Starting phenix.real_space_refine on Fri May 16 03:08:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tan_41138/05_2025/8tan_41138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tan_41138/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tan_41138/05_2025/8tan_41138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tan_41138/05_2025/8tan_41138.map" model { file = "/net/cci-nas-00/data/ceres_data/8tan_41138/05_2025/8tan_41138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tan_41138/05_2025/8tan_41138.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.81, per 1000 atoms: 0.56 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: 3.62 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.99 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: 5.57 Time building geometry restraints manager: 4.25 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 896 or resid 1001 through 10 \ 04)) 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.950 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.640 ------------------------------------------------------------------------------- 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 : 5.98 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (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 TRP 0.019 0.002 TRP B 402 HIS 0.009 0.001 HIS B 699 PHE 0.013 0.002 PHE B 790 TYR 0.018 0.002 TYR A 224 ARG 0.006 0.001 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00724 ( 14) link_NAG-ASN : angle 3.94204 ( 42) link_BETA1-4 : bond 0.02367 ( 4) link_BETA1-4 : angle 6.18307 ( 12) hydrogen bonds : bond 0.10349 ( 346) hydrogen bonds : angle 7.78293 ( 894) SS BOND : bond 0.00399 ( 37) SS BOND : angle 1.17403 ( 74) covalent geometry : bond 0.00368 (14171) covalent geometry : angle 0.77166 (19211) *********************** 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 : 1.439 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 248 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8387 (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: 0.6850 (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: 0.7726 (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: 0.8087 (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: 0.5570 (ptt90) REVERT: B 214 ASN cc_start: 0.3796 (OUTLIER) cc_final: 0.3492 (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: 0.5875 (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: 0.8013 (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: 0.8161 (p) REVERT: B 686 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8171 (mt-10) 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: 0.7857 (m-80) REVERT: B 837 ILE cc_start: 0.8937 (mt) cc_final: 0.8700 (mt) outliers start: 33 outliers final: 12 residues processed: 457 average time/residue: 0.2929 time to fit residues: 186.1911 Evaluate side-chains 257 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 242 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 142 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 80 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** A 364 HIS ** 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 = 0.4142 r_free = 0.4142 target = 0.127058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.101930 restraints weight = 30428.951| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.69 r_work: 0.3597 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14226 Z= 0.181 Angle : 0.786 10.497 19339 Z= 0.406 Chirality : 0.052 0.269 2118 Planarity : 0.005 0.049 2475 Dihedral : 9.874 70.121 2283 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.58 % Allowed : 12.58 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (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 TRP 0.012 0.001 TRP A 618 HIS 0.008 0.001 HIS B 699 PHE 0.017 0.002 PHE B 90 TYR 0.028 0.002 TYR A 628 ARG 0.008 0.001 ARG B 104 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 14) link_NAG-ASN : angle 3.47984 ( 42) link_BETA1-4 : bond 0.02076 ( 4) link_BETA1-4 : angle 4.91583 ( 12) hydrogen bonds : bond 0.04380 ( 346) hydrogen bonds : angle 6.96471 ( 894) SS BOND : bond 0.00578 ( 37) SS BOND : angle 2.21119 ( 74) covalent geometry : bond 0.00402 (14171) covalent geometry : angle 0.74954 (19211) *********************** 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 317 