Starting phenix.real_space_refine on Thu Sep 18 09:00:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lsj_63357/09_2025/9lsj_63357.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lsj_63357/09_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_63357/09_2025/9lsj_63357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lsj_63357/09_2025/9lsj_63357.map" model { file = "/net/cci-nas-00/data/ceres_data/9lsj_63357/09_2025/9lsj_63357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lsj_63357/09_2025/9lsj_63357.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.94, per 1000 atoms: 0.26 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: 1.39 Conformation dependent library (CDL) restraints added in 701.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.60 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: 3.00 Time building geometry restraints manager: 1.80 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: 1.440 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.200 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.690 ------------------------------------------------------------------------------- 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 : 10.52 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.001 ARG B 203 TYR 0.026 0.002 TYR C 74 PHE 0.030 0.002 PHE C 143 TRP 0.023 0.001 TRP C 656 HIS 0.011 0.001 HIS E 489 Details of bonding type rmsd covalent geometry : bond 0.00612 (15758) covalent geometry : angle 0.78717 (21390) SS BOND : bond 0.00364 ( 8) SS BOND : angle 1.12338 ( 16) hydrogen bonds : bond 0.18282 ( 678) hydrogen bonds : angle 7.16031 ( 1941) link_BETA1-3 : bond 0.04513 ( 1) link_BETA1-3 : angle 4.43043 ( 3) link_BETA1-4 : bond 0.02274 ( 4) link_BETA1-4 : angle 3.33328 ( 12) link_NAG-ASN : bond 0.00702 ( 8) link_NAG-ASN : angle 4.54291 ( 24) *********************** 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 : 0.534 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: 0.1247 time to fit residues: 21.8685 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 : 0.708 ------------------------------------------------------------------------------- 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 98 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 232 GLN C 684 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.066168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.041916 restraints weight = 52356.624| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 3.73 r_work: 0.2500 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 15779 Z= 0.302 Angle : 0.707 11.047 21445 Z= 0.356 Chirality : 0.047 0.427 2531 Planarity : 0.004 0.052 2669 Dihedral : 13.576 102.645 2401 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.30 % Allowed : 6.28 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.20), residues: 1979 helix: 1.18 (0.20), residues: 707 sheet: -0.87 (0.32), residues: 289 loop : -1.21 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 203 TYR 0.019 0.002 TYR A 31 PHE 0.021 0.002 PHE B 87 TRP 0.014 0.001 TRP B 382 HIS 0.006 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00685 (15758) covalent geometry : angle 0.68933 (21390) SS BOND : bond 0.00481 ( 8) SS BOND : angle 1.43459 ( 16) hydrogen bonds : bond 0.05527 ( 678) hydrogen bonds : angle 5.64595 ( 1941) link_BETA1-3 : bond 0.00732 ( 1) link_BETA1-3 : angle 5.65786 ( 3) link_BETA1-4 : bond 0.00731 ( 4) link_BETA1-4 : angle 2.01316 ( 12) link_NAG-ASN : bond 0.00455 ( 8) link_NAG-ASN : angle 3.89102 ( 24) *********************** 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 98 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.9020 (p0) cc_final: 0.8453 (p0) REVERT: A 85 MET cc_start: 0.8941 (tpp) cc_final: 0.8602 (tpp) REVERT: A 112 ASP cc_start: 0.8876 (t0) cc_final: 0.8587 (t0) REVERT: A 150 MET cc_start: 0.9203 (ptm) cc_final: 0.8940 (ptm) REVERT: A 444 MET cc_start: 0.8954 (tmm) cc_final: 0.8234 (tmm) REVERT: B 85 MET cc_start: 0.8912 (tpt) cc_final: 0.8586 (tpp) REVERT: B 150 MET cc_start: 0.9287 (ttm) cc_final: 0.8956 (ttm) REVERT: B 350 ASP cc_start: 0.8087 (t70) cc_final: 0.7441 (t0) REVERT: B 424 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8936 (mt0) REVERT: C 374 MET cc_start: 0.8989 (mtm) cc_final: 0.8699 (mtt) REVERT: D 73 ASP cc_start: 0.8223 (t0) cc_final: 0.7537 (t0) REVERT: D 76 LYS cc_start: 0.9618 (mtpp) cc_final: 0.9315 (mtpp) REVERT: D 148 ARG cc_start: 0.8484 (tpt-90) cc_final: 0.8257 (tpp80) REVERT: D 207 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.5136 (m-80) REVERT: E 286 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8742 (mmmm) REVERT: E 319 GLU cc_start: 0.8516 (tt0) cc_final: 0.8299 (tt0) outliers start: 5 outliers final: 3 residues processed: 98 average time/residue: 0.1246 time to fit residues: 19.2571 Evaluate side-chains 88 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.0870 chunk 147 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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 616 ASN 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 = 0.068751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.044606 restraints weight = 51799.732| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.78 r_work: 0.2616 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15779 Z= 0.127 Angle : 0.577 10.532 21445 Z= 0.290 Chirality : 0.044 0.415 2531 Planarity : 0.003 0.044 2669 Dihedral : 11.769 101.305 2401 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.84 % Allowed : 9.11 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.20), residues: 1979 helix: 1.52 (0.20), residues: 711 sheet: -0.79 (0.33), residues: 283 loop : -1.16 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 203 TYR 0.020 0.001 TYR A 31 PHE 0.017 0.001 PHE A 65 TRP 0.012 0.001 TRP B 382 HIS 0.006 0.001 HIS E 489 Details of bonding type rmsd covalent geometry : bond 0.00272 (15758) covalent geometry : angle 0.55930 (21390) SS BOND : bond 0.00334 ( 8) SS BOND : angle 1.06320 ( 16) hydrogen bonds : bond 0.04475 ( 678) hydrogen bonds : angle 5.03936 ( 1941) link_BETA1-3 : bond 0.00495 ( 1) link_BETA1-3 : angle 6.03345 ( 3) link_BETA1-4 : bond 0.00740 ( 4) link_BETA1-4 : angle 2.20464 ( 12) link_NAG-ASN : bond 0.00505 ( 8) link_NAG-ASN : angle 3.33951 ( 24) *********************** 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 111 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.8798 (p0) cc_final: 0.8544 (p0) REVERT: A 85 MET cc_start: 0.9004 (tpp) cc_final: 0.8699 (tpp) REVERT: A 112 ASP cc_start: 0.8942 (t0) cc_final: 0.8646 (t0) REVERT: A 350 ASP cc_start: 0.8384 (t0) cc_final: 0.8126 (t0) REVERT: A 352 GLN cc_start: 0.9047 (tp40) cc_final: 0.8801 (tp40) REVERT: A 444 MET cc_start: 0.8957 (tmm) cc_final: 0.8488 (tmm) REVERT: B 85 MET cc_start: 0.9018 (tpt) cc_final: 0.8579 (tpp) REVERT: B 150 MET cc_start: 0.9291 (ttm) cc_final: 0.8849 (ttm) REVERT: B 384 MET cc_start: 0.8500 (mpp) cc_final: 0.8188 (mpp) REVERT: C 94 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8483 (tp) REVERT: C 278 MET cc_start: 0.8496 (ptm) cc_final: 0.7858 (tmm) REVERT: C 374 MET cc_start: 0.9025 (mtm) cc_final: 0.8587 (mtm) REVERT: D 73 ASP cc_start: 0.8298 (t0) cc_final: 0.7637 (t0) REVERT: D 76 LYS cc_start: 0.9676 (mtpp) cc_final: 0.9424 (mtpp) REVERT: D 128 MET cc_start: 0.7823 (tpp) cc_final: 0.7388 (mmt) REVERT: D 207 PHE cc_start: 0.6382 (OUTLIER) cc_final: 0.4803 (m-80) REVERT: E 286 LYS cc_start: 0.9098 (mmmt) cc_final: 0.8741 (mmmm) REVERT: E 