Starting phenix.real_space_refine on Wed Feb 14 18:17:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5z_33629/02_2024/7y5z_33629_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5z_33629/02_2024/7y5z_33629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5z_33629/02_2024/7y5z_33629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5z_33629/02_2024/7y5z_33629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5z_33629/02_2024/7y5z_33629_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5z_33629/02_2024/7y5z_33629_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 39 5.16 5 C 6517 2.51 5 N 1576 2.21 5 O 1829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9962 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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: "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: "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: "J" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.08, per 1000 atoms: 0.61 Number of scatterers: 9962 At special positions: 0 Unit cell: (110.415, 95.26, 132.065, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 1 15.00 O 1829 8.00 N 1576 7.00 C 6517 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM 9783 O5 NAG A 802 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 5 " NAG-ASN " NAG A 801 " - " ASN A 387 " " NAG A 802 " - " ASN A 464 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " ASN A 580 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 4.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 4 sheets defined 49.0% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.508A pdb=" N VAL A 85 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 86 " --> pdb=" O GLN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.615A pdb=" N GLN A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 405 Processing helix chain 'A' and resid 426 through 432 removed outlier: 4.932A pdb=" N LEU A 431 " --> pdb=" O GLN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 482 through 501 removed outlier: 3.524A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 540 through 545 removed outlier: 3.903A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 575 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 666 through 692 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 93 through 109 removed outlier: 3.816A pdb=" N MET B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 180 removed outlier: 3.781A pdb=" N SER B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET B 178 " --> pdb=" O MET B 174 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.798A pdb=" N TYR B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 219 removed outlier: 3.509A pdb=" N LEU B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU B 206 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 213 " --> pdb=" O TRP B 209 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 214 " --> pdb=" O ASN B 210 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 246 removed outlier: 3.617A pdb=" N LEU B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.599A pdb=" N LEU B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.613A pdb=" N TYR B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 406 removed outlier: 3.723A pdb=" N ILE B 395 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 396 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 428 removed outlier: 3.674A pdb=" N PHE B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 443 removed outlier: 3.785A pdb=" N LEU B 441 " --> pdb=" O PHE B 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 31 through 59 removed outlier: 3.635A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 99 removed outlier: 4.028A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 141 removed outlier: 5.712A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 184 removed outlier: 3.707A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 205 removed outlier: 3.688A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N