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 1.461 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: A 84 ASN cc_start: 0.8752 (m-40) cc_final: 0.8347 (t0) REVERT: A 373 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8466 (mtmm) REVERT: A 429 ILE cc_start: 0.7882 (pt) cc_final: 0.7666 (mt) REVERT: A 477 ILE cc_start: 0.9004 (tt) cc_final: 0.8706 (mm) REVERT: A 494 THR cc_start: 0.8841 (p) cc_final: 0.8591 (p) REVERT: A 558 MET cc_start: 0.7580 (ttm) cc_final: 0.6753 (ttm) REVERT: A 586 ASP cc_start: 0.8670 (p0) cc_final: 0.8115 (p0) REVERT: A 602 ASN cc_start: 0.8977 (m-40) cc_final: 0.8721 (m-40) REVERT: A 617 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7232 (ttm170) REVERT: A 642 LYS cc_start: 0.8906 (mttt) cc_final: 0.8692 (mmtt) REVERT: A 643 TYR cc_start: 0.8069 (p90) cc_final: 0.7554 (p90) REVERT: A 704 VAL cc_start: 0.8775 (m) cc_final: 0.8514 (p) REVERT: A 754 ASN cc_start: 0.8067 (m-40) cc_final: 0.7724 (p0) REVERT: A 820 LEU cc_start: 0.9292 (mt) cc_final: 0.9038 (mm) REVERT: A 822 TRP cc_start: 0.7867 (p90) cc_final: 0.7282 (p90) REVERT: A 848 GLU cc_start: 0.7832 (tp30) cc_final: 0.7521 (tp30) REVERT: A 850 VAL cc_start: 0.8592 (t) cc_final: 0.8381 (t) REVERT: B 79 TRP cc_start: 0.7915 (t60) cc_final: 0.7587 (t60) REVERT: B 156 MET cc_start: 0.7578 (mmm) cc_final: 0.7058 (mtp) REVERT: B 174 ARG cc_start: 0.6609 (ptt90) cc_final: 0.5219 (ptt90) REVERT: B 388 TYR cc_start: 0.6511 (m-80) cc_final: 0.6301 (m-80) REVERT: B 415 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7961 (ptmt) REVERT: B 416 MET cc_start: 0.8793 (mtm) cc_final: 0.8446 (mtp) REVERT: B 476 ILE cc_start: 0.9052 (mt) cc_final: 0.8774 (mt) REVERT: B 572 LEU cc_start: 0.8667 (tp) cc_final: 0.8390 (tt) REVERT: B 686 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8402 (mt-10) REVERT: B 824 GLU cc_start: 0.8326 (tt0) cc_final: 0.8058 (tp30) REVERT: B 835 TYR cc_start: 0.8286 (m-80) cc_final: 0.7606 (m-80) REVERT: B 857 LYS cc_start: 0.9361 (tttt) cc_final: 0.9101 (ttmm) outliers start: 54 outliers final: 23 residues processed: 294 average time/residue: 0.2945 time to fit residues: 125.4835 Evaluate side-chains 240 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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 6 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 HIS ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.125699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.100667 restraints weight = 30685.725| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.68 r_work: 0.3595 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14226 Z= 0.170 Angle : 0.731 10.846 19339 Z= 0.374 Chirality : 0.050 0.274 2118 Planarity : 0.004 0.048 2475 Dihedral : 8.982 62.597 2268 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.11 % Favored : 92.83 % Rotamer: Outliers : 3.38 % Allowed : 15.30 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.20), residues: 1674 helix: -1.54 (0.36), residues: 181 sheet: -0.61 (0.28), residues: 333 loop : -1.07 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 618 HIS 0.009 0.001 HIS B 699 PHE 0.018 0.002 PHE C 61 TYR 0.018 0.002 TYR A 391 ARG 0.015 0.001 ARG A 565 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 14) link_NAG-ASN : angle 3.46274 ( 42) link_BETA1-4 : bond 0.01983 ( 4) link_BETA1-4 : angle 4.75338 ( 12) hydrogen bonds : bond 0.04048 ( 346) hydrogen bonds : angle 6.66187 ( 894) SS BOND : bond 0.00442 ( 37) SS BOND : angle 1.55035 ( 74) covalent geometry : bond 0.00378 (14171) covalent geometry : angle 0.69831 (19211) *********************** 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 273 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 1.454 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: 0.8461 (OUTLIER) cc_final: 0.8031 (ttp) REVERT: A 373 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8360 (mtmm) REVERT: A 384 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7804 (mp) REVERT: A 461 ASP cc_start: 0.8095 (m-30) cc_final: 0.7565 (m-30) REVERT: A 494 THR cc_start: 0.8836 (p) cc_final: 0.8604 (p) REVERT: A 586 ASP cc_start: 0.8716 (p0) cc_final: 0.8208 (p0) REVERT: A 602 ASN cc_start: 0.8944 (m-40) cc_final: 0.8692 (m-40) REVERT: A 617 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7274 (ttm170) REVERT: A 642 LYS cc_start: 0.8942 (mttt) cc_final: 0.8731 (mmtt) REVERT: A 643 