Starting phenix.real_space_refine on Sat Aug 23 18:31:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tan_41138/08_2025/8tan_41138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tan_41138/08_2025/8tan_41138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tan_41138/08_2025/8tan_41138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tan_41138/08_2025/8tan_41138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tan_41138/08_2025/8tan_41138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tan_41138/08_2025/8tan_41138.map" } resolution = 3.05 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 8738 2.51 5 N 2360 2.21 5 O 2653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13853 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6674 Classifications: {'peptide': 831} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 783} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 6530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6530 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 765} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 400 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain breaks: 1 Chain: "D" 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: "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: 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" 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: 3.33, per 1000 atoms: 0.24 Number of scatterers: 13853 At special positions: 0 Unit cell: (91.16, 120.84, 172.78, 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 102 16.00 O 2653 8.00 N 2360 7.00 C 8738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.02 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 458 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.02 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.04 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 298 " distance=2.04 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 458 " distance=2.04 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 849 " distance=2.03 Simple disulfide: pdb=" SG CYS B 776 " - pdb=" SG CYS B 785 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 47 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 62 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 53 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1001 " - " ASN A 592 " " NAG A1002 " - " ASN A 610 " " NAG A1003 " - " ASN A 577 " " NAG A1004 " - " ASN A 504 " " NAG A1005 " - " ASN A 21 " " NAG A1006 " - " ASN A 408 " " NAG A1007 " - " ASN A 387 " " NAG B1001 " - " ASN B 504 " " NAG B1002 " - " ASN B 610 " " NAG B1003 " - " ASN B 21 " " NAG B1004 " - " ASN B 214 " " NAG D 1 " - " ASN A 105 " " NAG E 1 " - " ASN B 105 " " NAG F 1 " - " ASN B 592 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 442.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3186 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 34 sheets defined 16.4% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.530A pdb=" N LYS A 17 " --> pdb=" O GLN A 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 18 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 20 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.756A pdb=" N ILE A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.635A pdb=" N CYS A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.299A pdb=" N MET A 319 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 349 removed outlier: 3.988A pdb=" N ASN A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.628A pdb=" N ASN A 448 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.719A pdb=" N LEU A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 703 Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'B' and resid 12 through 17 removed outlier: 3.699A pdb=" N LYS B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.590A pdb=" N TYR B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 4.073A pdb=" N LEU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 130 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 144 through 148 removed outlier: 4.197A pdb=" N GLU B 147 " --> pdb=" O PRO B 144 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS B 148 " --> pdb=" O PRO B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 148' Processing helix chain 'B' and resid 152 through 157 removed outlier: 4.080A pdb=" N GLU B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 190 Processing helix chain 'B' and resid 248 through 253 removed outlier: 4.238A pdb=" N CYS B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 319 Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 368 through 372 removed outlier: 4.349A pdb=" N PHE B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 437 removed outlier: 3.564A pdb=" N ILE B 429 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 441 Processing helix chain 'B' and resid 625 through 630 removed outlier: 3.631A pdb=" N ARG B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 699 removed outlier: 3.802A pdb=" N PHE B 694 " --> pdb=" O TYR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 852 through 859 removed outlier: 3.554A pdb=" N LYS B 857 " --> pdb=" O GLN B 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.500A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 57 through 62 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 9 removed outlier: 6.360A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 31 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE A 90 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 57 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ARG A 112 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLU A 114 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 167 removed outlier: 3.893A pdb=" N THR A 165 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN A 172 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 205 through 209 removed outlier: 3.634A pdb=" N ALA A 