PHE C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 232 Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'D' and resid 8 through 23 removed outlier: 4.143A pdb=" N LYS D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR D 19 " --> pdb=" O CYS D 15 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 36 Processing helix chain 'D' and resid 51 through 80 removed outlier: 3.633A pdb=" N VAL D 57 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 91 No H-bonds generated for 'chain 'D' and resid 88 through 91' Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 removed outlier: 8.584A pdb=" N ALA A 122 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 96 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N SER A 124 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 98 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET A 95 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL A 72 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU A 97 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS A 74 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N GLU A 99 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL A 76 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 73 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 657 " --> pdb=" O PHE A 218 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 248 through 250 Processing sheet with id= C, first strand: chain 'A' and resid 626 through 630 removed outlier: 3.837A pdb=" N VAL A 256 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL A 277 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 362 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA A 279 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU A 364 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N ARG A 281 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER A 437 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLU A 364 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A 439 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE A 412 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N MET A 378 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ARG A 414 " --> pdb=" O MET A 378 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.508A pdb=" N THR A 577 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 603 " --> pdb=" O VAL A 621 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1182 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: 2.87 Time building geometry restraints manager: 4.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1794 1.32 - 1.45: 2727 1.45 - 1.57: 5638 1.57 - 1.70: 4 1.70 - 1.82: 60 Bond restraints: 10223 Sorted by residual: bond pdb=" C1 BMA F 5 " pdb=" O5 BMA F 5 " ideal model delta sigma weight residual 1.410 1.470 -0.060 2.00e-02 2.50e+03 8.96e+00 bond pdb=" N VAL B 374 " pdb=" CA VAL B 374 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.58e+00 bond pdb=" N VAL A 465 " pdb=" CA VAL A 465 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.22e-02 6.72e+03 8.58e+00 bond pdb=" N VAL B 261 " pdb=" CA VAL B 261 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.24e+00 bond pdb=" N ILE B 368 " pdb=" CA ILE B 368 " ideal model delta sigma weight residual 1.463 1.495 -0.032 1.14e-02 7.69e+03 7.98e+00 ... (remaining 10218 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.60: 327 106.60 - 113.47: 5783 113.47 - 120.33: 4005 120.33 - 127.19: 3700 127.19 - 134.05: 138 Bond angle restraints: 13953 Sorted by residual: angle pdb=" C PRO B 248 " pdb=" N GLU B 249 " pdb=" CA GLU B 249 " ideal model delta sigma weight residual 120.79 127.44 -6.65 1.39e+00 5.18e-01 2.29e+01 angle pdb=" N ARG D 16 " pdb=" CA ARG D 16 " pdb=" C ARG D 16 " ideal model delta sigma weight residual 113.43 107.65 5.78 1.26e+00 6.30e-01 2.11e+01 angle pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" C PHE A 210 " ideal model delta sigma weight residual 109.81 119.54 -9.73 2.21e+00 2.05e-01 1.94e+01 angle pdb=" N VAL A 36 " pdb=" CA VAL A 36 " pdb=" C