TYR cc_start: 0.8067 (p90) cc_final: 0.7533 (p90) REVERT: A 681 LYS cc_start: 0.8799 (mttp) cc_final: 0.8592 (mptt) REVERT: A 704 VAL cc_start: 0.8773 (m) cc_final: 0.8491 (p) REVERT: A 820 LEU cc_start: 0.9287 (mt) cc_final: 0.9057 (mm) REVERT: A 833 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8432 (pt) REVERT: A 848 GLU cc_start: 0.7990 (tp30) cc_final: 0.7678 (tp30) REVERT: B 156 MET cc_start: 0.7583 (mmm) cc_final: 0.7024 (mtt) REVERT: B 270 ASP cc_start: 0.7858 (t0) cc_final: 0.7598 (t0) REVERT: B 309 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8227 (tttm) REVERT: B 388 TYR cc_start: 0.6545 (m-80) cc_final: 0.6031 (m-80) REVERT: B 415 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7890 (ptmt) REVERT: B 416 MET cc_start: 0.8552 (mtm) cc_final: 0.8292 (mtp) REVERT: B 477 ILE cc_start: 0.9361 (mt) cc_final: 0.9146 (mp) REVERT: B 572 LEU cc_start: 0.8737 (tp) cc_final: 0.8391 (tt) REVERT: B 686 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8409 (mt-10) REVERT: B 835 TYR cc_start: 0.8394 (m-80) cc_final: 0.7891 (m-80) REVERT: B 855 TYR cc_start: 0.8024 (t80) cc_final: 0.7428 (t80) REVERT: B 857 LYS cc_start: 0.9368 (tttt) cc_final: 0.9060 (ttmm) outliers start: 51 outliers final: 31 residues processed: 255 average time/residue: 0.2608 time to fit residues: 96.5874 Evaluate side-chains 234 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 384 LEU 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 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 298 CYS Chi-restraints excluded: chain B residue 309 LYS 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 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 100 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 11 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.127937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.102720 restraints weight = 30452.765| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 3.70 r_work: 0.3579 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14226 Z= 0.156 Angle : 0.711 10.949 19339 Z= 0.360 Chirality : 0.049 0.275 2118 Planarity : 0.004 0.044 2475 Dihedral : 8.402 59.972 2264 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.77 % Rotamer: Outliers : 3.71 % Allowed : 16.36 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.20), residues: 1674 helix: -1.43 (0.36), residues: 183 sheet: -0.55 (0.28), residues: 327 loop : -1.06 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 822 HIS 0.012 0.001 HIS A 563 PHE 0.015 0.001 PHE A 694 TYR 0.018 0.002 TYR A 391 ARG 0.009 0.000 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 14) link_NAG-ASN : angle 3.44298 ( 42) link_BETA1-4 : bond 0.01898 ( 4) link_BETA1-4 : angle 4.65348 ( 12) hydrogen bonds : bond 0.03721 ( 346) hydrogen bonds : angle 6.50453 ( 894) SS BOND : bond 0.00422 ( 37) SS BOND : angle 1.27980 ( 74) covalent geometry : bond 0.00347 (14171) covalent geometry : angle 0.68069 (19211) *********************** 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 264 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 1.465 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: 0.8437 (OUTLIER) cc_final: 0.8020 (ttp) REVERT: A 373 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8308 (mtmm) REVERT: A 385 GLU cc_start: 0.7827 (pm20) cc_final: 0.7598 (pm20) REVERT: A 430 TYR cc_start: 0.8894 (m-10) cc_final: 0.8669 (m-80) REVERT: A 461 ASP cc_start: 0.8105 (m-30) cc_final: 0.7824 (m-30) REVERT: A 494 THR cc_start: 0.8851 (p) cc_final: 0.8616 (p) REVERT: A 586 ASP cc_start: 0.8755 (p0) cc_final: 0.8296 (p0) REVERT: A 602 ASN cc_start: 0.8966 (m-40) cc_final: 0.8696 (m-40) REVERT: A 617 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7360 (ttm170) REVERT: A 642 LYS cc_start: 0.8955 (mttt) cc_final: 0.8735 (mmtt) REVERT: A 643 TYR cc_start: 0.8037 (p90) cc_final: 0.7461 (p90) REVERT: A 704 VAL cc_start: 0.8802 (m) cc_final: 0.8513 (p) REVERT: A 833 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8481 (pt) REVERT: A 848 GLU cc_start: 0.8035 (tp30) cc_final: 0.7756 (tp30) REVERT: B 156 MET cc_start: 0.7575 (mmm) cc_final: 0.7127 (mmp) REVERT: B 270 ASP cc_start: 0.7903 (t0) cc_final: 0.7594 (t0) REVERT: B 388 TYR cc_start: 0.6590 (m-80) cc_final: 0.6054 (m-80) REVERT: B 415 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7923 (ptmt) REVERT: B 416 MET