220 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N SER A 208 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N CYS A 218 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA7, first strand: chain 'A' and resid 245 through 247 removed outlier: 6.720A pdb=" N ARG A 240 " --> pdb=" O CYS A 273 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 281 through 283 Processing sheet with id=AA9, first strand: chain 'A' and resid 308 through 311 removed outlier: 6.254A pdb=" N LEU A 330 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ARG A 361 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE A 332 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N TYR A 417 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR A 391 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA A 419 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU A 393 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AB2, first strand: chain 'A' and resid 465 through 470 removed outlier: 3.573A pdb=" N SER A 467 " --> pdb=" O THR A 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 520 through 524 removed outlier: 3.721A pdb=" N SER A 492 " --> pdb=" O VAL A 554 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AB5, first strand: chain 'A' and resid 747 through 752 removed outlier: 3.581A pdb=" N TYR A 613 " --> pdb=" O CYS A 776 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 809 through 812 Processing sheet with id=AB7, first strand: chain 'A' and resid 846 through 851 Processing sheet with id=AB8, first strand: chain 'A' and resid 846 through 851 Processing sheet with id=AB9, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AC1, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.177A pdb=" N LEU B 29 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE B 58 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 31 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N PHE B 90 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU B 57 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ARG B 112 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLU B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE B 90 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 163 through 167 removed outlier: 4.796A pdb=" N GLU B 163 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AC4, first strand: chain 'B' and resid 245 through 247 removed outlier: 6.807A pdb=" N ARG B 240 " --> pdb=" O CYS B 273 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 281 through 283 Processing sheet with id=AC6, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AC7, first strand: chain 'B' and resid 308 through 311 removed outlier: 6.595A pdb=" N LYS B 309 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU B 330 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ARG B 361 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE B 332 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR B 388 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR B 417 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE B 390 " --> pdb=" O TYR B 417 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA B 419 " --> pdb=" O PHE B 390 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 392 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AC9, first strand: chain 'B' and resid 465 through 470 removed outlier: 3.681A pdb=" N SER B 467 " --> pdb=" O THR B 478 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 520 through 525 Processing sheet with id=AD2, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AD3, first strand: chain 'B' and resid 747 through 752 removed outlier: 3.982A pdb=" N TYR B 613 " --> pdb=" O CYS B 776 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 773 " --> pdb=" O ASN B 789 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD5, first strand: chain 'B' and resid 809 through 813 removed outlier: 3.579A pdb=" N SER B 817 " --> pdb=" O ARG B 813 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 846 through 851 Processing sheet with id=AD7, first strand: chain 'B' and resid 869 through 870 360 hydrogen bonds defined for protein. 894 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: 2.48 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4514 1.35 - 1.47: 3417 1.47 - 1.59: 6112 1.59 - 1.71: 0 1.71 - 1.84: 128 Bond restraints: 14171 Sorted by residual: bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.589 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.39e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.14e+00 ... (remaining 14166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 18331 1.71 - 3.42: 784 3.42 - 5.13: 81 5.13 - 6.84: 10 6.84 - 8.55: 5 Bond angle restraints: 19211 Sorted by residual: angle pdb=" N GLU C 21 " pdb=" CA GLU C 21 " pdb=" C GLU C 21 " ideal model delta sigma weight residual 114.75 109.91 4.84 1.26e+00 6.30e-01 1.48e+01 angle pdb=" N ILE A 340 " pdb=" CA ILE A 340 " pdb=" C ILE A 340 " ideal model delta sigma weight residual 110.42 114.02 -3.60 9.40e-01 1.13e+00 1.47e+01 angle pdb=" C PHE A 241 " pdb=" N GLU A 242 " pdb=" CA GLU A 242 " ideal model delta sigma weight residual 122.08 127.16 -5.08 1.47e+00 4.63e-01 1.19e+01 angle pdb=" C HIS A 223 " pdb=" N TYR A 224 " pdb=" CA TYR A 224 " ideal model delta sigma weight residual 122.59 117.59 5.00 1.57e+00 4.06e-01 1.02e+01 angle pdb=" CA TRP B 402 " pdb=" CB TRP B 402 " pdb=" CG TRP B 402 " ideal model delta sigma weight residual 113.60 119.64 -6.04 1.90e+00 2.77e-01 1.01e+01 ... (remaining 19206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 8327 21.26 - 42.52: 443 42.52 - 63.78: 78 63.78 - 85.04: 25 85.04 - 106.30: 6 Dihedral angle restraints: 8879 sinusoidal: 3916 harmonic: 4963 Sorted by residual: dihedral pdb=" CB CYS A 633 " pdb=" SG CYS A 633 " pdb=" SG CYS A 849 " pdb=" CB CYS A 849 " ideal model delta sinusoidal sigma weight residual -86.00 -148.89 62.89 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CB