VAL A 36 " ideal model delta sigma weight residual 111.81 108.03 3.78 8.60e-01 1.35e+00 1.93e+01 angle pdb=" N GLU B 249 " pdb=" CA GLU B 249 " pdb=" C GLU B 249 " ideal model delta sigma weight residual 111.02 116.34 -5.32 1.22e+00 6.72e-01 1.90e+01 ... (remaining 13948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.70: 6087 22.70 - 45.41: 210 45.41 - 68.11: 43 68.11 - 90.81: 19 90.81 - 113.52: 22 Dihedral angle restraints: 6381 sinusoidal: 2846 harmonic: 3535 Sorted by residual: dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -173.52 87.52 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -170.14 84.14 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CA LEU C 206 " pdb=" C LEU C 206 " pdb=" N ASN C 207 " pdb=" CA ASN C 207 " ideal model delta harmonic sigma weight residual -180.00 -148.29 -31.71 0 5.00e+00 4.00e-02 4.02e+01 ... (remaining 6378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1417 0.084 - 0.168: 230 0.168 - 0.253: 15 0.253 - 0.337: 5 0.337 - 0.421: 3 Chirality restraints: 1670 Sorted by residual: chirality pdb=" C2 NAG A 804 " pdb=" C1 NAG A 804 " pdb=" C3 NAG A 804 " pdb=" N2 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.49 -2.07 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1667 not shown) Planarity restraints: 1701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 464 " -0.034 2.00e-02 2.50e+03 7.85e-02 7.70e+01 pdb=" CG ASN A 464 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 464 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN A 464 " 0.142 2.00e-02 2.50e+03 pdb=" C1 NAG A 802 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 201 " 0.046 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO B 202 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 202 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 202 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO A 560 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.039 5.00e-02 4.00e+02 ... (remaining 1698 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1316 2.75 - 3.29: 9551 3.29 - 3.82: 16050 3.82 - 4.36: 19069 4.36 - 4.90: 33013 Nonbonded interactions: 78999 Sorted by model distance: nonbonded pdb=" O VAL B 374 " pdb=" N ALA B 377 " model vdw 2.210 2.520 nonbonded pdb=" O LEU B 433 " pdb=" OG SER C 50 " model vdw 2.252 2.440 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.258 2.440 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.295 2.440 nonbonded pdb=" O TRP C 227 " pdb=" OG1 THR C 231 " model vdw 2.303 2.440 ... (remaining 78994 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.490 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: 2.270 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.210 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.008 0.085 10223 Z= 0.542 Angle : 1.031 13.829 13953 Z= 0.554 Chirality : 0.063 0.421 1670 Planarity : 0.007 0.069 1689 Dihedral : 14.621 113.516 4091 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.96 % Allowed : 3.08 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.18), residues: 1202 helix: -2.78 (0.15), residues: 618 sheet: -2.90 (0.40), residues: 132 loop : -3.31 (0.24), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP D 36 HIS 0.016 0.003 HIS C 197 PHE 0.034 0.003 PHE C 132 TYR 0.042 0.003 TYR A 565 ARG 0.009 0.001 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 232 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.7793 (tpp80) cc_final: 0.7573 (mmm-85) REVERT: A 221 MET cc_start: 0.8783 (mmp) cc_final: 0.8547 (mmm) REVERT: A 476 ASP cc_start: 0.8774 (m-30) cc_final: 0.8528 (m-30) REVERT: A 639 GLN cc_start: 0.8282 (pt0) cc_final: 0.7772 (tm-30) REVERT: B 171 TRP cc_start: 0.4600 (t60) cc_final: 0.4173 (t60) REVERT: B 174 MET cc_start: 0.7699 (tmt) cc_final: 0.7155 (tmm) REVERT: B 180 LEU cc_start: 0.8818 (mt) cc_final: 0.8113 (mt) REVERT: B 190 GLU cc_start: 0.7989 (tp30) cc_final: 0.7779 (tp30) REVERT: C 12 VAL cc_start: 0.9367 (t) cc_final: 0.9055 (m) REVERT: C 215 LEU cc_start: 0.8744 (mm) cc_final: 0.8541 (mm) REVERT: D 85 TRP cc_start: 0.8421 (m-10) cc_final: 0.8064 (m100) REVERT: D 90 ASP cc_start: 0.8450 (t70) cc_final: 0.8096 (t0) REVERT: D 96 ILE cc_start: 0.8444 (mt) cc_final: 0.8121 (mt) outliers start: 10 outliers final: 6 residues processed: 239 average time/residue: 0.2194 time to fit residues: 72.8970 Evaluate side-chains 152 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 163 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 331 GLN A 358 ASN A 449 HIS A 540 GLN A 552 GLN A 606 GLN B 210 ASN B 386 ASN C 58 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10223 Z= 0.201 Angle : 0.670 10.909 13953 Z= 0.326 Chirality : 0.045 0.340 1670 Planarity : 0.005 0.047 1689 Dihedral : 13.489 107.522 1979 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.89 % Allowed : 9.44 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.22), residues: 1202 helix: -0.82 (0.19), residues: 626 sheet: -2.39 (0.43), residues: 122 loop : -3.00 (0.24), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 PHE 0.023 0.002 PHE A 302 TYR 0.026 0.002 TYR B 262 ARG 0.003 0.000 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 172 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.7638 (tpp80) cc_final: 0.7395 (mmm-85) REVERT: A 476 ASP cc_start: 0.8744 (m-30) cc_final: 0.8538 (m-30) REVERT: B 171 TRP cc_start: 0.4462 (t60) cc_final: 0.4059 (t60) REVERT: B 174 MET cc_start: 0.7607 (tmt) cc_final: 0.6881 (tmm) REVERT: B 193 LYS cc_start: 0.8874 (mttm) cc_final: 0.8662 (mttt) REVERT: B 229 GLN cc_start: 0.8982 (mt0) cc_final: 0.8573 (mp10) REVERT: B 239 MET cc_start: 0.8375 (mmm) cc_final: 0.8035 (mmm) REVERT: B 424 LEU cc_start: 0.9383 (mt) cc_final: 0.8429 (pp) REVERT: B 435 ARG cc_start: 0.8326 (ttp80) cc_final: 0.7837 (ttp80) REVERT: B 439 ASP cc_start: 0.8453 (m-30) cc_final: 0.8226 (m-30) REVERT: C 136 ASN cc_start: 0.8160 (m-40) cc_final: 0.7904 (m-40) REVERT: C 170 LEU cc_start: 0.9379 (mt) cc_final: 0.9116 (mt) REVERT: C 180 ASP cc_start: 0.8493 (t0) cc_final: 0.8268 (t0) REVERT: C 196 SER cc_start: 0.9029 (m) cc_final: 0.8803 (t) REVERT: D 51 SER cc_start: 0.8629 (m) cc_final: 0.8285 (t) REVERT: D 85 TRP cc_start: 0.8476 (m-10) cc_final: 0.8189 (m100) outliers start: 30 outliers final: 24 residues processed: 189 average time/residue: 0.2282 time to fit residues: 64.5946 Evaluate side-chains 172 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 73 optimal weight: 0.0010 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 0.1980 chunk 107 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 355 GLN B 210 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10223 Z= 0.149 Angle : 0.613 9.742 13953 Z= 0.291 Chirality : 0.044 0.292 1670 Planarity : 0.004 0.041 1689 Dihedral : 11.387 105.668 1973 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.99 % Allowed : 11.56 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.23), residues: 1202 helix: 0.10 (0.21), residues: 629 sheet: -2.17 (0.42), residues: 134 loop : -2.68 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 67 HIS 0.004 0.001 HIS A 553 PHE 0.023 0.001 PHE A 302 TYR 0.015 0.001 TYR D 18 ARG 0.002 0.000 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.8431 (tp30) cc_final: 0.8208 (tp30) REVERT: B 171 TRP cc_start: 0.4447 (t60) cc_final: 0.4038 (t60) REVERT: B 174 MET cc_start: 0.7705 (tmt) cc_final: 0.7093 (tmm) REVERT: B 193 LYS cc_start: 0.8919 (mttm) cc_final: 0.8694 (mttt) REVERT: B 229 GLN cc_start: 0.8859 (mt0) cc_final: 0.8410 (mp10) REVERT: B 239 MET cc_start: 0.8318 (mmm) cc_final: 0.7907 (mmm) REVERT: B 424 LEU cc_start: 0.9361 (mt) cc_final: 0.8401 (pp) REVERT: B 435 ARG cc_start: 0.8355 (ttp80) cc_final: 0.7814 (ttp80) REVERT: B 439 ASP cc_start: 0.8495 (m-30) cc_final: 0.8227 (m-30) REVERT: C 136 ASN cc_start: 0.8149 (m-40) cc_final: 0.7908 (m-40) REVERT: C 180 ASP cc_start: 0.8615 (t0) cc_final: 0.8329 (t0) REVERT: C 196 SER cc_start: 0.9103 (m) cc_final: 0.8897 (t) REVERT: D 85 TRP cc_start: 0.8481 (m-10) cc_final: 0.8134 (m100) outliers start: 31 outliers final: 