cc_start: 0.8518 (mtm) cc_final: 0.8269 (mtp) REVERT: B 686 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8403 (mt-10) REVERT: B 789 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8219 (t0) REVERT: B 857 LYS cc_start: 0.9373 (tttt) cc_final: 0.9111 (ttmm) REVERT: B 885 SER cc_start: 0.9160 (t) cc_final: 0.8907 (p) outliers start: 56 outliers final: 32 residues processed: 244 average time/residue: 0.2746 time to fit residues: 97.1223 Evaluate side-chains 231 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 433 GLU 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 880 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 310 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 597 LEU 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 Chi-restraints excluded: chain C residue 63 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 40 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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** ** B 11 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 = 0.4133 r_free = 0.4133 target = 0.126220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.102599 restraints weight = 30434.248| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.47 r_work: 0.3598 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14226 Z= 0.157 Angle : 0.693 10.986 19339 Z= 0.352 Chirality : 0.049 0.271 2118 Planarity : 0.004 0.063 2475 Dihedral : 8.098 59.591 2262 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.05 % Favored : 92.89 % Rotamer: Outliers : 3.91 % Allowed : 16.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.20), residues: 1674 helix: -1.44 (0.36), residues: 183 sheet: -0.39 (0.29), residues: 313 loop : -1.06 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 618 HIS 0.008 0.001 HIS B 699 PHE 0.022 0.001 PHE C 61 TYR 0.029 0.002 TYR A 835 ARG 0.010 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 14) link_NAG-ASN : angle 3.38991 ( 42) link_BETA1-4 : bond 0.01886 ( 4) link_BETA1-4 : angle 4.58335 ( 12) hydrogen bonds : bond 0.03530 ( 346) hydrogen bonds : angle 6.42988 ( 894) SS BOND : bond 0.00390 ( 37) SS BOND : angle 1.32974 ( 74) covalent geometry : bond 0.00352 (14171) covalent geometry : angle 0.66240 (19211) *********************** 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 265 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 1.554 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 319 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8085 (ttp) REVERT: A 373 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8372 (mtmm) REVERT: A 412 LYS cc_start: 0.8505 (tmtt) cc_final: 0.8270 (tptp) REVERT: A 461 ASP cc_start: 0.8056 (m-30) cc_final: 0.7784 (m-30) REVERT: A 494 THR cc_start: 0.8854 (p) cc_final: 0.8626 (p) REVERT: A 586 ASP cc_start: 0.8750 (p0) cc_final: 0.8314 (p0) REVERT: A 602 ASN cc_start: 0.8963 (m-40) cc_final: 0.8711 (m-40) REVERT: A 617 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7430 (tpp80) REVERT: A 643 TYR cc_start: 0.8027 (p90) cc_final: 0.7592 (p90) REVERT: A 704 VAL cc_start: 0.8777 (m) cc_final: 0.8493 (p) REVERT: A 848 GLU cc_start: 0.8255 (tp30) cc_final: 0.7745 (tp30) REVERT: B 156 MET cc_start: 0.7524 (mmm) cc_final: 0.7037 (mmp) REVERT: B 270 ASP cc_start: 0.7899 (t0) cc_final: 0.7566 (t0) REVERT: B 388 TYR cc_start: 0.6701 (m-80) cc_final: 0.6036 (m-80) REVERT: B 415 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7975 (ptmt) REVERT: B 416 MET cc_start: 0.8437 (mtm) cc_final: 0.8084 (mtm) REVERT: B 686 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8360 (mt-10) REVERT: B 789 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8196 (t0) REVERT: B 835 TYR cc_start: 0.8235 (m-80) cc_final: 0.7762 (m-80) REVERT: B 857 LYS cc_start: 0.9353 (tttt) cc_final: 0.9137 (ttmm) REVERT: B 885 SER cc_start: 0.9107 (t) cc_final: 0.8853 (p) REVERT: C 13 ASP cc_start: 0.8547 (m-30) cc_final: 0.8300 (m-30) outliers start: 59 outliers final: 36 residues processed: 244 average time/residue: 0.2591 time to fit residues: 92.1194 Evaluate side-chains 229 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 333 ASN 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 605 SER 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 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 367 VAL 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 