through 453 Processing helix chain 'C' and resid 522 through 526 removed outlier: 4.189A pdb=" N LEU C 526 " --> pdb=" O ASP C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 653 through 664 removed outlier: 4.144A pdb=" N PHE C 657 " --> pdb=" O SER C 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.688A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 74 through 77 Processing helix chain 'E' and resid 336 through 339 Processing helix chain 'E' and resid 428 through 431 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 23 Processing sheet with id=AA4, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.510A pdb=" N LEU C 80 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN C 105 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 82 " --> pdb=" O ASN C 105 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN C 107 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 128 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP C 153 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 130 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU C 176 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU C 202 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN C 229 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 256 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 253 " --> pdb=" O MET C 278 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU C 279 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N PHE C 303 " --> pdb=" O ASN C 328 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU C 360 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU C 436 " --> pdb=" O TYR C 462 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 185 through 186 Processing sheet with id=AA6, first strand: chain 'C' and resid 262 through 263 Processing sheet with id=AA7, first strand: chain 'C' and resid 312 through 313 Processing sheet with id=AA8, first strand: chain 'C' and resid 395 through 396 Processing sheet with id=AA9, first strand: chain 'C' and resid 444 through 446 removed outlier: 7.133A pdb=" N GLN C 445 " --> pdb=" O GLN C 470 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 469 " --> pdb=" O LYS C 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 676 through 677 removed outlier: 3.606A pdb=" N PHE C 686 " --> pdb=" O CYS C 677 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 2 through 4 removed outlier: 3.947A pdb=" N LEU D 4 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.697A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR D 113 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA D 33 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.697A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR D 113 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL D 108 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 18 through 20 Processing sheet with id=AB6, first strand: chain 'D' and resid 128 through 130 removed outlier: 3.896A pdb=" N VAL D 143 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP D 194 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 157 through 162 Processing sheet with id=AB8, first strand: chain 'E' and resid 276 through 279 removed outlier: 3.744A pdb=" N THR E 351 " --> pdb=" O ASP E 346 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 283 through 285 removed outlier: 6.307A pdb=" N GLU E 283 " --> pdb=" O THR E 391 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP E 306 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY E 322 " --> pdb=" O TRP E 309 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG E 311 " --> pdb=" O TRP E 320 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TRP E 320 " --> pdb=" O ARG E 311 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 283 through 285 removed outlier: 6.307A pdb=" N GLU E 283 " --> pdb=" O THR E 391 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER E 383 " --> pdb=" O ARG E 371 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 409 through 411 removed outlier: 6.194A pdb=" N LEU E 410 " --> pdb=" O GLU E 505 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP E 435 " --> pdb=" O LEU E 447 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 420 through 423 removed outlier: 3.548A pdb=" N LEU E 473 " --> pdb=" O LEU E 420 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR E 472 " --> pdb=" O SER E 465 " (cutoff:3.500A) 685 hydrogen bonds defined for protein. 