319 GLU cc_start: 0.8735 (tt0) cc_final: 0.8478 (tt0) outliers start: 14 outliers final: 7 residues processed: 107 average time/residue: 0.1156 time to fit residues: 19.6393 Evaluate side-chains 95 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 94 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 136 optimal weight: 0.8980 chunk 149 optimal weight: 0.0010 chunk 81 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 0.0670 chunk 48 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 overall best weight: 0.7928 ------------------------------------------------------------------------------- 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 424 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.069080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.044916 restraints weight = 51071.817| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.74 r_work: 0.2634 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15779 Z= 0.115 Angle : 0.553 10.378 21445 Z= 0.276 Chirality : 0.043 0.411 2531 Planarity : 0.003 0.043 2669 Dihedral : 10.814 98.893 2401 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.97 % Allowed : 10.56 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.20), residues: 1979 helix: 1.70 (0.20), residues: 716 sheet: -0.69 (0.32), residues: 286 loop : -1.12 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 428 TYR 0.020 0.001 TYR A 31 PHE 0.016 0.001 PHE B 87 TRP 0.015 0.001 TRP C 656 HIS 0.006 0.001 HIS E 489 Details of bonding type rmsd covalent geometry : bond 0.00248 (15758) covalent geometry : angle 0.53650 (21390) SS BOND : bond 0.00329 ( 8) SS BOND : angle 0.91951 ( 16) hydrogen bonds : bond 0.04112 ( 678) hydrogen bonds : angle 4.83199 ( 1941) link_BETA1-3 : bond 0.00699 ( 1) link_BETA1-3 : angle 5.72233 ( 3) link_BETA1-4 : bond 0.00541 ( 4) link_BETA1-4 : angle 2.37340 ( 12) link_NAG-ASN : bond 0.00484 ( 8) link_NAG-ASN : angle 3.11953 ( 24) *********************** 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 113 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.9002 (tpp) cc_final: 0.8722 (tpp) REVERT: A 112 ASP cc_start: 0.8930 (t0) cc_final: 0.8628 (t0) REVERT: A 150 MET cc_start: 0.9312 (ptm) cc_final: 0.9096 (ptm) REVERT: A 350 ASP cc_start: 0.8391 (t0) cc_final: 0.8026 (t0) REVERT: A 352 GLN cc_start: 0.9063 (tp40) cc_final: 0.8843 (tp40) REVERT: A 444 MET cc_start: 0.8974 (tmm) cc_final: 0.8153 (tmm) REVERT: B 85 MET cc_start: 0.9001 (tpt) cc_final: 0.8568 (tpp) REVERT: B 150 MET cc_start: 0.9160 (ttm) cc_final: 0.8691 (ttm) REVERT: C 94 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8411 (tp) REVERT: C 146 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: C 278 MET cc_start: 0.8504 (ptm) cc_final: 0.7845 (tmm) REVERT: C 374 MET cc_start: 0.9032 (mtm) cc_final: 0.8616 (mtm) REVERT: D 73 ASP cc_start: 0.8215 (t0) cc_final: 0.7589 (t0) REVERT: D 76 LYS cc_start: 0.9658 (mtpp) cc_final: 0.9398 (mtpp) REVERT: D 128 MET cc_start: 0.7935 (tpp) cc_final: 0.7491 (mmt) REVERT: D 207 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.4854 (m-80) REVERT: E 286 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8543 (mmmt) REVERT: E 319 GLU cc_start: 0.8764 (tt0) cc_final: 0.8492 (tt0) REVERT: E 364 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.9024 (t) outliers start: 16 outliers final: 9 residues processed: 109 average time/residue: 0.1163 time to fit residues: 20.2933 Evaluate side-chains 99 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 317 CYS 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 94 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 131 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 180 ASN E 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.068950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.044714 