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 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 154 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 ASN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** 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 = 0.4023 r_free = 0.4023 target = 0.122134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096703 restraints weight = 30904.974| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.69 r_work: 0.3450 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14226 Z= 0.236 Angle : 0.736 10.923 19339 Z= 0.372 Chirality : 0.050 0.256 2118 Planarity : 0.005 0.041 2475 Dihedral : 8.107 58.799 2262 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.66 % Favored : 91.28 % Rotamer: Outliers : 3.51 % Allowed : 17.35 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.20), residues: 1674 helix: -1.14 (0.38), residues: 177 sheet: -0.55 (0.28), residues: 329 loop : -1.03 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 618 HIS 0.008 0.001 HIS B 699 PHE 0.024 0.002 PHE C 61 TYR 0.033 0.002 TYR A 430 ARG 0.007 0.001 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 14) link_NAG-ASN : angle 3.45154 ( 42) link_BETA1-4 : bond 0.01728 ( 4) link_BETA1-4 : angle 4.63850 ( 12) hydrogen bonds : bond 0.03618 ( 346) hydrogen bonds : angle 6.39543 ( 894) SS BOND : bond 0.00597 ( 37) SS BOND : angle 1.45020 ( 74) covalent geometry : bond 0.00533 (14171) covalent geometry : angle 0.70520 (19211) *********************** 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 254 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 201 time to evaluate : 1.807 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: A 319 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8263 (ttp) REVERT: A 373 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8219 (mtmm) REVERT: A 412 LYS cc_start: 0.8615 (tmtt) cc_final: 0.8226 (tmtt) REVERT: A 461 ASP cc_start: 0.8354 (m-30) cc_final: 0.8004 (m-30) REVERT: A 494 THR cc_start: 0.8872 (p) cc_final: 0.8632 (p) REVERT: A 586 ASP cc_start: 0.8748 (p0) cc_final: 0.8358 (p0) REVERT: A 602 ASN cc_start: 0.9103 (m-40) cc_final: 0.8741 (m-40) REVERT: A 643 TYR cc_start: 0.8140 (p90) cc_final: 0.7621 (p90) REVERT: A 704 VAL cc_start: 0.8791 (m) cc_final: 0.8481 (p) REVERT: A 822 TRP cc_start: 0.8208 (p90) cc_final: 0.7455 (p90) REVERT: A 848 GLU cc_start: 0.8211 (tp30) cc_final: 0.7589 (tp30) REVERT: B 26 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7494 (tt0) REVERT: B 156 MET cc_start: 0.7527 (mmm) cc_final: 0.7032 (mmp) REVERT: B 270 ASP cc_start: 0.8059 (t0) cc_final: 0.7680 (t0) REVERT: B 336 ARG cc_start: 0.8380 (tpp80) cc_final: 0.8016 (ttp-170) REVERT: B 374 ASN cc_start: 0.8940 (m110) cc_final: 0.8255 (t0) REVERT: B 388 TYR cc_start: 0.6946 (m-80) cc_final: 0.5995 (m-80) REVERT: B 415 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7972 (ttpt) REVERT: B 416 MET cc_start: 0.8549 (mtm) cc_final: 0.8164 (mtm) REVERT: B 789 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8248 (t0) REVERT: B 835 TYR cc_start: 0.8245 (m-80) cc_final: 0.7867 (m-80) REVERT: B 857 LYS cc_start: 0.9468 (tttt) cc_final: 0.9202 (ttmm) outliers start: 53 outliers final: 35 residues processed: 240 average time/residue: 0.2448 time to fit residues: 86.4225 Evaluate side-chains 230 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 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 433 GLU Chi-restraints excluded: chain A residue 525 ASP 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 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 272 GLU 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 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 789 ASN Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 846 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 23 optimal weight: 0.0000 chunk 119 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 145 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 96 optimal weight: 0.0870 overall best weight: 0.