1941 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: 5.64 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4857 1.34 - 1.46: 3374 1.46 - 1.58: 7403 1.58 - 1.70: 0 1.70 - 1.81: 124 Bond restraints: 15758 Sorted by residual: bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" N GLY E 499 " pdb=" CA GLY E 499 " ideal model delta sigma weight residual 1.444 1.474 -0.030 1.02e-02 9.61e+03 8.63e+00 bond pdb=" CA SER E 495 " pdb=" CB SER E 495 " ideal model delta sigma weight residual 1.529 1.497 0.032 1.13e-02 7.83e+03 8.11e+00 bond pdb=" N PHE E 498 " pdb=" CA PHE E 498 " ideal model delta sigma weight residual 1.454 1.486 -0.033 1.17e-02 7.31e+03 7.74e+00 bond pdb=" N ILE E 494 " pdb=" CA ILE E 494 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.39e+00 ... (remaining 15753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 20555 1.81 - 3.61: 683 3.61 - 5.42: 114 5.42 - 7.22: 33 7.22 - 9.03: 5 Bond angle restraints: 21390 Sorted by residual: angle pdb=" N PRO C 681 " pdb=" CA PRO C 681 " pdb=" C PRO C 681 " ideal model delta sigma weight residual 113.65 107.54 6.11 1.35e+00 5.49e-01 2.05e+01 angle pdb=" C TYR B 144 " pdb=" N ILE B 145 " pdb=" CA ILE B 145 " ideal model delta sigma weight residual 120.24 122.90 -2.66 6.30e-01 2.52e+00 1.79e+01 angle pdb=" N TYR E 377 " pdb=" CA TYR E 377 " pdb=" C TYR E 377 " ideal model delta sigma weight residual 112.30 107.11 5.19 1.36e+00 5.41e-01 1.46e+01 angle pdb=" N ILE D 153 " pdb=" CA ILE D 153 " pdb=" C ILE D 153 " ideal model delta sigma weight residual 112.80 108.53 4.27 1.15e+00 7.56e-01 1.38e+01 angle pdb=" C PHE B 252 " pdb=" N LYS B 253 " pdb=" CA LYS B 253 " ideal model delta sigma weight residual 121.19 127.09 -5.90 1.59e+00 3.96e-01 1.38e+01 ... (remaining 21385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.26: 8898 23.26 - 46.52: 446 46.52 - 69.78: 63 69.78 - 93.04: 25 93.04 - 116.30: 27 Dihedral angle restraints: 9459 sinusoidal: 3771 harmonic: 5688 Sorted by residual: dihedral pdb=" CB CYS C 95 " pdb=" SG CYS C 95 " pdb=" SG CYS C 122 " pdb=" CB CYS C 122 " ideal model delta sinusoidal sigma weight residual 93.00 166.19 -73.19 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CA MET C 642 " pdb=" C MET C 642 " pdb=" N ARG C 643 " pdb=" CA ARG C 643 " ideal model delta harmonic sigma weight residual -180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " pdb=" SG CYS C 677 " pdb=" CB CYS C 677 " ideal model delta sinusoidal sigma weight residual 93.00 56.29 36.71 1 1.00e+01 1.00e-02 1.90e+01 ... (remaining 9456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2328 0.092 - 0.184: 186 0.184 - 0.276: 16 0.276 - 0.369: 0 0.369 - 0.461: 1 Chirality restraints: 2531 Sorted by residual: chirality pdb=" C1 BMA G 3 " pdb=" O3 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.32e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.50e+01 chirality pdb=" C1 NAG C1004 " pdb=" ND2 ASN C 398 " pdb=" C2 NAG C1004 " pdb=" O5 NAG C1004 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 2528 not shown) Planarity restraints: 2677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " 0.053 2.00e-02 2.50e+03 4.42e-02 2.44e+01 pdb=" C7 NAG G 2 " -0.013 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.040 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " -0.071 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 413 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO E 414 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 414 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 414 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 145 " 0.032 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO B 146 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " 0.027 5.00e-02 4.00e+02 ... (remaining 2674 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1841 2.74 - 3.28: 16475 3.28 - 3.82: 26419 3.82 - 4.36: 31442 4.36 - 4.90: 53588 Nonbonded interactions: 129765 Sorted by model distance: nonbonded pdb=" OE2 GLU B 195 " pdb=" OH TYR B 348 " model vdw 2.205 3.040 nonbonded pdb=" O TYR B 144 " pdb=" OG1 THR B 147 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR C 556 " pdb=" OE2 GLU C 580 " model vdw 2.236 3.040 nonbonded pdb=" O3 CIT A 501 " pdb=" O7 CIT A 501 " model vdw 2.236 3.040 nonbonded pdb=" O ALA C 68 " pdb=" OG1 THR C 72 " model vdw 2.254 3.040 ... (remaining 129760 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 257 or (resid 258 through 259 and (name N or na \ me CA or name C or name O or name CB )) or resid 260 through 446)) selection = (chain 'B' and (resid 16 through 248 or (resid 249 through 250 and (name N or na \ me CA or name C or name O or name CB )) or resid 251 through 446)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 37.660 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.006 0.078 15779 Z= 0.300 Angle : 0.807 11.908 21445 Z= 0.433 Chirality : 0.052 0.461 2531 Planarity : 0.004 0.063 2669 Dihedral : 15.933 116.303 5799 