restraints weight = 51525.518| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.75 r_work: 0.2568 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15779 Z= 0.128 Angle : 0.556 10.409 21445 Z= 0.276 Chirality : 0.043 0.404 2531 Planarity : 0.003 0.042 2669 Dihedral : 10.297 97.825 2401 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.09 % Allowed : 11.71 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.20), residues: 1979 helix: 1.72 (0.20), residues: 720 sheet: -0.62 (0.32), residues: 286 loop : -1.10 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 148 TYR 0.020 0.001 TYR A 31 PHE 0.015 0.001 PHE B 87 TRP 0.021 0.001 TRP A 382 HIS 0.005 0.001 HIS E 489 Details of bonding type rmsd covalent geometry : bond 0.00283 (15758) covalent geometry : angle 0.54049 (21390) SS BOND : bond 0.00303 ( 8) SS BOND : angle 0.88974 ( 16) hydrogen bonds : bond 0.04058 ( 678) hydrogen bonds : angle 4.73427 ( 1941) link_BETA1-3 : bond 0.00796 ( 1) link_BETA1-3 : angle 5.27988 ( 3) link_BETA1-4 : bond 0.00631 ( 4) link_BETA1-4 : angle 2.39568 ( 12) link_NAG-ASN : bond 0.00464 ( 8) link_NAG-ASN : angle 3.03777 ( 24) *********************** 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 116 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 85 MET cc_start: 0.8810 (tpp) cc_final: 0.8567 (tpp) REVERT: A 112 ASP cc_start: 0.8856 (t0) cc_final: 0.8556 (t0) REVERT: A 262 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8778 (tp-100) REVERT: A 350 ASP cc_start: 0.8296 (t0) cc_final: 0.7889 (t0) REVERT: A 352 GLN cc_start: 0.9008 (tp40) cc_final: 0.8805 (tp40) REVERT: A 444 MET cc_start: 0.8924 (tmm) cc_final: 0.8450 (tmm) REVERT: B 85 MET cc_start: 0.8845 (tpt) cc_final: 0.8417 (tpp) REVERT: B 150 MET cc_start: 0.9160 (ttm) cc_final: 0.8717 (ttm) REVERT: B 384 MET cc_start: 0.8671 (mpp) cc_final: 0.7611 (mpp) REVERT: C 94 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8326 (tp) REVERT: C 146 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: C 278 MET cc_start: 0.8347 (ptm) cc_final: 0.7675 (tmm) REVERT: D 34 MET cc_start: 0.9220 (mmm) cc_final: 0.8692 (mmt) REVERT: D 73 ASP cc_start: 0.7956 (t0) cc_final: 0.7323 (t0) REVERT: D 76 LYS cc_start: 0.9598 (mtpp) cc_final: 0.9321 (mtpp) REVERT: D 128 MET cc_start: 0.7665 (tpp) cc_final: 0.7318 (mmt) REVERT: D 130 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6760 (mm-40) REVERT: D 207 PHE cc_start: 0.6276 (OUTLIER) cc_final: 0.4868 (m-80) REVERT: E 283 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8400 (mm-30) REVERT: E 286 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8328 (mmmt) REVERT: E 319 GLU cc_start: 0.8606 (tt0) cc_final: 0.8330 (tt0) REVERT: E 364 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8936 (t) outliers start: 18 outliers final: 7 residues processed: 113 average time/residue: 0.1110 time to fit residues: 20.3229 Evaluate side-chains 100 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 94 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 109 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.067095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.042921 restraints weight = 51620.479| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 3.70 r_work: 0.2531 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15779 Z= 0.238 Angle : 0.618 10.853 21445 Z= 0.306 Chirality : 0.044 0.404 2531 Planarity : 0.003 0.044 2669 Dihedral : 9.877 95.616 2401 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.03 % Allowed : 13.34 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.20), residues: 1979 helix: 1.76 (0.20), residues: 713 sheet: -0.75 (0.31), residues: 300 loop : -1.06 