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** 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 = 0.4076 r_free = 0.4076 target = 0.125665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.100686 restraints weight = 30572.804| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.72 r_work: 0.3521 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4287 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= 0.122 Angle : 0.686 13.214 19339 Z= 0.343 Chirality : 0.048 0.253 2118 Planarity : 0.004 0.040 2475 Dihedral : 7.653 59.095 2258 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.57 % Favored : 93.37 % Rotamer: Outliers : 3.31 % Allowed : 18.28 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1674 helix: -0.86 (0.40), residues: 169 sheet: -0.44 (0.29), residues: 318 loop : -1.00 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 618 HIS 0.004 0.001 HIS B 699 PHE 0.017 0.001 PHE C 61 TYR 0.016 0.002 TYR B 835 ARG 0.007 0.000 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 14) link_NAG-ASN : angle 3.26881 ( 42) link_BETA1-4 : bond 0.01837 ( 4) link_BETA1-4 : angle 4.34015 ( 12) hydrogen bonds : bond 0.03425 ( 346) hydrogen bonds : angle 6.29518 ( 894) SS BOND : bond 0.00249 ( 37) SS BOND : angle 1.07139 ( 74) covalent geometry : bond 0.00266 (14171) covalent geometry : angle 0.65916 (19211) *********************** 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 259 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 1.691 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: A 91 GLU cc_start: 0.8048 (mp0) cc_final: 0.7763 (mp0) REVERT: A 319 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8099 (ttp) REVERT: A 373 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8193 (mtmm) REVERT: A 461 ASP cc_start: 0.8238 (m-30) cc_final: 0.7921 (m-30) REVERT: A 494 THR cc_start: 0.8855 (p) cc_final: 0.8597 (p) REVERT: A 586 ASP cc_start: 0.8743 (p0) cc_final: 0.8333 (p0) REVERT: A 600 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8699 (ptpt) REVERT: A 602 ASN cc_start: 0.8982 (m-40) cc_final: 0.8621 (m-40) REVERT: A 643 TYR cc_start: 0.8087 (p90) cc_final: 0.7554 (p90) REVERT: A 704 VAL cc_start: 0.8751 (m) cc_final: 0.8442 (p) REVERT: A 822 TRP cc_start: 0.8259 (p90) cc_final: 0.7468 (p90) REVERT: A 847 ARG cc_start: 0.8066 (tpp80) cc_final: 0.7850 (mmm-85) REVERT: A 848 GLU cc_start: 0.8244 (tp30) cc_final: 0.7690 (tp30) REVERT: B 156 MET cc_start: 0.7431 (mmm) cc_final: 0.7135 (mmt) REVERT: B 270 ASP cc_start: 0.8117 (t0) cc_final: 0.7753 (t0) REVERT: B 336 ARG cc_start: 0.8462 (tpp80) cc_final: 0.8081 (ttp-170) REVERT: B 343 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8556 (mp0) REVERT: B 388 TYR cc_start: 0.6965 (m-80) cc_final: 0.5995 (m-80) REVERT: B 415 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7830 (ptmt) REVERT: B 416 MET cc_start: 0.8419 (mtm) cc_final: 0.7638 (mtm) REVERT: B 789 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8176 (t0) REVERT: B 857 LYS cc_start: 0.9479 (tttt) cc_final: 0.9248 (ttmm) REVERT: B 885 SER cc_start: 0.9141 (t) cc_final: 0.8866 (p) REVERT: C 13 ASP cc_start: 0.8613 (m-30) cc_final: 0.8386 (m-30) outliers start: 50 outliers final: 38 residues processed: 243 average time/residue: 0.2460 time to fit residues: 88.7645 Evaluate side-chains 236 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 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 416 MET 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 600 LYS 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 A residue 837 ILE Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 81 LEU 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 272 GLU 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 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 846 GLN 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 131 optimal weight: 4.9990 chunk 129 optimal weight: 0.0980 chunk 121 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4067 r_free = 0.4067 target = 0.124924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.099886 restraints weight = 30522.772| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.72 r_work: 0.3512 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14226 Z= 0.142 Angle : 0.686 10.946 19339 Z= 0.343 Chirality : 0.048 0.255 2118 Planarity : 0.004 0.041 2475 Dihedral : 7.422 59.623 2258 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.59 % Favored : 92.35 % Rotamer: Outliers : 3.31 % Allowed : 19.07 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.20), residues: 1674 helix: -0.85 (0.40), residues: 172 sheet: -0.43 (0.29), residues: 318 loop : -0.99 