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.12 % Allowed : 0.48 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 1979 helix: 0.84 (0.20), residues: 694 sheet: -0.86 (0.33), residues: 286 loop : -1.27 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 656 HIS 0.011 0.001 HIS E 489 PHE 0.030 0.002 PHE C 143 TYR 0.026 0.002 TYR C 74 ARG 0.014 0.001 ARG B 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 8) link_NAG-ASN : angle 4.54291 ( 24) link_BETA1-4 : bond 0.02274 ( 4) link_BETA1-4 : angle 3.33328 ( 12) hydrogen bonds : bond 0.18282 ( 678) hydrogen bonds : angle 7.16031 ( 1941) SS BOND : bond 0.00364 ( 8) SS BOND : angle 1.12338 ( 16) link_BETA1-3 : bond 0.04513 ( 1) link_BETA1-3 : angle 4.43043 ( 3) covalent geometry : bond 0.00612 (15758) covalent geometry : angle 0.78717 (21390) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.9102 (tpp) cc_final: 0.8629 (tpp) REVERT: A 112 ASP cc_start: 0.8562 (t0) cc_final: 0.8250 (t0) REVERT: A 444 MET cc_start: 0.8828 (tmm) cc_final: 0.7880 (tmm) REVERT: B 85 MET cc_start: 0.8794 (tpt) cc_final: 0.8320 (tpp) REVERT: B 111 MET cc_start: 0.9169 (mmm) cc_final: 0.8873 (mtp) REVERT: B 350 ASP cc_start: 0.8710 (t70) cc_final: 0.8302 (t0) REVERT: B 424 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8949 (mt0) REVERT: D 73 ASP cc_start: 0.8578 (t0) cc_final: 0.7987 (t0) REVERT: D 206 ASP cc_start: 0.8325 (m-30) cc_final: 0.8093 (p0) REVERT: E 319 GLU cc_start: 0.8067 (tt0) cc_final: 0.7519 (tt0) outliers start: 2 outliers final: 1 residues processed: 112 average time/residue: 0.2554 time to fit residues: 44.7709 Evaluate side-chains 90 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 683 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 93 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS C 169 GLN C 684 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.067304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.043150 restraints weight = 51715.040| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 3.73 r_work: 0.2536 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15779 Z= 0.205 Angle : 0.649 10.648 21445 Z= 0.328 Chirality : 0.046 0.427 2531 Planarity : 0.004 0.050 2669 Dihedral : 13.394 102.268 2401 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.30 % Allowed : 5.61 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1979 helix: 1.24 (0.20), residues: 712 sheet: -0.82 (0.32), residues: 299 loop : -1.17 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 382 HIS 0.005 0.001 HIS E 489 PHE 0.019 0.001 PHE B 87 TYR 0.019 0.001 TYR A 31 ARG 0.003 0.000 ARG B 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 8) link_NAG-ASN : angle 3.83196 ( 24) link_BETA1-4 : bond 0.00359 ( 4) link_BETA1-4 : angle 2.06740 ( 12) hydrogen bonds : bond 0.05282 ( 678) hydrogen bonds : angle 5.52174 ( 1941) SS BOND : bond 0.00430 ( 8) SS BOND : angle 1.27524 ( 16) link_BETA1-3 : bond 0.00410 ( 1) link_BETA1-3 : angle 5.81957 ( 3) covalent geometry : bond 0.00459 (15758) covalent geometry : angle 0.63085 (21390) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8954 (p0) cc_final: 0.8423 (p0) REVERT: A 85 MET cc_start: 0.8952 (tpp) cc_final: 0.8621 (tpp) REVERT: A 112 ASP cc_start: 0.8908 (t0) cc_final: 0.8615 (t0) REVERT: A 150 MET cc_start: 0.9196 (ptm) cc_final: 0.8950 (ptm) REVERT: A 317 CYS cc_start: 0.8945 (p) cc_final: 0.8733 (p) REVERT: A 444 MET cc_start: 0.8967 (tmm) cc_final: 0.8247 (tmm) REVERT: A 445 MET cc_start: 0.7198 (mmt) cc_final: 0.6833 (mmt) REVERT: B 85 MET cc_start: 0.8931 (tpt) cc_final: 0.8493 (tpp) REVERT: B 150 MET cc_start: 0.9285 (ttm) cc_final: 0.8946 (ttm) REVERT: B 350 ASP cc_start: 0.7989 (t70) cc_final: 0.7413 (t0) REVERT: C 374 MET cc_start: 0.8976 (mtm) cc_final: 0.8716 (mtt) REVERT: D 73 ASP cc_start: 0.8248 (t0) cc_final: 0.7601 (t0) REVERT: D 76 LYS cc_start: 0.9640 (mtpp) cc_final: 0.9364 (mtpp) REVERT: D 148 ARG cc_start: 0.8422 (tpt-90) cc_final: 0.8222 (tpp80) REVERT: D 206 ASP cc_start: 0.8468 (m-30) cc_final: 0.7878 (p0) REVERT: D 207 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.5127 (m-80) REVERT: D 227 LYS cc_start: 0.7318 (mmtt) cc_final: 0.6865 (mmmt) REVERT: E 319 GLU cc_start: 0.8592 (tt0) cc_final: 0.8349 (tt0) outliers start: 5 outliers final: 3 residues processed: 105 average time/residue: 0.2582 time to fit residues: 42.6763 Evaluate side-chains 90 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain D residue 207 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 52 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 80 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.067302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.043120 restraints weight = 