CYS A 205 " pdb=" SG CYS A 205 " pdb=" SG CYS A 218 " pdb=" CB CYS A 218 " ideal model delta sinusoidal sigma weight residual -86.00 -144.08 58.08 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CB CYS B 425 " pdb=" SG CYS B 425 " pdb=" SG CYS B 458 " pdb=" CB CYS B 458 " ideal model delta sinusoidal sigma weight residual 93.00 143.95 -50.95 1 1.00e+01 1.00e-02 3.55e+01 ... (remaining 8876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1813 0.074 - 0.148: 286 0.148 - 0.223: 13 0.223 - 0.297: 3 0.297 - 0.371: 3 Chirality restraints: 2118 Sorted by residual: chirality pdb=" C1 NAG A1004 " pdb=" ND2 ASN A 504 " pdb=" C2 NAG A1004 " pdb=" O5 NAG A1004 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" C1 NAG A1006 " pdb=" ND2 ASN A 408 " pdb=" C2 NAG A1006 " pdb=" O5 NAG A1006 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C1 NAG B1004 " pdb=" ND2 ASN B 214 " pdb=" C2 NAG B1004 " pdb=" O5 NAG B1004 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 2115 not shown) Planarity restraints: 2489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 638 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A 639 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 639 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 639 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 580 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A 581 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 581 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 581 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 484 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B 485 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.026 5.00e-02 4.00e+02 ... (remaining 2486 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 831 2.73 - 3.28: 13970 3.28 - 3.82: 22585 3.82 - 4.36: 29072 4.36 - 4.90: 47349 Nonbonded interactions: 113807 Sorted by model distance: nonbonded pdb=" O MET A 432 " pdb=" OG1 THR A 436 " model vdw 2.194 3.040 nonbonded pdb=" O PRO A 584 " pdb=" ND2 ASN A 789 " model vdw 2.202 3.120 nonbonded pdb=" OE2 GLU B 26 " pdb=" NE ARG B 245 " model vdw 2.254 3.120 nonbonded pdb=" O ASP B 215 " pdb=" OG1 THR B 216 " model vdw 2.294 3.040 nonbonded pdb=" O SER A 313 " pdb=" OG SER A 316 " model vdw 2.321 3.040 ... (remaining 113802 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 1 through 256 or resid 264 through 294 or resid 297 throug \ h 555 or resid 564 through 642 or resid 677 through 1004)) selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.830 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14226 Z= 0.194 Angle : 0.809 12.117 19339 Z= 0.437 Chirality : 0.052 0.371 2118 Planarity : 0.005 0.053 2475 Dihedral : 13.803 106.299 5582 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.19 % Allowed : 7.02 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.74 (0.20), residues: 1674 helix: -2.20 (0.33), residues: 183 sheet: -0.74 (0.27), residues: 350 loop : -1.13 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 112 TYR 0.018 0.002 TYR A 224 PHE 0.013 0.002 PHE B 790 TRP 0.019 0.002 TRP B 402 HIS 0.009 0.001 HIS B 699 Details of bonding type rmsd covalent geometry : bond 0.00368 (14171) covalent geometry : angle 0.77166 (19211) SS BOND : bond 0.00399 ( 37) SS BOND : angle 1.17403 ( 74) hydrogen bonds : bond 0.10349 ( 346) hydrogen bonds : angle 7.78293 ( 894) link_BETA1-4 : bond 0.02367 ( 4) link_BETA1-4 : angle 6.18307 ( 12) link_NAG-ASN : bond 0.00724 ( 14) link_NAG-ASN : angle 3.94204 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 434 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8386 (p0) REVERT: A 494 THR cc_start: 0.8827 (p) cc_final: 0.8609 (p) REVERT: A 617 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6849 (ttm-80) REVERT: A 642 LYS cc_start: 0.8972 (mttt) cc_final: 0.8696 (mmtt) REVERT: A 643 TYR cc_start: 0.7974 (p90) cc_final: 0.7352 (p90) REVERT: A 754 ASN cc_start: 0.7959 (m-40) cc_final: 0.7643 (p0) REVERT: A 820 LEU cc_start: 0.9264 (mt) cc_final: 0.8864 (mm) REVERT: A 822 TRP cc_start: 0.7541 (p90) cc_final: 0.7061 (p90) REVERT: A 848 GLU cc_start: 0.7887 (tp30) cc_final: 0.7683 (tp30) REVERT: A 850 VAL cc_start: 0.8481 (t) cc_final: 0.8218 (t) REVERT: A 893 TYR cc_start: 0.8067 (p90) cc_final: 0.7612 (p90) REVERT: B 83 TYR cc_start: 0.8573 (t80) cc_final: 0.8065 (t80) REVERT: B 92 MET cc_start: 0.8925 (mmm) cc_final: 0.8691 (mmm) REVERT: B 156 MET cc_start: 0.7631 (mmm) cc_final: 0.7151 (mtt) REVERT: B 174 ARG cc_start: 0.6762 (ptt90) cc_final: 0.5571 (ptt90) REVERT: B 214 ASN cc_start: 0.3796 (OUTLIER) cc_final: 0.3493 (t160) REVERT: B 350 LEU cc_start: 0.8641 (mt) cc_final: 0.8318 (mm) REVERT: B 352 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7329 (mm-30) REVERT: B 374 ASN cc_start: 0.8653 (m-40) cc_final: 0.8449 (m110) REVERT: B 388 TYR cc_start: 0.6573 (m-80) cc_final: 0.5874 (m-80) REVERT: B 415 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7727 (ptmt) REVERT: B 416 MET cc_start: 0.8437 (mtm) cc_final: 0.8014 (mtt) REVERT: B 477 ILE cc_start: 0.9394 (mt) cc_final: 0.9121 (mp) REVERT: B 572 LEU cc_start: 0.8670 (tp) cc_final: 0.8210 (tt) REVERT: B 612 SER cc_start: 0.8713 (m) cc_final: 0.8162 (p) REVERT: B 686 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8172 (mt-10) REVERT: B 770 ARG cc_start: 0.8429 (ttp80) cc_final: 0.8147 (ttt90) REVERT: B 772 ASP cc_start: 0.8459 (m-30) cc_final: 0.8214 (m-30) REVERT: B 824 GLU cc_start: 0.8318 (tt0) cc_final: 0.8030 (tp30) REVERT: B 835 TYR cc_start: 0.8256 (m-80) cc_final: 0.7856 (m-80) REVERT: B 837 ILE cc_start: 0.8937 (mt) cc_final: 0.8699 (mt) outliers start: 33 outliers final: 12 residues processed: 457 average time/residue: 0.1114 time to fit residues: 71.2899 Evaluate side-chains 258 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 243 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 699 HIS Chi-restraints excluded: chain B residue 776 