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 148 TYR 0.021 0.001 TYR A 31 PHE 0.019 0.001 PHE B 87 TRP 0.015 0.001 TRP C 656 HIS 0.003 0.001 HIS C 674 Details of bonding type rmsd covalent geometry : bond 0.00540 (15758) covalent geometry : angle 0.60398 (21390) SS BOND : bond 0.00377 ( 8) SS BOND : angle 1.09283 ( 16) hydrogen bonds : bond 0.04484 ( 678) hydrogen bonds : angle 4.85775 ( 1941) link_BETA1-3 : bond 0.00900 ( 1) link_BETA1-3 : angle 4.85476 ( 3) link_BETA1-4 : bond 0.00642 ( 4) link_BETA1-4 : angle 2.44313 ( 12) link_NAG-ASN : bond 0.00385 ( 8) link_NAG-ASN : angle 3.08411 ( 24) *********************** 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 109 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8916 (t0) cc_final: 0.8677 (t0) REVERT: A 262 GLN cc_start: 0.9055 (tp-100) cc_final: 0.8818 (tp-100) REVERT: A 350 ASP cc_start: 0.8326 (t0) cc_final: 0.7927 (t0) REVERT: A 444 MET cc_start: 0.8993 (tmm) cc_final: 0.8553 (tmm) REVERT: B 85 MET cc_start: 0.8996 (tpt) cc_final: 0.8683 (tpp) REVERT: B 350 ASP cc_start: 0.7897 (t70) cc_final: 0.7219 (t0) REVERT: C 146 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: C 278 MET cc_start: 0.8469 (ptm) cc_final: 0.7829 (tmm) REVERT: C 374 MET cc_start: 0.9078 (mtm) cc_final: 0.8711 (mtt) REVERT: D 73 ASP cc_start: 0.8153 (t0) cc_final: 0.7485 (t0) REVERT: D 76 LYS cc_start: 0.9625 (mtpp) cc_final: 0.9346 (mtpp) REVERT: D 128 MET cc_start: 0.8051 (tpp) cc_final: 0.7425 (mmt) REVERT: D 130 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7166 (mm-40) REVERT: D 207 PHE cc_start: 0.6413 (OUTLIER) cc_final: 0.4970 (m-80) REVERT: E 286 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8358 (mmmt) REVERT: E 319 GLU cc_start: 0.8662 (tt0) cc_final: 0.8407 (tt0) REVERT: E 364 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8949 (t) outliers start: 17 outliers final: 9 residues processed: 105 average time/residue: 0.1192 time to fit residues: 20.0579 Evaluate side-chains 101 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 317 CYS Chi-restraints excluded: chain B residue 339 VAL 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 130 GLN 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 109 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 185 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.068651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.044416 restraints weight = 50777.759| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.70 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: 0.8304 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15779 Z= 0.119 Angle : 0.558 10.242 21445 Z= 0.276 Chirality : 0.043 0.397 2531 Planarity : 0.003 0.043 2669 Dihedral : 9.489 95.609 2401 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.91 % Allowed : 14.24 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.20), residues: 1979 helix: 1.86 (0.20), residues: 716 sheet: -0.62 (0.31), residues: 301 loop : -1.06 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 148 TYR 0.020 0.001 TYR A 31 PHE 0.015 0.001 PHE B 65 TRP 0.010 0.001 TRP A 382 HIS 0.006 0.001 HIS E 489 Details of bonding type rmsd covalent geometry : bond 0.00261 (15758) covalent geometry : angle 0.54301 (21390) SS BOND : bond 0.00325 ( 8) SS BOND : angle 0.91447 ( 16) hydrogen bonds : bond 0.04047 ( 678) hydrogen bonds : angle 4.67848 ( 1941) link_BETA1-3 : bond 0.00794 ( 1) link_BETA1-3 : angle 4.62269 ( 3) link_BETA1-4 : bond 0.00636 ( 4) link_BETA1-4 : angle 2.50630 ( 12) link_NAG-ASN : bond 0.00478 ( 8) link_NAG-ASN : angle 2.93305 ( 24) *********************** 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 107 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 ASP cc_start: 0.8389 (t0) cc_final: 0.7974 (t0) REVERT: A 444 MET cc_start: 0.9012 (tmm) cc_final: 0.8547 (tmm) REVERT: B 85 MET cc_start: 0.9079 (tpt) cc_final: 0.8648 (tpp) REVERT: B 150 MET cc_start: 0.9004 (ttm) cc_final: 0.8802 (mmt) REVERT: C 131 MET cc_start: 0.9010 (mmp) cc_final: 0.8703 (mpp) REVERT: C 146 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: C 278 MET cc_start: 0.8577 (ptm) cc_final: 0.7882 (tmm) REVERT: C 374 MET cc_start: 0.9052 (mtm) cc_final: 0.8629 (mtt) REVERT: D 73 ASP cc_start: 0.8275 (t0) cc_final: 0.7620 (t0) REVERT: D 76 LYS cc_start: 0.9670 (mtpp) cc_final: 0.9413 (mtpp) REVERT: D 128 MET cc_start: 0.7739 (tpp) cc_final: 0.7287 (mmt) REVERT: D 207 PHE cc_start: 0.6341 (OUTLIER) cc_final: 0.4877 (m-80) REVERT: E 283 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8530 (mm-30) REVERT: E 286 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8525 (mmmt) REVERT: E 319 GLU cc_start: 0.8793 (tt0) cc_final: 0.8259 (tt0) REVERT: E 364 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8928 (t) outliers start: 15 outliers final: 8 residues processed: 104 average time/residue: 0.1117 time to fit residues: 18.8669 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 : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 339 VAL 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 130 GLN 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 193 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.066766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.042428 restraints weight = 52223.217| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 3.74 r_work: 0.2518 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15779 Z= 0.256 Angle : 0.633 10.853 21445 Z= 0.313 Chirality : 0.044 0.401 2531 Planarity : 0.003 0.042 2669 Dihedral : 9.134 93.492 2401 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.09 % Allowed : 14.18 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.20), residues: 1979 helix: 1.75 (0.20), residues: 715 sheet: -0.82 (0.31), residues: 300 loop : -1.05 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 148 TYR 0.022 0.001 TYR A 31 PHE 0.020 0.001 PHE B 87 TRP 0.014 0.001 TRP B 382 HIS 0.003 0.001 HIS C 674 Details of bonding type rmsd covalent geometry : bond 0.00580 (15758) covalent geometry : angle 0.61890 (21390) SS BOND : bond 0.00408 ( 8) SS BOND : angle 1.12676 ( 16) hydrogen bonds : bond 0.04523 ( 678) hydrogen bonds : angle 4.84315 ( 1941) link_BETA1-3 : bond 0.00894 ( 1) link_BETA1-3 : angle 4.61133 ( 3) link_BETA1-4 : bond 0.00688 ( 4) link_BETA1-4 : angle 2.56386 ( 12) link_NAG-ASN : bond 0.00368 ( 8) link_NAG-ASN : angle 3.06465 ( 24) *********************** 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 109 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.9279 (ptm) cc_final: 0.9070 (ptm) REVERT: A 350 ASP cc_start: 0.8315 (t0) cc_final: 0.7902 (t0) REVERT: A 398 CYS cc_start: 0.9264 (m) cc_final: 0.8975 (m) REVERT: A 444 MET cc_start: 0.9053 (tmm) cc_final: 0.8195 (tmm) REVERT: B 85 MET cc_start: 0.9016 (tpt) cc_final: 0.8702 (tpp) REVERT: B 150 MET cc_start: 0.8948 (ttm) cc_final: 0.8690 (mpp) REVERT: B 350 ASP cc_start: 0.7937 (t70) cc_final: 0.7258 (t0) REVERT: C 131 MET cc_start: 0.9083 (mmp) cc_final: 0.8706 (mpp) REVERT: C 146 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: C 278 MET cc_start: 0.8472 (ptm) cc_final: 0.7848 (tmm) REVERT: C 374 MET cc_start: 0.9144 (mtm) cc_final: 0.8943 (mtm) REVERT: D 73 ASP cc_start: 0.8177 (t0) cc_final: 0.7487 (t0) REVERT: D 76 LYS cc_start: 0.9621 (mtpp) cc_final: 0.9309 (mtpp) REVERT: D 207 PHE cc_start: 0.6407 (OUTLIER) cc_final: 0.4995 (m-80) REVERT: E 286 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8302 (mmmt) REVERT: E 319 GLU cc_start: 0.8642 (tt0) cc_final: 0.8376 (tt0) outliers start: 18 outliers final: 11 residues processed: 105 average time/residue: 0.1102 time to fit residues: 18.7664 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 : 0.599 ------------------------------------------------------------------------------- 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 162 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 339 VAL 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 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 46 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3379 r_free = 0.3379 target = 0.068555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.044237 restraints weight = 50916.467| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.74 r_work: 0.2616 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2033 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= 0.117 Angle : 0.569 10.273 21445 Z= 0.281 Chirality : 0.043 0.393 2531 Planarity : 0.003 0.043 2669 Dihedral : 8.812 94.088 2401 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.84 % Allowed : 14.48 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.20), residues: 1979 helix: 1.87 (0.20), residues: 715 sheet: -0.68 (0.31), residues: 301 loop : -1.05 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 148 TYR 0.020 0.001 TYR A 31 PHE 0.016 0.001 PHE B 65 TRP 0.011 0.001 TRP B 382 HIS 0.007 0.001 HIS E 489 Details of bonding type rmsd covalent geometry : bond 0.00253 (15758) covalent geometry : angle 0.55431 (21390) SS BOND : bond 0.00320 ( 8) SS BOND : angle 0.87528 ( 16) hydrogen bonds : bond 0.04048 ( 678) hydrogen bonds : angle 4.68544 ( 1941) link_BETA1-3 : bond 0.00798 ( 1) link_BETA1-3 : angle 4.56256 ( 3) link_BETA1-4 : bond 0.00677 ( 4) link_BETA1-4 : angle 2.66440 ( 12) link_NAG-ASN : bond 0.00477 ( 8) link_NAG-ASN : angle 2.89534 ( 24) *********************** 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 105 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 ASP cc_start: 0.8357 (t0) cc_final: 0.7937 (t0) REVERT: A 444 MET cc_start: 0.9059 (tmm) cc_final: 0.8190 (tmm) REVERT: B 85 MET cc_start: 0.9054 (tpt) cc_final: 0.8613 (tpp) REVERT: C 132 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.8885 (p) REVERT: C 146 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: C 278 MET cc_start: 0.8497 (ptm) cc_final: 0.7808 (tmm) REVERT: D 73 ASP cc_start: 0.8165 (t0) cc_final: 0.7470 (t0) REVERT: D 76 LYS cc_start: 0.9651 (mtpp) cc_final: 0.9355 (mtpp) REVERT: D 128 MET cc_start: 0.7953 (tpp) cc_final: 0.7707 (mmt) REVERT: D 207 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.4936 (m-80) REVERT: E 283 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8463 (mm-30) REVERT: E 286 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8306 (mmmt) REVERT: E 319 GLU cc_start: 0.8756 (tt0) cc_final: 0.8492 (tt0) outliers start: 14 outliers final: 9 residues processed: 102 average time/residue: 0.1085 time to fit residues: 17.9160 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 : 0.619 ------------------------------------------------------------------------------- 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 317 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 427 SER 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 93 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.0040 chunk 184 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.069620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.045529 restraints weight = 51028.319| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.73 r_work: 0.2645 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15779 Z= 0.111 Angle : 0.569 10.053 21445 Z= 0.279 Chirality : 0.043 0.383 2531 Planarity : 0.003 0.040 2669 Dihedral : 8.335 93.779 2401 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.72 % Allowed : 14.60 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.20), residues: 1979 helix: 1.99 (0.20), residues: 709 sheet: -0.65 (0.32), residues: 291 loop : -1.09 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 148 TYR 0.019 0.001 TYR A 31 PHE 0.015 0.001 PHE B 65 TRP 0.011 0.001 TRP B 382 HIS 0.007 0.001 HIS E 489 Details of bonding type rmsd covalent geometry : bond 0.00242 (15758) covalent geometry : angle 0.55457 (21390) SS BOND : bond 0.00398 ( 8) SS BOND : angle 0.90947 ( 16) hydrogen bonds : bond 0.03839 ( 678) hydrogen bonds : angle 4.59157 ( 1941) link_BETA1-3 : bond 0.00893 ( 1) link_BETA1-3 : angle 4.61346 ( 3) link_BETA1-4 : bond 0.00622 ( 4) link_BETA1-4 : angle 2.83132 ( 12) link_NAG-ASN : bond 0.00505 ( 8) link_NAG-ASN : angle 2.79031 ( 24) ********************** 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 107 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.9306 (ptm) cc_final: 0.8130 (ppp) REVERT: A 350 ASP cc_start: 0.8395 (t0) cc_final: 0.7977 (t0) REVERT: A 444 MET cc_start: 0.9083 (tmm) cc_final: 0.8267 (tmm) REVERT: B 85 MET cc_start: 0.9177 (tpt) cc_final: 0.8728 (tpp) REVERT: B 150 MET cc_start: 0.8634 (mmt) cc_final: 0.8190 (mmt) REVERT: B 175 MET cc_start: 0.9249 (mtm) cc_final: 0.9029 (mtm) REVERT: C 132 SER cc_start: 0.9128 (OUTLIER) cc_final: 0.8884 (p) REVERT: C 278 MET cc_start: 0.8580 (ptm) cc_final: 0.7964 (tmm) REVERT: D 73 ASP cc_start: 0.8290 (t0) cc_final: 0.7603 (t0) REVERT: D 76 LYS cc_start: 0.9672 (mtpp) cc_final: 0.9392 (mtpp) REVERT: D 207 PHE cc_start: 0.6449 (OUTLIER) cc_final: 0.5174 (m-80) REVERT: E 283 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8529 (mm-30) REVERT: E 319 GLU cc_start: 0.8826 (tt0) cc_final: 0.8532 (tt0) REVERT: E 431 ASN cc_start: 0.8802 (m-40) cc_final: 0.8567 (m-40) outliers start: 12 outliers final: 9 residues processed: 104 average time/residue: 0.1202 time to fit residues: 19.6412 Evaluate side-chains 103 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 317 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 132 SER 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 141 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 160 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 146 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 = 0.3363 r_free = 0.3363 target = 0.067784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.043513 restraints weight = 50929.219| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.71 r_work: 0.2596 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15779 Z= 0.195 Angle : 0.615 10.403 21445 Z= 0.301 Chirality : 0.043 0.384 2531 Planarity : 0.003 0.041 2669 Dihedral : 8.044 92.568 2401 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.72 % Allowed : 14.60 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.20), residues: 1979 helix: 1.90 (0.20), residues: 716 sheet: -0.74 (0.31), residues: 300 loop : -1.03 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 454 TYR 0.020 0.001 TYR A 31 PHE 0.018 0.001 PHE B 87 TRP 0.013 0.001 TRP B 382 HIS 0.002 0.001 HIS C 674 Details of bonding type rmsd covalent geometry : bond 0.00442 (15758) covalent geometry : angle 0.60189 (21390) SS BOND : bond 0.00377 ( 8) SS BOND : angle 0.92039 ( 16) hydrogen bonds : bond 0.04189 ( 678) hydrogen bonds : angle 4.68346 ( 1941) link_BETA1-3 : bond 0.00876 ( 1) link_BETA1-3 : angle 4.57290 ( 3) link_BETA1-4 : bond 0.00732 ( 4) link_BETA1-4 : angle 2.85237 ( 12) link_NAG-ASN : bond 0.00392 ( 8) link_NAG-ASN : angle 2.87210 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3881.91 seconds wall clock time: 67 minutes 28.25 seconds (4048.25 seconds total)