51658.944| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 3.74 r_work: 0.2536 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15779 Z= 0.199 Angle : 0.610 11.031 21445 Z= 0.306 Chirality : 0.045 0.422 2531 Planarity : 0.003 0.047 2669 Dihedral : 11.808 100.394 2401 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.91 % Allowed : 9.54 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1979 helix: 1.47 (0.20), residues: 709 sheet: -0.83 (0.32), residues: 293 loop : -1.12 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 382 HIS 0.005 0.001 HIS E 489 PHE 0.018 0.001 PHE B 87 TYR 0.021 0.001 TYR A 31 ARG 0.003 0.000 ARG B 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 8) link_NAG-ASN : angle 3.39677 ( 24) link_BETA1-4 : bond 0.00461 ( 4) link_BETA1-4 : angle 2.23001 ( 12) hydrogen bonds : bond 0.04754 ( 678) hydrogen bonds : angle 5.13441 ( 1941) SS BOND : bond 0.00395 ( 8) SS BOND : angle 1.13754 ( 16) link_BETA1-3 : bond 0.00515 ( 1) link_BETA1-3 : angle 6.09275 ( 3) covalent geometry : bond 0.00451 (15758) covalent geometry : angle 0.59295 (21390) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.567 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8648 (p0) cc_final: 0.8431 (p0) REVERT: A 51 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8745 (tt) REVERT: A 85 MET cc_start: 0.8946 (tpp) cc_final: 0.8634 (tpp) REVERT: A 112 ASP cc_start: 0.8896 (t0) cc_final: 0.8596 (t0) REVERT: A 317 CYS cc_start: 0.8911 (p) cc_final: 0.8699 (p) REVERT: A 350 ASP cc_start: 0.8322 (t0) cc_final: 0.8077 (t0) REVERT: A 398 CYS cc_start: 0.9339 (m) cc_final: 0.9009 (m) REVERT: A 444 MET cc_start: 0.9024 (tmm) cc_final: 0.8407 (tmm) REVERT: A 445 MET cc_start: 0.7121 (mmt) cc_final: 0.6618 (mmm) REVERT: B 85 MET cc_start: 0.8946 (tpt) cc_final: 0.8625 (tpp) REVERT: B 150 MET cc_start: 0.9295 (ttm) cc_final: 0.8879 (ttm) REVERT: B 350 ASP cc_start: 0.7921 (t70) cc_final: 0.7271 (t0) REVERT: B 384 MET cc_start: 0.8467 (mpp) cc_final: 0.8150 (mpp) REVERT: D 73 ASP cc_start: 0.8210 (t0) cc_final: 0.7519 (t0) REVERT: D 76 LYS cc_start: 0.9651 (mtpp) cc_final: 0.9353 (mtpp) REVERT: D 128 MET cc_start: 0.8003 (tpp) cc_final: 0.7418 (mmt) REVERT: D 207 PHE cc_start: 0.6425 (OUTLIER) cc_final: 0.4874 (m-80) REVERT: E 286 LYS cc_start: 0.9042 (mmmt) cc_final: 0.8443 (mmmt) REVERT: E 289 GLU cc_start: 0.9210 (pt0) cc_final: 0.8965 (pm20) REVERT: E 319 GLU cc_start: 0.8633 (tt0) cc_final: 0.8378 (tt0) outliers start: 15 outliers final: 7 residues processed: 105 average time/residue: 0.2521 time to fit residues: 41.6960 Evaluate side-chains 96 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain D residue 207 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 124 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 616 ASN D 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.068070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.044058 restraints weight = 51524.449| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.73 r_work: 0.2562 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15779 Z= 0.144 Angle : 0.567 10.599 21445 Z= 0.284 Chirality : 0.043 0.416 2531 Planarity : 0.003 0.043 2669 Dihedral : 10.970 98.652 2401 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.03 % Allowed : 11.16 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1979 helix: 1.65 (0.20), residues: 712 sheet: -0.77 (0.32), residues: 296 loop : -1.11 (0.21), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 382 HIS 0.006 0.001 HIS E 489 PHE 0.016 0.001 PHE B 87 TYR 0.020 0.001 TYR A 31 ARG 0.003 0.000 ARG D 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 8) link_NAG-ASN : angle 3.19322 ( 24) link_BETA1-4 : bond 0.00484 ( 4) link_BETA1-4 : angle 2.37012 ( 12) hydrogen bonds : bond 0.04340 ( 678) hydrogen bonds : angle 4.91166 ( 1941) SS BOND : bond 0.00342 ( 8) SS BOND : angle 1.00350 ( 16) link_BETA1-3 : bond 0.00607 ( 1) link_BETA1-3 : angle 5.56396 ( 3) covalent geometry : bond 0.00321 (15758) covalent geometry : angle 0.54961 (21390) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8743 (tt) REVERT: A 112 ASP cc_start: 0.8885 (t0) cc_final: 0.8581 (t0) REVERT: A 150 MET cc_start: 0.9184 (ptm) cc_final: 0.8837 (ptm) REVERT: A 317 CYS cc_start: 0.8888 (p) cc_final: 0.8687 (p) REVERT: A 350 ASP cc_start: 0.8352 (t0) cc_final: 0.7995 (t0) REVERT: A 444 MET cc_start: 0.9020 (tmm) cc_final: 0.8362 (tmm) REVERT: B 85 MET cc_start: 0.8947 (tpt) cc_final: 0.8544 (tpp) REVERT: B 150 MET cc_start: 0.9173 (ttm) cc_final: 0.8718 (ttm) REVERT: B 350 ASP cc_start: 0.7803 (t70) cc_final: 0.7109 (t0) REVERT: C 146 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: C 278 MET cc_start: 0.8488 (ptm) cc_final: 