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.0030 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 511 GLN A 876 GLN B 399 GLN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 HIS B 696 ASN B 699 HIS ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.127103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.102028 restraints weight = 30550.833| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.70 r_work: 0.3608 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 14226 Z= 0.181 Angle : 0.788 10.496 19339 Z= 0.406 Chirality : 0.052 0.270 2118 Planarity : 0.005 0.049 2475 Dihedral : 9.857 69.860 2283 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.51 % Allowed : 12.58 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.61 (0.20), residues: 1674 helix: -1.78 (0.34), residues: 186 sheet: -0.64 (0.28), residues: 332 loop : -1.10 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 104 TYR 0.026 0.002 TYR A 628 PHE 0.017 0.002 PHE B 90 TRP 0.011 0.001 TRP A 618 HIS 0.011 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00407 (14171) covalent geometry : angle 0.75243 (19211) SS BOND : bond 0.00564 ( 37) SS BOND : angle 2.10092 ( 74) hydrogen bonds : bond 0.04356 ( 346) hydrogen bonds : angle 6.95163 ( 894) link_BETA1-4 : bond 0.01891 ( 4) link_BETA1-4 : angle 4.86283 ( 12) link_NAG-ASN : bond 0.00513 ( 14) link_NAG-ASN : angle 3.47784 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 257 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8742 (m-40) cc_final: 0.8344 (t0) REVERT: A 373 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8465 (mtmm) REVERT: A 429 ILE cc_start: 0.7880 (pt) cc_final: 0.7661 (mt) REVERT: A 477 ILE cc_start: 0.9004 (tt) cc_final: 0.8714 (mm) REVERT: A 494 THR cc_start: 0.8845 (p) cc_final: 0.8596 (p) REVERT: A 558 MET cc_start: 0.7574 (ttm) cc_final: 0.7271 (ttm) REVERT: A 586 ASP cc_start: 0.8665 (p0) cc_final: 0.8109 (p0) REVERT: A 602 ASN cc_start: 0.8978 (m-40) cc_final: 0.8720 (m-40) REVERT: A 617 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7262 (ttm170) REVERT: A 642 LYS cc_start: 0.8903 (mttt) cc_final: 0.8691 (mmtt) REVERT: A 643 TYR cc_start: 0.8075 (p90) cc_final: 0.7565 (p90) REVERT: A 704 VAL cc_start: 0.8778 (m) cc_final: 0.8480 (p) REVERT: A 754 ASN cc_start: 0.8117 (m-40) cc_final: 0.7772 (p0) REVERT: A 820 LEU cc_start: 0.9292 (mt) cc_final: 0.9037 (mm) REVERT: A 822 TRP cc_start: 0.7855 (p90) cc_final: 0.7276 (p90) REVERT: A 848 GLU cc_start: 0.7842 (tp30) cc_final: 0.7527 (tp30) REVERT: A 850 VAL cc_start: 0.8602 (t) cc_final: 0.8391 (t) REVERT: B 79 TRP cc_start: 0.7917 (t60) cc_final: 0.7589 (t60) REVERT: B 83 TYR cc_start: 0.8447 (t80) cc_final: 0.8172 (t80) REVERT: B 156 MET cc_start: 0.7560 (mmm) cc_final: 0.7119 (mmm) REVERT: B 388 TYR cc_start: 0.6531 (m-80) cc_final: 0.6315 (m-80) REVERT: B 415 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7963 (ptmt) REVERT: B 416 MET cc_start: 0.8797 (mtm) cc_final: 0.8345 (mtt) REVERT: B 476 ILE cc_start: 0.9048 (mt) cc_final: 0.8770 (mt) REVERT: B 572 LEU cc_start: 0.8643 (tp) cc_final: 0.8364 (tt) REVERT: B 686 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8407 (mt-10) REVERT: B 772 ASP cc_start: 0.8256 (m-30) cc_final: 0.7998 (m-30) REVERT: B 824 GLU cc_start: 0.8311 (tt0) cc_final: 0.8051 (tp30) REVERT: B 835 TYR cc_start: 0.8329 (m-80) cc_final: 0.7626 (m-80) REVERT: B 857 LYS cc_start: 0.9365 (tttt) cc_final: 0.9072 (ttmm) outliers start: 53 outliers final: 23 residues processed: 288 average time/residue: 0.1047 time to fit residues: 43.3754 Evaluate side-chains 235 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 699 HIS Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 68 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 HIS ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN B 846 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.126766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.101805 restraints weight = 30913.954| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.69 r_work: 0.3615 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14226 Z= 0.148 Angle : 0.711 10.857 19339 Z= 0.364 Chirality : 0.049 0.277 2118 Planarity : 0.004 0.048 2475 Dihedral : 8.886 58.723 2268 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.87 % Favored : 93.07 % Rotamer: Outliers : 3.25 % Allowed : 15.23 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.54 (0.20), residues: 1674 helix: -1.53 (0.36), residues: 182 sheet: -0.62 (0.27), residues: 336 loop : -1.08 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 192 TYR 0.017 0.002 TYR A 391 PHE 0.015 0.001 PHE C 61 TRP 0.011 0.001 TRP A 618 HIS 0.009 0.001 HIS B 699 Details of bonding type rmsd covalent geometry : bond 0.00325 (14171) covalent geometry : angle 0.67860 (19211) SS BOND : bond 0.00445 ( 37) SS BOND : angle 1.49035 ( 74) hydrogen bonds : bond 0.04017 ( 346) hydrogen bonds : angle 6.67062 ( 894) link_BETA1-4 : bond 0.02053 ( 4) link_BETA1-4 : angle 4.69898 ( 12) link_NAG-ASN : bond 0.00580 ( 14) link_NAG-ASN : angle 3.43483 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 222 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8003 (ttp) REVERT: A 373 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8280 (mtmm) REVERT: A 461 ASP cc_start: 0.8108 (m-30) cc_final: 0.6559 (m-30) REVERT: A 494 THR cc_start: 0.8827 (p) cc_final: 0.8609 (p) REVERT: A 565 ARG cc_start: 0.8190 (mmm160) cc_final: 0.7632 (mmm160) REVERT: A 586 ASP cc_start: 0.8702 (p0) cc_final: 0.8172 (p0) REVERT: A 602 ASN cc_start: 0.8954 (m-40) cc_final: 0.8695 (m-40) REVERT: A 617 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7275 (ttm170) REVERT: A 642 LYS cc_start: 0.8925 (mttt) cc_final: 0.8724 (mmtt) REVERT: A 643 TYR cc_start: 0.8045 (p90) cc_final: 0.7538 (p90) REVERT: A 704 VAL cc_start: 0.8788 (m) cc_final: 0.8533 (p) REVERT: A 754 ASN cc_start: 0.8170 (m-40) cc_final: 0.7766 (p0) REVERT: A 