24 residues processed: 177 average time/residue: 0.1856 time to fit residues: 48.2851 Evaluate side-chains 158 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 385 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10223 Z= 0.386 Angle : 0.726 9.628 13953 Z= 0.346 Chirality : 0.048 0.301 1670 Planarity : 0.004 0.045 1689 Dihedral : 10.795 105.370 1971 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.53 % Allowed : 12.43 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.24), residues: 1202 helix: 0.36 (0.21), residues: 640 sheet: -2.11 (0.42), residues: 134 loop : -2.43 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 36 HIS 0.005 0.001 HIS A 553 PHE 0.026 0.002 PHE A 302 TYR 0.022 0.002 TYR D 18 ARG 0.004 0.001 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 135 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 TRP cc_start: 0.4592 (t60) cc_final: 0.4106 (t60) REVERT: B 174 MET cc_start: 0.7774 (tmt) cc_final: 0.7031 (tmm) REVERT: B 193 LYS cc_start: 0.8937 (mttm) cc_final: 0.8724 (mttt) REVERT: B 239 MET cc_start: 0.8357 (mmm) cc_final: 0.7906 (mmm) REVERT: B 435 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8014 (ttp80) REVERT: B 439 ASP cc_start: 0.8592 (m-30) cc_final: 0.8388 (m-30) REVERT: C 90 TYR cc_start: 0.8941 (t80) cc_final: 0.8494 (t80) REVERT: C 136 ASN cc_start: 0.8359 (m-40) cc_final: 0.7941 (m-40) REVERT: C 180 ASP cc_start: 0.8690 (t0) cc_final: 0.8339 (t0) REVERT: D 85 TRP cc_start: 0.8604 (m-10) cc_final: 0.8175 (m100) outliers start: 47 outliers final: 38 residues processed: 166 average time/residue: 0.1850 time to fit residues: 45.4119 Evaluate side-chains 167 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 129 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10223 Z= 0.239 Angle : 0.646 9.825 13953 Z= 0.305 Chirality : 0.045 0.289 1670 Planarity : 0.004 0.044 1689 Dihedral : 10.272 105.981 1971 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.05 % Allowed : 13.87 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.25), residues: 1202 helix: 0.61 (0.21), residues: 642 sheet: -1.83 (0.44), residues: 134 loop : -2.25 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 67 HIS 0.005 0.001 HIS A 553 PHE 0.023 0.002 PHE A 302 TYR 0.024 0.002 TYR C 119 ARG 0.003 0.000 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 139 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 TRP cc_start: 0.4590 (t60) cc_final: 0.4109 (t60) REVERT: B 174 MET cc_start: 0.7814 (tmt) cc_final: 0.7157 (tmm) REVERT: B 239 MET cc_start: 0.8300 (mmm) cc_final: 0.7896 (mmm) REVERT: B 435 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8012 (ttp80) REVERT: B 439 ASP cc_start: 0.8581 (m-30) cc_final: 0.8380 (m-30) REVERT: C 136 ASN cc_start: 0.8141 (m-40) cc_final: 0.7882 (m-40) REVERT: C 170 LEU cc_start: 0.9381 (mt) cc_final: 0.9135 (mt) REVERT: C 180 ASP cc_start: 0.8717 (t0) cc_final: 0.8317 (t0) REVERT: C 190 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9247 (mp) REVERT: D 85 TRP cc_start: 0.8605 (m-10) cc_final: 0.8173 (m100) outliers start: 42 outliers final: 31 residues processed: 166 average time/residue: 0.1793 time to fit residues: 44.4725 Evaluate side-chains 161 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10223 Z= 0.202 Angle : 0.616 10.190 13953 Z= 0.292 Chirality : 0.045 0.280 1670 Planarity : 0.003 0.042 1689 Dihedral : 9.827 106.602 1969 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.95 % Allowed : 14.45 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1202 helix: 0.82 (0.21), residues: 643 sheet: -1.64 (0.45), residues: 133 loop : -2.08 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 253 HIS 0.004 0.001 HIS A 553 PHE 0.023 0.001 PHE A 302 TYR 0.022 0.001 TYR C 119 ARG 0.002 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9247 (mp) REVERT: A 364 GLU cc_start: 0.8576 (tp30) cc_final: 0.8363 (tp30) REVERT: B 171 TRP cc_start: 0.4597 (t60) cc_final: 0.4111 (t60) REVERT: B 174 MET cc_start: 0.7845 (tmt) cc_final: 0.7184 (tmm) REVERT: B 239 MET cc_start: 