0.7841 (tmm) REVERT: D 73 ASP cc_start: 0.8150 (t0) cc_final: 0.7494 (t0) REVERT: D 76 LYS cc_start: 0.9626 (mtpp) cc_final: 0.9318 (mtpp) REVERT: D 128 MET cc_start: 0.7881 (tpp) cc_final: 0.7281 (mmt) REVERT: D 207 PHE cc_start: 0.6358 (OUTLIER) cc_final: 0.4770 (m-80) REVERT: E 286 LYS cc_start: 0.9108 (mmmt) cc_final: 0.8552 (mmmt) REVERT: E 289 GLU cc_start: 0.9133 (pt0) cc_final: 0.8896 (pm20) REVERT: E 319 GLU cc_start: 0.8624 (tt0) cc_final: 0.8335 (tt0) REVERT: E 364 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8983 (t) REVERT: E 378 MET cc_start: 0.8764 (ptm) cc_final: 0.8525 (ptp) outliers start: 17 outliers final: 6 residues processed: 109 average time/residue: 0.2362 time to fit residues: 41.3024 Evaluate side-chains 97 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain E residue 364 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 140 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN D 130 GLN ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.067259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.043169 restraints weight = 52001.270| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 3.72 r_work: 0.2532 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15779 Z= 0.206 Angle : 0.603 10.856 21445 Z= 0.300 Chirality : 0.044 0.413 2531 Planarity : 0.003 0.044 2669 Dihedral : 10.537 97.043 2401 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.09 % Allowed : 12.73 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.20), residues: 1979 helix: 1.66 (0.20), residues: 713 sheet: -0.76 (0.32), residues: 290 loop : -1.11 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 656 HIS 0.004 0.001 HIS E 489 PHE 0.018 0.001 PHE B 87 TYR 0.020 0.001 TYR A 31 ARG 0.005 0.000 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 8) link_NAG-ASN : angle 3.15751 ( 24) link_BETA1-4 : bond 0.00549 ( 4) link_BETA1-4 : angle 2.40348 ( 12) hydrogen bonds : bond 0.04472 ( 678) hydrogen bonds : angle 4.90325 ( 1941) SS BOND : bond 0.00354 ( 8) SS BOND : angle 1.09673 ( 16) link_BETA1-3 : bond 0.00763 ( 1) link_BETA1-3 : angle 5.23730 ( 3) covalent geometry : bond 0.00466 (15758) covalent geometry : angle 0.58774 (21390) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8874 (t0) cc_final: 0.8577 (t0) REVERT: A 262 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8759 (tp-100) REVERT: A 317 CYS cc_start: 0.8905 (p) cc_final: 0.8690 (p) REVERT: A 350 ASP cc_start: 0.8320 (t0) cc_final: 0.7938 (t0) REVERT: A 444 MET cc_start: 0.9061 (tmm) cc_final: 0.8495 (tmm) REVERT: B 85 MET cc_start: 0.8914 (tpt) cc_final: 0.8637 (tpp) REVERT: B 350 ASP cc_start: 0.7841 (t70) cc_final: 0.7155 (t0) REVERT: B 384 MET cc_start: 0.8647 (mpp) cc_final: 0.7627 (mpp) REVERT: C 146 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: C 278 MET cc_start: 0.8455 (ptm) cc_final: 0.7848 (tmm) REVERT: D 73 ASP cc_start: 0.8111 (t0) cc_final: 0.7451 (t0) REVERT: D 76 LYS cc_start: 0.9615 (mtpp) cc_final: 0.9314 (mtpp) REVERT: D 128 MET cc_start: 0.8082 (tpp) cc_final: 0.7514 (mmt) REVERT: D 207 PHE cc_start: 0.6433 (OUTLIER) cc_final: 0.4925 (m-80) REVERT: E 286 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8670 (mmmm) REVERT: E 289 GLU cc_start: 0.9163 (pt0) cc_final: 0.8873 (pm20) REVERT: E 319 GLU cc_start: 0.8592 (tt0) cc_final: 0.8330 (tt0) REVERT: E 364 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8915 (t) REVERT: E 375 GLN cc_start: 0.8347 (tt0) cc_final: 0.8025 (tt0) outliers start: 18 outliers final: 10 residues processed: 109 average time/residue: 0.2383 time to fit residues: 42.4959 Evaluate side-chains 102 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain E residue 364 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 65 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.068712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.044530 restraints weight = 51391.129| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.75 r_work: 0.2581 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15779 Z= 0.120 Angle : 0.561 10.389 21445 Z= 0.279 Chirality : 0.043 0.407 2531 Planarity : 0.003 0.044 2669 Dihedral : 10.111 96.611 2401 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.84 % Allowed : 13.76 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1979 helix: 1.77 (0.20), residues: 711 sheet: -0.72 (0.32), residues: 296 loop : -1.12 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 656 HIS 0.006 0.001 HIS E 489 PHE 0.016 0.001 PHE B 65 TYR 0.020 0.001 TYR A 31 ARG 0.005 0.000 ARG D 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 8) link_NAG-ASN : angle 3.01925 ( 24) link_BETA1-4 : bond 0.00580 ( 4) link_BETA1-4 : angle 2.43387 ( 12) hydrogen