820 LEU cc_start: 0.9291 (mt) cc_final: 0.9055 (mm) REVERT: A 833 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8421 (pt) REVERT: A 848 GLU cc_start: 0.7977 (tp30) cc_final: 0.7669 (tp30) REVERT: B 79 TRP cc_start: 0.7978 (t60) cc_final: 0.7563 (t60) REVERT: B 83 TYR cc_start: 0.8400 (t80) cc_final: 0.8160 (t80) REVERT: B 156 MET cc_start: 0.7560 (mmm) cc_final: 0.7011 (mtt) REVERT: B 270 ASP cc_start: 0.7836 (t0) cc_final: 0.7571 (t0) REVERT: B 309 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8223 (tttm) REVERT: B 388 TYR cc_start: 0.6469 (m-80) cc_final: 0.5991 (m-80) REVERT: B 415 LYS cc_start: 0.8229 (ttmt) cc_final: 0.7900 (ptmt) REVERT: B 416 MET cc_start: 0.8657 (mtm) cc_final: 0.8045 (mtt) REVERT: B 477 ILE cc_start: 0.9367 (mt) cc_final: 0.9158 (mp) REVERT: B 572 LEU cc_start: 0.8739 (tp) cc_final: 0.8385 (tt) REVERT: B 686 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8413 (mt-10) REVERT: B 835 TYR cc_start: 0.8356 (m-80) cc_final: 0.7808 (m-80) REVERT: B 855 TYR cc_start: 0.7950 (t80) cc_final: 0.7307 (t80) REVERT: B 857 LYS cc_start: 0.9372 (tttt) cc_final: 0.9112 (ttmm) REVERT: C 13 ASP cc_start: 0.8621 (m-30) cc_final: 0.8399 (m-30) REVERT: C 21 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8017 (mm-30) outliers start: 49 outliers final: 29 residues processed: 256 average time/residue: 0.1205 time to fit residues: 44.8177 Evaluate side-chains 232 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 12 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 47 optimal weight: 0.0870 chunk 154 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.3560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 HIS ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.128350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.103470 restraints weight = 30892.080| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.63 r_work: 0.3598 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14226 Z= 0.152 Angle : 0.707 10.958 19339 Z= 0.360 Chirality : 0.049 0.272 2118 Planarity : 0.004 0.044 2475 Dihedral : 8.292 59.544 2264 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.11 % Favored : 92.83 % Rotamer: Outliers : 3.38 % Allowed : 15.89 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.43 (0.20), residues: 1674 helix: -1.41 (0.36), residues: 176 sheet: -0.50 (0.28), residues: 327 loop : -1.03 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 847 TYR 0.018 0.002 TYR C 25 PHE 0.014 0.001 PHE C 61 TRP 0.021 0.001 TRP A 822 HIS 0.008 0.001 HIS B 699 Details of bonding type rmsd covalent geometry : bond 0.00337 (14171) covalent geometry : angle 0.67678 (19211) SS BOND : bond 0.00340 ( 37) SS BOND : angle 1.27436 ( 74) hydrogen bonds : bond 0.03780 ( 346) hydrogen bonds : angle 6.54652 ( 894) link_BETA1-4 : bond 0.01965 ( 4) link_BETA1-4 : angle 4.66778 ( 12) link_NAG-ASN : bond 0.00677 ( 14) link_NAG-ASN : angle 3.39586 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7964 (ttp) REVERT: A 373 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8352 (mtmm) REVERT: A 461 ASP cc_start: 0.8040 (m-30) cc_final: 0.7714 (m-30) REVERT: A 494 THR cc_start: 0.8835 (p) cc_final: 0.8626 (p) REVERT: A 586 ASP cc_start: 0.8714 (p0) cc_final: 0.8222 (p0) REVERT: A 602 ASN cc_start: 0.8906 (m-40) cc_final: 0.8672 (m-40) REVERT: A 617 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7416 (ttm170) REVERT: A 643 TYR cc_start: 0.8039 (p90) cc_final: 0.7540 (p90) REVERT: A 704 VAL cc_start: 0.8805 (m) cc_final: 0.8526 (p) REVERT: A 833 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8487 (pt) REVERT: A 848 GLU cc_start: 0.8039 (tp30) cc_final: 0.7690 (tp30) REVERT: B 83 TYR cc_start: 0.8375 (t80) cc_final: 0.8139 (t80) REVERT: B 156 MET cc_start: 0.7530 (mmm) cc_final: 0.7093 (mmp) REVERT: B 270 ASP cc_start: 0.7819 (t0) cc_final: 0.7528 (t0) REVERT: B 388 TYR cc_start: 0.6562 (m-80) cc_final: 0.6047 (m-80) REVERT: B 415 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7937 (ptmt) REVERT: B 416 MET cc_start: 0.8664 (mtm) cc_final: 0.8146 (mtp) REVERT: B 686 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8399 (mt-10) REVERT: B 789 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8216 (t0) REVERT: B 857 LYS cc_start: 0.9347 (tttt) cc_final: 0.9110 (ttmm) REVERT: B 885 SER cc_start: 0.9142 (t) cc_final: 0.8896 (p) REVERT: C 21 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8047 (mm-30) outliers start: 51 outliers final: 31 residues processed: 243 average time/residue: 0.1306 time to fit residues: 46.1852 Evaluate side-chains 224 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 789 ASN Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 144 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.126155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.100806 restraints weight = 30971.564| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.66 r_work: 0.3571 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14226 Z= 0.189 Angle : 0.705 10.929 19339 Z= 0.357 Chirality : 0.049 0.264 2118 Planarity : 0.004 0.041 2475 Dihedral : 8.054 59.876 2264 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.53 % Favored : 92.41 % Rotamer: Outliers : 3.71 % Allowed : 16.56 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.38 (0.20), residues: 1674 helix: -1.26 (0.37), residues: 177 sheet: -0.43 (0.29), residues: 321 loop : -1.03 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 376 TYR 0.022 0.002 TYR C 25 PHE 0.021 0.002 PHE C 61 TRP 0.014 0.002 TRP A 618 HIS 0.009 0.001 HIS B 699 Details of bonding type rmsd covalent geometry : bond 0.00423 (14171) covalent geometry : angle 0.67449 (19211) SS BOND : bond 0.00536 ( 37) SS BOND : angle 1.36388 ( 74) hydrogen bonds : bond 0.03597 ( 346) hydrogen bonds : angle 6.45475 ( 894) link_BETA1-4 : bond 0.01806 ( 4) link_BETA1-4 : angle 4.63967 ( 12) link_NAG-ASN : bond 0.00639 ( 14) link_NAG-ASN : angle 3.39427 