0.8288 (mmm) cc_final: 0.7883 (mmm) REVERT: B 250 TRP cc_start: 0.4668 (p90) cc_final: 0.3904 (p-90) REVERT: B 435 ARG cc_start: 0.8361 (ttp80) cc_final: 0.7950 (ttp80) REVERT: C 90 TYR cc_start: 0.8814 (t80) cc_final: 0.8254 (t80) REVERT: C 136 ASN cc_start: 0.8128 (m-40) cc_final: 0.7887 (m-40) REVERT: C 180 ASP cc_start: 0.8726 (t0) cc_final: 0.8261 (t0) REVERT: D 85 TRP cc_start: 0.8603 (m-10) cc_final: 0.8175 (m100) outliers start: 41 outliers final: 37 residues processed: 161 average time/residue: 0.1786 time to fit residues: 43.5786 Evaluate side-chains 168 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 73 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 96 optimal weight: 0.0570 chunk 64 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10223 Z= 0.147 Angle : 0.590 9.610 13953 Z= 0.277 Chirality : 0.043 0.273 1670 Planarity : 0.003 0.041 1689 Dihedral : 9.449 106.756 1969 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.95 % Allowed : 15.22 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.25), residues: 1202 helix: 1.00 (0.21), residues: 641 sheet: -1.53 (0.45), residues: 133 loop : -1.98 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 67 HIS 0.004 0.001 HIS A 553 PHE 0.022 0.001 PHE A 302 TYR 0.021 0.001 TYR C 119 ARG 0.002 0.000 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9239 (mp) REVERT: A 364 GLU cc_start: 0.8486 (tp30) cc_final: 0.8275 (tp30) REVERT: B 174 MET cc_start: 0.7806 (tmt) cc_final: 0.7164 (tmm) REVERT: B 180 LEU cc_start: 0.8659 (mt) cc_final: 0.8333 (mt) REVERT: B 239 MET cc_start: 0.8256 (mmm) cc_final: 0.7949 (mmm) REVERT: B 250 TRP cc_start: 0.4425 (p90) cc_final: 0.3841 (p-90) REVERT: B 435 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7886 (ttp80) REVERT: C 90 TYR cc_start: 0.8762 (t80) cc_final: 0.8191 (t80) REVERT: C 136 ASN cc_start: 0.8059 (m-40) cc_final: 0.7850 (m-40) REVERT: C 180 ASP cc_start: 0.8657 (t0) cc_final: 0.8161 (t0) REVERT: C 240 GLN cc_start: 0.7118 (mt0) cc_final: 0.6174 (tp40) REVERT: D 66 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7495 (m-10) REVERT: D 85 TRP cc_start: 0.8650 (m-10) cc_final: 0.8135 (m100) outliers start: 41 outliers final: 33 residues processed: 160 average time/residue: 0.1765 time to fit residues: 43.3404 Evaluate side-chains 166 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 18 TYR Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 73 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN A 531 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10223 Z= 0.167 Angle : 0.598 9.673 13953 Z= 0.278 Chirality : 0.043 0.271 1670 Planarity : 0.003 0.042 1689 Dihedral : 9.008 107.022 1969 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.56 % Allowed : 15.70 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1202 helix: 1.10 (0.21), residues: 644 sheet: -1.42 (0.46), residues: 133 loop : -1.89 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 67 HIS 0.004 0.001 HIS A 553 PHE 0.023 0.001 PHE A 302 TYR 0.020 0.001 TYR C 119 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9215 (mp) REVERT: A 364 GLU cc_start: 0.8467 (tp30) cc_final: 0.8253 (tp30) REVERT: B 174 MET cc_start: 0.7795 (tmt) cc_final: 0.7205 (tmm) REVERT: B 239 MET cc_start: 0.8258 (mmm) cc_final: 0.8011 (mmm) REVERT: B 250 TRP cc_start: 0.4612 (p90) cc_final: 0.3845 (p-90) REVERT: C 90 TYR cc_start: 0.8639 (t80) cc_final: 0.8213 (t80) REVERT: C 136 ASN cc_start: 0.8070 (m-40) cc_final: 0.7850 (m-40) REVERT: C 180 ASP cc_start: 0.8648 (t0) cc_final: 0.8176 (t0) REVERT: D 85 TRP cc_start: 0.8662 (m-10) cc_final: 0.8185 (m100) outliers start: 37 outliers final: 36 residues processed: 154 average time/residue: 0.1718 time to fit residues: 40.4489 Evaluate side-chains 165 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 128 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 18 TYR Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 73 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN C 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 