bonds : bond 0.04114 ( 678) hydrogen bonds : angle 4.74037 ( 1941) SS BOND : bond 0.00351 ( 8) SS BOND : angle 0.98678 ( 16) link_BETA1-3 : bond 0.00716 ( 1) link_BETA1-3 : angle 4.84892 ( 3) covalent geometry : bond 0.00262 (15758) covalent geometry : angle 0.54613 (21390) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 1.728 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8883 (t0) cc_final: 0.8582 (t0) REVERT: A 150 MET cc_start: 0.9114 (ptm) cc_final: 0.8861 (ptm) REVERT: A 262 GLN cc_start: 0.8990 (tp-100) cc_final: 0.8748 (tp-100) REVERT: A 350 ASP cc_start: 0.8318 (t0) cc_final: 0.7891 (t0) REVERT: A 444 MET cc_start: 0.9031 (tmm) cc_final: 0.8466 (tmm) REVERT: B 85 MET cc_start: 0.8935 (tpt) cc_final: 0.8523 (tpp) REVERT: C 146 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: C 278 MET cc_start: 0.8426 (ptm) cc_final: 0.7735 (tmm) REVERT: D 73 ASP cc_start: 0.8106 (t0) cc_final: 0.7446 (t0) REVERT: D 76 LYS cc_start: 0.9617 (mtpp) cc_final: 0.9343 (mtpp) REVERT: D 207 PHE cc_start: 0.6327 (OUTLIER) cc_final: 0.4902 (m-80) REVERT: E 286 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8683 (mmmm) REVERT: E 289 GLU cc_start: 0.9225 (pt0) cc_final: 0.9023 (pm20) REVERT: E 319 GLU cc_start: 0.8674 (tt0) cc_final: 0.8391 (tt0) REVERT: E 364 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8885 (t) REVERT: E 378 MET cc_start: 0.8835 (ptm) cc_final: 0.8589 (ptp) outliers start: 14 outliers final: 8 residues processed: 108 average time/residue: 0.2392 time to fit residues: 41.8448 Evaluate side-chains 102 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain E residue 364 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 84 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.068623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.044369 restraints weight = 51609.079| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.76 r_work: 0.2612 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15779 Z= 0.136 Angle : 0.560 10.403 21445 Z= 0.278 Chirality : 0.043 0.399 2531 Planarity : 0.003 0.043 2669 Dihedral : 9.643 95.564 2401 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.03 % Allowed : 14.18 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1979 helix: 1.79 (0.20), residues: 712 sheet: -0.79 (0.31), residues: 306 loop : -1.04 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 382 HIS 0.005 0.001 HIS E 489 PHE 0.016 0.001 PHE B 87 TYR 0.021 0.001 TYR A 31 ARG 0.003 0.000 ARG D 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 8) link_NAG-ASN : angle 2.95773 ( 24) link_BETA1-4 : bond 0.00689 ( 4) link_BETA1-4 : angle 2.47042 ( 12) hydrogen bonds : bond 0.04089 ( 678) hydrogen bonds : angle 4.69330 ( 1941) SS BOND : bond 0.00300 ( 8) SS BOND : angle 0.90269 ( 16) link_BETA1-3 : bond 0.00661 ( 1) link_BETA1-3 : angle 4.64369 ( 3) covalent geometry : bond 0.00302 (15758) covalent geometry : angle 0.54507 (21390) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.797 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8938 (t0) cc_final: 0.8627 (t0) REVERT: A 150 MET cc_start: 0.9129 (ptm) cc_final: 0.8870 (ptm) REVERT: A 262 GLN cc_start: 0.9010 (tp-100) cc_final: 0.8740 (tp-100) REVERT: A 304 MET cc_start: 0.9273 (tpp) cc_final: 0.9013 (tpp) REVERT: A 350 ASP cc_start: 0.8361 (t0) cc_final: 0.7935 (t0) REVERT: A 444 MET cc_start: 0.9076 (tmm) cc_final: 0.8513 (tmm) REVERT: B 85 MET cc_start: 0.9083 (tpt) cc_final: 0.8657 (tpp) REVERT: C 146 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: C 278 MET cc_start: 0.8502 (ptm) cc_final: 0.7797 (tmm) REVERT: D 73 ASP cc_start: 0.8232 (t0) cc_final: 0.7528 (t0) REVERT: D 76 LYS cc_start: 0.9641 (mtpp) cc_final: 0.9336 (mtpp) REVERT: D 207 PHE cc_start: 0.6346 (OUTLIER) cc_final: 0.4900 (m-80) REVERT: E 286 LYS cc_start: 0.9144 (mmmt) cc_final: 0.8714 (mmmm) REVERT: E 319 GLU cc_start: 0.8781 (tt0) cc_final: 0.8527 (tt0) REVERT: E 364 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8865 (t) REVERT: E 378 MET cc_start: 0.8931 (ptm) cc_final: 0.8704 (ptp) outliers start: 17 outliers final: 9 residues processed: 107 average time/residue: 0.2448 time to fit residues: 42.7371 Evaluate side-chains 102 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain E residue 364 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 105 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 203 GLN E 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.069344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.045086 restraints weight = 50862.787| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.72 r_work: 0.2637 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15779 Z= 0.111 Angle : 0.553 10.308 21445 Z= 