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ARG cc_start: 0.8157 (mtm110) cc_final: 0.7574 (mtp-110) REVERT: A 319 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8217 (ttp) REVERT: A 373 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8353 (mtmm) REVERT: A 412 LYS cc_start: 0.8568 (tmtt) cc_final: 0.8338 (tptp) REVERT: A 461 ASP cc_start: 0.8169 (m-30) cc_final: 0.7789 (m-30) REVERT: A 494 THR cc_start: 0.8877 (p) cc_final: 0.8649 (p) REVERT: A 586 ASP cc_start: 0.8792 (p0) cc_final: 0.8380 (p0) REVERT: A 602 ASN cc_start: 0.9008 (m-40) cc_final: 0.8732 (m-40) REVERT: A 643 TYR cc_start: 0.8098 (p90) cc_final: 0.7650 (p90) REVERT: A 704 VAL cc_start: 0.8844 (m) cc_final: 0.8552 (p) REVERT: A 754 ASN cc_start: 0.8259 (m-40) cc_final: 0.7852 (p0) REVERT: A 848 GLU cc_start: 0.8276 (tp30) cc_final: 0.7673 (tp30) REVERT: A 857 LYS cc_start: 0.8897 (mttp) cc_final: 0.8694 (mttp) REVERT: B 83 TYR cc_start: 0.8447 (t80) cc_final: 0.8150 (t80) REVERT: B 156 MET cc_start: 0.7551 (mmm) cc_final: 0.7100 (mmm) REVERT: B 270 ASP cc_start: 0.7933 (t0) cc_final: 0.7582 (t0) REVERT: B 374 ASN cc_start: 0.8875 (m110) cc_final: 0.8221 (t0) REVERT: B 388 TYR cc_start: 0.6787 (m-80) cc_final: 0.6216 (m-80) REVERT: B 415 LYS cc_start: 0.8233 (ttmt) cc_final: 0.8031 (ttpt) REVERT: B 835 TYR cc_start: 0.8226 (m-80) cc_final: 0.7683 (m-80) REVERT: B 857 LYS cc_start: 0.9375 (tttt) cc_final: 0.9143 (ttmm) outliers start: 56 outliers final: 34 residues processed: 245 average time/residue: 0.1180 time to fit residues: 42.1980 Evaluate side-chains 224 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 64 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 36 optimal weight: 0.0570 chunk 73 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 92 optimal weight: 0.0040 chunk 123 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN B 846 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.125826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.101098 restraints weight = 30802.522| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.64 r_work: 0.3602 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14226 Z= 0.144 Angle : 0.685 11.057 19339 Z= 0.346 Chirality : 0.048 0.260 2118 Planarity : 0.005 0.070 2475 Dihedral : 7.796 59.913 2258 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.87 % Favored : 93.07 % Rotamer: Outliers : 3.18 % Allowed : 17.55 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.28 (0.20), residues: 1674 helix: -0.90 (0.39), residues: 170 sheet: -0.38 (0.29), residues: 317 loop : -1.01 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 59 TYR 0.021 0.002 TYR C 25 PHE 0.022 0.001 PHE C 61 TRP 0.013 0.001 TRP A 618 HIS 0.007 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00320 (14171) covalent geometry : angle 0.65602 (19211) SS BOND : bond 0.00455 ( 37) SS BOND : angle 1.24247 ( 74) hydrogen bonds : bond 0.03420 ( 346) hydrogen bonds : angle 6.39531 ( 894) link_BETA1-4 : bond 0.01857 ( 4) link_BETA1-4 : angle 4.43471 ( 12) link_NAG-ASN : bond 0.00604 ( 14) link_NAG-ASN : angle 3.31899 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7564 (mtp-110) REVERT: A 319 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8156 (ttp) REVERT: A 373 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8377 (mtmm) REVERT: A 461 ASP cc_start: 0.8104 (m-30) cc_final: 0.7835 (m-30) REVERT: A 494 THR cc_start: 0.8887 (p) cc_final: 0.8678 (p) REVERT: A 586 ASP cc_start: 0.8781 (p0) cc_final: 0.8403 (p0) REVERT: A 602 ASN cc_start: 0.8952 (m-40) cc_final: 0.8712 (m-40) REVERT: A 643 TYR cc_start: 0.8065 (p90) cc_final: 0.7702 (p90) REVERT: A 704 VAL cc_start: 0.8721 (m) cc_final: 0.8433 (p) REVERT: A 848 GLU cc_start: 0.8285 (tp30) cc_final: 0.7850 (tp30) REVERT: B 156 MET cc_start: 0.7469 (mmm) cc_final: 0.7020 (mmm) REVERT: B 336 ARG cc_start: 0.8298 (tpp80) cc_final: 0.7982 (ttp-170) REVERT: B 343 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8534 (mp0) REVERT: B 374 ASN cc_start: 0.8808 (m110) cc_final: 0.8189 (t0) REVERT: B 388 TYR cc_start: 0.6898 (m-80) cc_final: 0.6430 (m-80) REVERT: B 415 LYS cc_start: 0.8335 (ttmt) cc_final: 0.8086 (ttpt) REVERT: B 835 TYR cc_start: 0.8201 (m-80) cc_final: 0.7776 (m-80) REVERT: B 857 LYS cc_start: 0.9352 (tttt) cc_final: 0.9135 (ttmm) REVERT: B 885 SER cc_start: 0.9107 (t) cc_final: 0.8844 (p) outliers start: 48 outliers final: 34 residues processed: 230 average time/residue: 0.1243 time to fit residues: 41.9733 Evaluate side-chains 221 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 130 optimal weight: 0.0370 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 ASN ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.127173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.102685 restraints weight = 30867.974| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.63 r_work: 0.3607 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14226 Z= 0.127 Angle : 0.673 11.352 19339 Z= 0.338 Chirality : 0.048 0.265 2118 Planarity : 0.005 0.049 2475 Dihedral : 7.529 59.793 2258 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.11 % Favored : 92.83 % Rotamer: Outliers : 2.98 % Allowed : 17.81 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.21 (0.21), residues: 1674 helix: -0.63 (0.41), residues: 163 sheet: -0.40 (0.29), residues: 318 loop : -0.98 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 847 TYR 0.043 0.002 TYR A 430 PHE 0.019 0.001 PHE C 61 TRP 0.014 0.001 TRP B 79 HIS 0.005 0.001 HIS B 699 Details of bonding type rmsd covalent geometry : bond 0.00280 (14171) covalent geometry : angle 0.64570 (19211) SS BOND : bond 0.00318 ( 37) SS BOND : angle 1.11652 ( 74) hydrogen bonds : bond 0.03351 ( 346) hydrogen bonds : angle 6.31344 ( 894) link_BETA1-4 : bond 0.01808 ( 4) link_BETA1-4 : angle 4.33662 ( 12) link_NAG-ASN : bond 0.00589 ( 14) link_NAG-ASN : angle 3.22893 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8142 (ttp) REVERT: A 373 