10223 Z= 0.389 Angle : 0.734 12.307 13953 Z= 0.346 Chirality : 0.048 0.278 1670 Planarity : 0.004 0.046 1689 Dihedral : 9.230 108.019 1969 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.24 % Allowed : 15.32 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 1202 helix: 0.92 (0.21), residues: 645 sheet: -1.51 (0.46), residues: 134 loop : -1.95 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 36 HIS 0.006 0.001 HIS A 553 PHE 0.027 0.002 PHE C 41 TYR 0.027 0.002 TYR D 18 ARG 0.010 0.001 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 124 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9237 (mp) REVERT: B 171 TRP cc_start: 0.4678 (t60) cc_final: 0.4169 (t60) REVERT: B 174 MET cc_start: 0.7820 (tmt) cc_final: 0.7211 (tmm) REVERT: B 216 MET cc_start: 0.7424 (tpp) cc_final: 0.7101 (tpp) REVERT: B 250 TRP cc_start: 0.4488 (p90) cc_final: 0.3887 (p-90) REVERT: C 90 TYR cc_start: 0.8905 (t80) cc_final: 0.8327 (t80) REVERT: C 136 ASN cc_start: 0.8201 (m-40) cc_final: 0.7954 (m-40) REVERT: C 180 ASP cc_start: 0.8626 (t0) cc_final: 0.8181 (t0) REVERT: C 224 MET cc_start: 0.8837 (tpp) cc_final: 0.8302 (mmp) outliers start: 44 outliers final: 41 residues processed: 153 average time/residue: 0.1782 time to fit residues: 41.3640 Evaluate side-chains 161 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 119 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 18 TYR Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 73 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10223 Z= 0.206 Angle : 0.646 12.677 13953 Z= 0.300 Chirality : 0.044 0.262 1670 Planarity : 0.003 0.044 1689 Dihedral : 8.977 107.947 1969 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.66 % Allowed : 16.28 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1202 helix: 1.01 (0.21), residues: 647 sheet: -1.39 (0.46), residues: 133 loop : -1.85 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 85 HIS 0.005 0.001 HIS A 553 PHE 0.022 0.001 PHE A 302 TYR 0.020 0.001 TYR C 119 ARG 0.010 0.000 ARG D 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 128 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9246 (mp) REVERT: B 171 TRP cc_start: 0.4656 (t60) cc_final: 0.4156 (t60) REVERT: B 174 MET cc_start: 0.7873 (tmt) cc_final: 0.7258 (tmm) REVERT: B 250 TRP cc_start: 0.4516 (p90) cc_final: 0.3899 (p-90) REVERT: C 90 TYR cc_start: 0.8768 (t80) cc_final: 0.8239 (t80) REVERT: C 136 ASN cc_start: 0.8103 (m-40) cc_final: 0.7896 (m-40) REVERT: C 180 ASP cc_start: 0.8644 (t0) cc_final: 0.8200 (t0) REVERT: C 224 MET cc_start: 0.8855 (tpp) cc_final: 0.8280 (mmp) REVERT: D 66 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7439 (m-10) REVERT: D 85 TRP cc_start: 0.7740 (m-10) cc_final: 0.6975 (m100) outliers start: 38 outliers final: 35 residues processed: 152 average time/residue: 0.1794 time to fit residues: 41.1097 Evaluate side-chains 161 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 18 TYR Chi-restraints excluded: chain D residue 19 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 73 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.0570 chunk 83 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.098062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076796 restraints weight = 23043.108| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.82 r_work: 0.2948 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10223 Z= 0.205 Angle : 0.644 12.992 13953 Z= 0.298 Chirality : 0.044 0.260 1670 Planarity : 0.003 0.043 1689 Dihedral : 8.787 108.249 1969 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.47 % Allowed : 16.86 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1202 helix: 1.08 (0.21), residues: 646 sheet: -1.34 (0.46), residues: 133 loop : -1.82 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 67 HIS 0.005 0.001 HIS A 553 PHE 0.023 0.001 PHE A 302 TYR 0.021 0.001 TYR C 119 ARG 0.003 0.000 ARG D 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1976.09 seconds wall clock time: 36 minutes 49.88 seconds (2209.88 seconds total)