0.272 Chirality : 0.043 0.392 2531 Planarity : 0.003 0.043 2669 Dihedral : 9.222 95.141 2401 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.09 % Allowed : 14.48 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.20), residues: 1979 helix: 1.89 (0.20), residues: 708 sheet: -0.72 (0.32), residues: 296 loop : -1.10 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 382 HIS 0.006 0.001 HIS E 489 PHE 0.015 0.001 PHE B 65 TYR 0.019 0.001 TYR A 31 ARG 0.003 0.000 ARG D 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 8) link_NAG-ASN : angle 2.87335 ( 24) link_BETA1-4 : bond 0.00644 ( 4) link_BETA1-4 : angle 2.56586 ( 12) hydrogen bonds : bond 0.03905 ( 678) hydrogen bonds : angle 4.60110 ( 1941) SS BOND : bond 0.00291 ( 8) SS BOND : angle 0.84901 ( 16) link_BETA1-3 : bond 0.00779 ( 1) link_BETA1-3 : angle 4.62508 ( 3) covalent geometry : bond 0.00241 (15758) covalent geometry : angle 0.53827 (21390) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 1.963 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8954 (t0) cc_final: 0.8640 (t0) REVERT: A 150 MET cc_start: 0.9133 (ptm) cc_final: 0.8867 (ptm) REVERT: A 350 ASP cc_start: 0.8404 (t0) cc_final: 0.7981 (t0) REVERT: A 444 MET cc_start: 0.9085 (tmm) cc_final: 0.8520 (tmm) REVERT: B 85 MET cc_start: 0.9149 (tpt) cc_final: 0.8706 (tpp) REVERT: C 146 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: C 278 MET cc_start: 0.8551 (ptm) cc_final: 0.7827 (tmm) REVERT: D 73 ASP cc_start: 0.8312 (t0) cc_final: 0.7610 (t0) REVERT: D 76 LYS cc_start: 0.9658 (mtpp) cc_final: 0.9365 (mtpp) REVERT: D 128 MET cc_start: 0.8664 (mmt) cc_final: 0.7935 (mmt) REVERT: D 130 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7059 (mt0) REVERT: D 207 PHE cc_start: 0.6342 (OUTLIER) cc_final: 0.4958 (m-80) REVERT: E 283 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8514 (mm-30) REVERT: E 286 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8453 (mmmt) REVERT: E 319 GLU cc_start: 0.8828 (tt0) cc_final: 0.8548 (tt0) REVERT: E 378 MET cc_start: 0.8968 (ptm) cc_final: 0.8743 (ptp) outliers start: 18 outliers final: 8 residues processed: 112 average time/residue: 0.3151 time to fit residues: 56.9067 Evaluate side-chains 101 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 207 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 196 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.068920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.044726 restraints weight = 50927.582| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.68 r_work: 0.2624 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15779 Z= 0.141 Angle : 0.568 10.283 21445 Z= 0.280 Chirality : 0.043 0.389 2531 Planarity : 0.003 0.042 2669 Dihedral : 8.960 94.574 2401 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.66 % Allowed : 14.73 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1979 helix: 1.88 (0.20), residues: 715 sheet: -0.68 (0.31), residues: 291 loop : -1.09 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 382 HIS 0.004 0.001 HIS E 489 PHE 0.016 0.001 PHE B 87 TYR 0.019 0.001 TYR A 31 ARG 0.004 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 8) link_NAG-ASN : angle 2.86496 ( 24) link_BETA1-4 : bond 0.00652 ( 4) link_BETA1-4 : angle 2.61246 ( 12) hydrogen bonds : bond 0.03949 ( 678) hydrogen bonds : angle 4.62214 ( 1941) SS BOND : bond 0.00351 ( 8) SS BOND : angle 0.97422 ( 16) link_BETA1-3 : bond 0.00818 ( 1) link_BETA1-3 : angle 4.64769 ( 3) covalent geometry : bond 0.00318 (15758) covalent geometry : angle 0.55426 (21390) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.606 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8961 (t0) cc_final: 0.8641 (t0) REVERT: A 150 MET cc_start: 0.9137 (ptm) cc_final: 0.8866 (ptm) REVERT: A 350 ASP cc_start: 0.8419 (t0) cc_final: 0.8022 (t0) REVERT: A 444 MET cc_start: 0.9088 (tmm) cc_final: 0.8506 (tmm) REVERT: B 85 MET cc_start: 0.9159 (tpt) cc_final: 0.8719 (tpp) REVERT: B 150 MET cc_start: 0.9024 (tpp) cc_final: 0.8670 (mpp) REVERT: C 132 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8819 (p) REVERT: C 146 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: C 278 MET cc_start: 0.8547 (ptm) cc_final: 0.7861 (tmm) REVERT: D 73 ASP cc_start: 0.8328 (t0) cc_final: 0.7641 (t0) REVERT: D 76 LYS cc_start: 0.9659 (mtpp) cc_final: 0.9364 (mtpp) REVERT: D 128 MET cc_start: 0.8385 (mmt) cc_final: 0.7641 (mmt) REVERT: D 207 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.4977 (m-80) REVERT: E 283 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8531 (mm-30) REVERT: E 286 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8433 (mmmt) REVERT: E 319 GLU cc_start: 0.8819 (tt0) cc_final: 0.8294 (tt0) REVERT: E 378 MET cc_start: 0.8939 (ptm) cc_final: 0.8701 (ptp) outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.2444 time to fit residues: 39.8363 Evaluate side-chains 102 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain D residue 207 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 109 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 166 optimal weight: 0.0270 chunk 127 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.068690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.044505 restraints weight = 51149.573| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.71 r_work: 0.2620 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15779 Z= 0.143 Angle : 0.573 10.236 21445 Z= 0.282 Chirality : 0.043 0.385 2531 Planarity : 0.003 0.042 2669 Dihedral : 8.501 93.632 2401 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.78 % Allowed : 14.67 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1979 helix: 1.88 (0.20), residues: 715 sheet: -0.70 (0.31), residues: 291 loop : -1.11 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 382 HIS 0.003 0.001 HIS E 489 PHE 0.016 0.001 PHE B 87 TYR 0.019 0.001 TYR A 31 ARG 0.007 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 8) link_NAG-ASN : angle 2.83915 ( 24) link_BETA1-4 : bond 0.00663 ( 4) link_BETA1-4 : angle 2.74434 ( 12) hydrogen bonds : bond 0.03993 ( 678) hydrogen bonds : angle 4.61699 ( 1941) SS BOND : bond 0.00336 ( 8) SS BOND : angle 0.91768 ( 16) link_BETA1-3 : bond 0.00862 ( 1) link_BETA1-3 : angle 4.64657 ( 3) covalent geometry : bond 0.00323 (15758) covalent geometry : angle 0.55851 (21390) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3958 Ramachandran restraints generated. 1979 Oldfield, 0 Emsley, 1979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.608 Fit side-chains revert: symmetry clash REVERT: A 350 ASP cc_start: 0.8385 (t0) cc_final: 0.7963 (t0) REVERT: A 444 MET cc_start: 0.9109 (tmm) cc_final: 0.8376 (tmm) REVERT: B 85 MET cc_start: 0.9114 (tpt) cc_final: 0.8679 (tpp) REVERT: C 132 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8827 (p) REVERT: C 146 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: C 278 MET cc_start: 0.8498 (ptm) cc_final: 0.7814 (tmm) REVERT: D 73 ASP cc_start: 0.8266 (t0) cc_final: 0.7567 (t0) REVERT: D 76 LYS cc_start: 0.9643 (mtpp) cc_final: 0.9342 (mtpp) REVERT: D 128 MET cc_start: 0.8432 (mmt) cc_final: 0.7662 (mmt) REVERT: D 207 PHE cc_start: 0.6371 (OUTLIER) cc_final: 0.5053 (m-80) REVERT: E 283 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8513 (mm-30) REVERT: E 286 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8345 (mmmt) REVERT: E 319 GLU cc_start: 0.8781 (tt0) cc_final: 0.8230 (tt0) REVERT: E 366 MET cc_start: 0.8600 (tpt) cc_final: 0.7910 (tpt) REVERT: E 378 MET cc_start: 0.8877 (ptm) cc_final: 0.8640 (ptp) outliers start: 13 outliers final: 9 residues processed: 106 average time/residue: 0.2640 time to fit residues: 44.5411 Evaluate side-chains 103 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 146 GLN Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 207 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 187 optimal weight: 0.5980 chunk 179 optimal weight: 0.0980 chunk 193 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 138 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS D 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.069342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.045123 restraints weight = 51139.479| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.73 r_work: 0.2632 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15779 Z= 0.119 Angle : 0.570 10.091 21445 Z= 0.280 Chirality : 0.043 0.384 2531 Planarity : 0.003 0.043 2669 Dihedral : 8.336 93.440 2401 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.72 % Allowed : 14.91 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1979 helix: 1.90 (0.20), residues: 715 sheet: -0.70 (0.31), residues: 291 loop : -1.11 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 382 HIS 0.004 0.001 HIS E 489 PHE 0.015 0.001 PHE B 87 TYR 0.019 0.001 TYR A 31 ARG 0.007 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 8) link_NAG-ASN : angle 2.79940 ( 24) link_BETA1-4 : bond 0.00663 ( 4) link_BETA1-4 : angle 2.79791 ( 12) hydrogen bonds : bond 0.03920 ( 678) hydrogen bonds : angle 4.58920 ( 1941) SS BOND : bond 0.00334 ( 8) SS BOND : angle 0.92940 ( 16) link_BETA1-3 : bond 0.00860 ( 1) link_BETA1-3 : angle 4.62251 ( 3) covalent geometry : bond 0.00264 (15758) covalent geometry : angle 0.55565 (21390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7850.91 seconds wall clock time: 137 minutes 36.05 seconds (8256.05 seconds total)