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8396 (mtmm) REVERT: A 432 MET cc_start: 0.7703 (tpp) cc_final: 0.7080 (ttm) REVERT: A 586 ASP cc_start: 0.8754 (p0) cc_final: 0.8381 (p0) REVERT: A 602 ASN cc_start: 0.8880 (m-40) cc_final: 0.8648 (m-40) REVERT: A 643 TYR cc_start: 0.8014 (p90) cc_final: 0.7666 (p90) REVERT: A 704 VAL cc_start: 0.8697 (m) cc_final: 0.8420 (p) REVERT: A 848 GLU cc_start: 0.8361 (tp30) cc_final: 0.7892 (tp30) REVERT: B 156 MET cc_start: 0.7425 (mmm) cc_final: 0.7010 (mmm) REVERT: B 336 ARG cc_start: 0.8393 (tpp80) cc_final: 0.8113 (ttp-170) REVERT: B 343 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8510 (mp0) REVERT: B 374 ASN cc_start: 0.8784 (m110) cc_final: 0.8161 (t0) REVERT: B 388 TYR cc_start: 0.6900 (m-80) cc_final: 0.6204 (m-80) REVERT: B 415 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8118 (ttpt) REVERT: B 416 MET cc_start: 0.8235 (mtm) cc_final: 0.7881 (ttm) REVERT: B 835 TYR cc_start: 0.8131 (m-80) cc_final: 0.7679 (m-80) REVERT: B 885 SER cc_start: 0.9077 (t) cc_final: 0.8836 (p) REVERT: C 13 ASP cc_start: 0.8576 (m-30) cc_final: 0.8367 (m-30) REVERT: C 60 LYS cc_start: 0.8813 (tttt) cc_final: 0.8603 (tttp) outliers start: 45 outliers final: 32 residues processed: 235 average time/residue: 0.1299 time to fit residues: 44.5951 Evaluate side-chains 220 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 91 optimal weight: 0.3980 chunk 23 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 120 optimal weight: 0.0970 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** 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 = 0.4044 r_free = 0.4044 target = 0.123462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.098348 restraints weight = 30374.857| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.70 r_work: 0.3483 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14226 Z= 0.180 Angle : 0.706 10.837 19339 Z= 0.354 Chirality : 0.049 0.255 2118 Planarity : 0.005 0.049 2475 Dihedral : 7.547 59.926 2258 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.71 % Favored : 92.23 % Rotamer: Outliers : 2.98 % Allowed : 18.74 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.17 (0.21), residues: 1674 helix: -0.50 (0.42), residues: 165 sheet: -0.41 (0.30), residues: 314 loop : -0.95 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 376 TYR 0.024 0.002 TYR A 835 PHE 0.021 0.002 PHE C 61 TRP 0.015 0.001 TRP A 618 HIS 0.005 0.001 HIS B 699 Details of bonding type rmsd covalent geometry : bond 0.00405 (14171) covalent geometry : angle 0.67843 (19211) SS BOND : bond 0.00438 ( 37) SS BOND : angle 1.21538 ( 74) hydrogen bonds : bond 0.03369 ( 346) hydrogen bonds : angle 6.31341 ( 894) link_BETA1-4 : bond 0.01688 ( 4) link_BETA1-4 : angle 4.39398 ( 12) link_NAG-ASN : bond 0.00557 ( 14) link_NAG-ASN : angle 3.25911 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8212 (mtmm) REVERT: A 430 TYR cc_start: 0.8970 (m-10) cc_final: 0.8744 (m-80) REVERT: A 586 ASP cc_start: 0.8747 (p0) cc_final: 0.8388 (p0) REVERT: A 602 ASN cc_start: 0.9048 (m-40) cc_final: 0.8697 (m-40) REVERT: A 643 TYR cc_start: 0.8105 (p90) cc_final: 0.7595 (p90) REVERT: A 754 ASN cc_start: 0.8297 (m-40) cc_final: 0.7824 (p0) REVERT: A 848 GLU cc_start: 0.8377 (tp30) cc_final: 0.8124 (tp30) REVERT: A 857 LYS cc_start: 0.8800 (ptpt) cc_final: 0.8291 (ptpt) REVERT: A 858 TYR cc_start: 0.8904 (m-10) cc_final: 0.8635 (m-10) REVERT: B 156 MET cc_start: 0.7466 (mmm) cc_final: 0.7050 (mmm) REVERT: B 343 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8562 (mp0) REVERT: B 374 ASN cc_start: 0.8950 (m110) cc_final: 0.8285 (t0) REVERT: B 388 TYR cc_start: 0.7047 (m-80) cc_final: 0.6116 (m-80) REVERT: B 415 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7955 (ttpt) REVERT: B 835 TYR cc_start: 0.8008 (m-80) cc_final: 0.7631 (m-80) REVERT: C 13 ASP cc_start: 0.8628 (m-30) cc_final: 0.8416 (m-30) REVERT: C 60 LYS cc_start: 0.8799 (tttt) cc_final: 0.8436 (tttp) outliers start: 45 outliers final: 37 residues processed: 215 average time/residue: 0.1255 time to fit residues: 40.1991 Evaluate side-chains 205 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 64 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 119 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 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 = 0.4047 r_free = 0.4047 target = 0.123740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.098431 restraints weight = 30588.996| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.72 r_work: 0.3482 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14226 Z= 0.176 Angle : 0.718 10.814 19339 Z= 0.361 Chirality : 0.049 0.252 2118 Planarity : 0.005 0.050 2475 Dihedral : 7.508 59.349 2258 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.71 % Favored : 92.23 % Rotamer: Outliers : 2.91 % Allowed : 19.01 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.25 (0.21), residues: 1674 helix: -0.75 (0.40), residues: 172 sheet: -0.43 (0.30), residues: 314 loop : -0.98 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 376 TYR 0.038 0.002 TYR A 835 PHE 0.021 0.001 PHE C 61 TRP 0.015 0.001 TRP A 618 HIS 0.005 0.001 HIS B 699 Details of bonding type rmsd covalent geometry : bond 0.00398 (14171) covalent geometry : angle 0.69039 (19211) SS BOND : bond 0.00491 ( 37) SS BOND : angle 1.37207 ( 74) hydrogen bonds : bond 0.03426 ( 346) hydrogen bonds : angle 6.42310 ( 894) link_BETA1-4 : bond 0.01587 ( 4) link_BETA1-4 : angle 4.29734 ( 12) link_NAG-ASN : bond 0.00542 ( 14) link_NAG-ASN : angle 3.23342 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8107 (mp0) cc_final: 0.7792 (mp0) REVERT: A 373 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8187 (mtmm) REVERT: A 430 TYR cc_start: 0.8985 (m-10) cc_final: 0.8772 (m-10) REVERT: A 494 THR cc_start: 0.8977 (p) cc_final: 0.8768 (t) REVERT: A 586 ASP cc_start: 0.8776 (p0) cc_final: 0.8438 (p0) REVERT: A 602 ASN cc_start: 0.9067 (m-40) cc_final: 0.8712 (m-40) REVERT: A 643 TYR cc_start: 0.8057 (p90) cc_final: 0.7493 (p90) REVERT: A 754 ASN cc_start: 0.8317 (m-40) cc_final: 0.7813 (p0) REVERT: A 822 TRP cc_start: 0.8319 (p90) cc_final: 0.7691 (p90) REVERT: A 846 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8363 (mt0) REVERT: A 848 GLU cc_start: 0.8413 (tp30) cc_final: 0.7860 (tp30) REVERT: A 857 LYS cc_start: 0.8810 (ptpt) cc_final: 0.8220 (ptpt) REVERT: A 858 TYR cc_start: 0.8920 (m-10) cc_final: 0.8504 (m-10) REVERT: B 26 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7122 (tt0) REVERT: B 156 MET cc_start: 0.7451 (mmm) cc_final: 0.7010 (mmm) REVERT: B 343 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8528 (mp0) REVERT: B 374 ASN cc_start: 0.8988 (m110) cc_final: 0.8315 (t0) REVERT: B 388 TYR cc_start: 0.7069 (m-80) cc_final: 0.5971 (m-80) REVERT: B 415 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7901 (ttpt) REVERT: C 13 ASP cc_start: 0.8578 (m-30) cc_final: 0.8369 (m-30) REVERT: C 60 LYS cc_start: 0.8793 (tttt) cc_final: 0.8543 (tttp) outliers start: 44 outliers final: 34 residues processed: 211 average time/residue: 0.1242 time to fit residues: 39.2629 Evaluate side-chains 207 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 633 CYS Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 57 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 96 optimal weight: 0.1980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 339 ASN B 400 GLN B 406 HIS ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.124530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.099557 restraints weight = 30552.676| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.73 r_work: 0.3507 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14226 Z= 0.148 Angle : 0.714 15.726 19339 Z= 0.356 Chirality : 0.048 0.249 2118 Planarity : 0.005 0.050 2475 Dihedral : 7.314 59.121 2258 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.47 % Favored : 92.47 % Rotamer: Outliers : 2.52 % Allowed : 19.40 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.21 (0.21), residues: 1674 helix: -0.71 (0.40), residues: 172 sheet: -0.36 (0.29), residues: 321 loop : -0.98 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 376 TYR 0.035 0.002 TYR A 835 PHE 0.018 0.001 PHE C 61 TRP 0.030 0.001 TRP B 404 HIS 0.005 0.001 HIS B 699 Details of bonding type rmsd covalent geometry : bond 0.00334 (14171) covalent geometry : angle 0.69006 (19211) SS BOND : bond 0.00361 ( 37) SS BOND : angle 1.07171 ( 74) hydrogen bonds : bond 0.03307 ( 346) hydrogen bonds : angle 6.35295 ( 894) link_BETA1-4 : bond 0.01602 ( 4) link_BETA1-4 : angle 4.18849 ( 12) link_NAG-ASN : bond 0.00548 ( 14) link_NAG-ASN : angle 3.17267 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8055 (mp0) cc_final: 0.7739 (mp0) REVERT: A 373 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8255 (mtmm) REVERT: A 494 THR cc_start: 0.8989 (p) cc_final: 0.8773 (t) REVERT: A 586 ASP cc_start: 0.8774 (p0) cc_final: 0.8425 (p0) REVERT: A 602 ASN cc_start: 0.9027 (m-40) cc_final: 0.8673 (m-40) REVERT: A 643 TYR cc_start: 0.8019 (p90) cc_final: 0.7480 (p90) REVERT: A 754 ASN cc_start: 0.8296 (m-40) cc_final: 0.7817 (p0) REVERT: A 822 TRP cc_start: 0.8314 (p90) cc_final: 0.7294 (p90) REVERT: A 846 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8358 (mt0) REVERT: A 857 LYS cc_start: 0.8821 (ptpt) cc_final: 0.8134 (ptpt) REVERT: A 858 TYR cc_start: 0.8870 (m-10) cc_final: 0.8444 (m-10) REVERT: B 26 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7036 (tt0) REVERT: B 156 MET cc_start: 0.7478 (mmm) cc_final: 0.7016 (mmm) REVERT: B 174 ARG cc_start: 0.6455 (ptt90) cc_final: 0.5322 (ptt90) REVERT: B 184 MET cc_start: 0.7207 (tpt) cc_final: 0.6785 (tmm) REVERT: B 343 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8512 (mp0) REVERT: B 374 ASN cc_start: 0.8984 (m110) cc_final: 0.8283 (t0) REVERT: B 388 TYR cc_start: 0.7073 (m-80) cc_final: 0.5938 (m-80) REVERT: B 415 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7839 (ttpt) REVERT: B 416 MET cc_start: 0.8422 (mtm) cc_final: 0.7545 (mtm) REVERT: B 751 ARG cc_start: 0.8202 (ttt90) cc_final: 0.7722 (mtp85) REVERT: C 60 LYS cc_start: 0.8808 (tttt) cc_final: 0.8574 (tttp) outliers start: 38 outliers final: 31 residues processed: 213 average time/residue: 0.0934 time to fit residues: 29.4944 Evaluate side-chains 215 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 633 CYS Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 120 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 400 GLN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.122770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.097367 restraints weight = 30481.743| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.73 r_work: 0.3464 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14226 Z= 0.201 Angle : 0.744 17.548 19339 Z= 0.372 Chirality : 0.050 0.242 2118 Planarity : 0.005 0.051 2475 Dihedral : 7.320 58.199 2258 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.84 % Favored : 91.10 % Rotamer: Outliers : 2.45 % Allowed : 19.47 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.15 (0.21), residues: 1674 helix: -0.45 (0.42), residues: 163 sheet: -0.20 (0.31), residues: 289 loop : -1.00 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 59 TYR 0.037 0.002 TYR A 430 PHE 0.032 0.002 PHE B 241 TRP 0.044 0.002 TRP B 404 HIS 0.006 0.001 HIS B 699 Details of bonding type rmsd covalent geometry : bond 0.00455 (14171) covalent geometry : angle 0.71969 (19211) SS BOND : bond 0.00525 ( 37) SS BOND : angle 1.29543 ( 74) hydrogen bonds : bond 0.03418 ( 346) hydrogen bonds : angle 6.34901 ( 894) link_BETA1-4 : bond 0.01433 ( 4) link_BETA1-4 : angle 4.22337 ( 12) link_NAG-ASN : bond 0.00524 ( 14) link_NAG-ASN : angle 3.17340 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3644.30 seconds wall clock time: 63 minutes 36.04 seconds (3816.04 seconds total)