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 618 HIS 0.005 0.001 HIS B 699 PHE 0.020 0.001 PHE C 61 TYR 0.025 0.002 TYR A 391 ARG 0.011 0.000 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 14) link_NAG-ASN : angle 3.24779 ( 42) link_BETA1-4 : bond 0.01740 ( 4) link_BETA1-4 : angle 4.35518 ( 12) hydrogen bonds : bond 0.03381 ( 346) hydrogen bonds : angle 6.18904 ( 894) SS BOND : bond 0.00347 ( 37) SS BOND : angle 1.10617 ( 74) covalent geometry : bond 0.00319 (14171) covalent geometry : angle 0.65908 (19211) *********************** 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 247 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 1.643 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 91 GLU cc_start: 0.8031 (mp0) cc_final: 0.7692 (mp0) REVERT: A 319 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8194 (ttp) REVERT: A 340 ILE cc_start: 0.8954 (tp) cc_final: 0.8476 (pt) REVERT: A 373 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8200 (mtmm) REVERT: A 461 ASP cc_start: 0.8289 (m-30) cc_final: 0.7940 (m-30) REVERT: A 494 THR cc_start: 0.8896 (p) cc_final: 0.8658 (p) REVERT: A 586 ASP cc_start: 0.8724 (p0) cc_final: 0.8337 (p0) REVERT: A 602 ASN cc_start: 0.9002 (m-40) cc_final: 0.8641 (m-40) REVERT: A 643 TYR cc_start: 0.8089 (p90) cc_final: 0.7542 (p90) REVERT: A 704 VAL cc_start: 0.8744 (m) cc_final: 0.8433 (p) REVERT: A 754 ASN cc_start: 0.8297 (m-40) cc_final: 0.7822 (p0) REVERT: A 822 TRP cc_start: 0.8197 (p90) cc_final: 0.7383 (p90) REVERT: A 847 ARG cc_start: 0.8101 (tpp80) cc_final: 0.7885 (mmm-85) REVERT: A 848 GLU cc_start: 0.8285 (tp30) cc_final: 0.7737 (tp30) REVERT: B 156 MET cc_start: 0.7409 (mmm) cc_final: 0.7144 (mmt) REVERT: B 242 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7801 (mt-10) REVERT: B 336 ARG cc_start: 0.8441 (tpp80) cc_final: 0.8216 (ttp-170) REVERT: B 343 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8549 (mp0) REVERT: B 388 TYR cc_start: 0.6964 (m-80) cc_final: 0.5908 (m-80) REVERT: B 415 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7759 (ptmt) REVERT: B 416 MET cc_start: 0.8509 (mtm) cc_final: 0.7587 (mtm) REVERT: B 477 ILE cc_start: 0.9531 (mt) cc_final: 0.9330 (mp) REVERT: B 834 MET cc_start: 0.7463 (ppp) cc_final: 0.7191 (ttt) REVERT: B 857 LYS cc_start: 0.9495 (tttt) cc_final: 0.9265 (ttmm) REVERT: B 878 THR cc_start: 0.8978 (m) cc_final: 0.8640 (p) REVERT: B 885 SER cc_start: 0.9117 (t) cc_final: 0.8840 (p) REVERT: C 13 ASP cc_start: 0.8536 (m-30) cc_final: 0.8312 (m-30) outliers start: 50 outliers final: 38 residues processed: 232 average time/residue: 0.2575 time to fit residues: 88.1810 Evaluate side-chains 231 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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 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 319 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 373 LYS 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 743 THR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 81 LEU 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 339 ASN Chi-restraints excluded: chain B residue 401 LEU 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 846 GLN Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 9 LYS 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 62 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.122895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.097591 restraints weight = 30633.449| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.70 r_work: 0.3467 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14226 Z= 0.210 Angle : 0.726 15.430 19339 Z= 0.363 Chirality : 0.049 0.249 2118 Planarity : 0.005 0.042 2475 Dihedral : 7.457 58.588 2258 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.36 % Favored : 91.58 % Rotamer: Outliers : 2.91 % Allowed : 19.34 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1674 helix: -0.82 (0.40), residues: 172 sheet: -0.46 (0.29), residues: 312 loop : -1.01 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 79 HIS 0.006 0.001 HIS B 699 PHE 0.023 0.001 PHE C 61 TYR 0.030 0.002 TYR A 391 ARG 0.009 0.001 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 14) link_NAG-ASN : angle 3.24945 ( 42) link_BETA1-4 : bond 0.01571 ( 4) link_BETA1-4 : angle 4.42389 ( 12) hydrogen bonds : bond 0.03539 ( 346) hydrogen bonds : angle 6.30411 ( 894) SS BOND : bond 0.00481 ( 37) SS BOND : angle 1.38167 ( 74) covalent geometry : bond 0.00475 (14171) covalent geometry : angle 0.69868 (19211) *********************** 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 230 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 1.464 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: A 340 ILE cc_start: 0.8929 (tp) cc_final: 0.8538 (pt) REVERT: A 373 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8260 (mtmm) REVERT: A 461 ASP cc_start: 0.8321 (m-30) cc_final: 0.7848 (m-30) REVERT: A 494 THR cc_start: 0.8985 (p) cc_final: 0.8754 (p) REVERT: A 586 ASP cc_start: 0.8781 (p0) cc_final: 0.8453 (p0) REVERT: A 602 ASN cc_start: 0.9096 (m-40) cc_final: 0.8749 (m-40) REVERT: A 643 TYR cc_start: 0.8061 (p90) cc_final: 0.7510 (p90) REVERT: A 704 VAL cc_start: 0.8776 (m) cc_final: 0.8486 (p) REVERT: A 754 ASN cc_start: 0.8298 (m-40) cc_final: 0.7815 (p0) REVERT: A 822 TRP cc_start: 0.8236 (p90) cc_final: 0.7132 (p90) REVERT: A 847 ARG cc_start: 0.8151 (tpp80) cc_final: 0.7944 (mmm-85) REVERT: A 848 GLU cc_start: 0.8281 (tp30) cc_final: 0.7784 (tp30) REVERT: B 156 MET cc_start: 0.7523 (mmm) cc_final: 0.7228 (mmp) REVERT: B 242 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7739 (mt-10) REVERT: B 336 ARG cc_start: 0.8538 (tpp80) cc_final: 0.8240 (ttp-170) REVERT: B 343 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8541 (mp0) REVERT: B 388 TYR cc_start: 0.7125 (m-80) cc_final: 0.6483 (m-80) REVERT: B 416 MET cc_start: 0.8685 (mtm) cc_final: 0.8056 (mtm) REVERT: B 857 LYS cc_start: 0.9485 (tttt) cc_final: 0.9269 (ttmm) REVERT: C 13 ASP cc_start: 0.8568 (m-30) cc_final: 0.8341 (m-30) outliers start: 44 outliers final: 38 residues processed: 220 average time/residue: 0.2463 time to fit residues: 79.6065 Evaluate side-chains 218 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 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 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 401 LEU 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 845 ASP Chi-restraints excluded: chain B residue 846 GLN Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 9 LYS 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 62 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 113 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 146 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.125045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.100061 restraints weight = 30630.629| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.73 r_work: 0.3511 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14226 Z= 0.136 Angle : 0.697 17.287 19339 Z= 0.348 Chirality : 0.048 0.248 2118 Planarity : 0.004 0.041 2475 Dihedral : 7.285 58.610 2258 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 2.38 % Allowed : 20.46 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.20), residues: 1674 helix: -1.06 (0.39), residues: 179 sheet: -0.51 (0.29), residues: 316 loop : -1.04 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 79 HIS 0.004 0.001 HIS B 699 PHE 0.017 0.001 PHE C 61 TYR 0.025 0.001 TYR A 391 ARG 0.010 0.000 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 14) link_NAG-ASN : angle 3.12481 ( 42) link_BETA1-4 : bond 0.01664 ( 4) link_BETA1-4 : angle 4.18788 ( 12) hydrogen bonds : bond 0.03397 ( 346) hydrogen bonds : angle 6.22575 ( 894) SS BOND : bond 0.00339 ( 37) SS BOND : angle 1.04745 ( 74) covalent geometry : bond 0.00304 (14171) covalent geometry : angle 0.67237 (19211) ********************** 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 230 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 1.473 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 91 GLU cc_start: 0.8052 (mp0) cc_final: 0.7764 (mp0) REVERT: A 373 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8248 (mtmm) REVERT: A 461 ASP cc_start: 0.8375 (m-30) cc_final: 0.7888 (m-30) REVERT: A 494 THR cc_start: 0.8946 (p) cc_final: 0.8676 (p) REVERT: A 586 ASP cc_start: 0.8778 (p0) cc_final: 0.8413 (p0) REVERT: A 602 ASN cc_start: 0.9022 (m-40) cc_final: 0.8663 (m-40) REVERT: A 643 TYR cc_start: 0.8068 (p90) cc_final: 0.7538 (p90) REVERT: A 704 VAL cc_start: 0.8790 (m) cc_final: 0.8485 (p) REVERT: A 847 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7924 (mmm-85) REVERT: A 848 GLU cc_start: 0.8294 (tp30) cc_final: 0.7700 (tp30) REVERT: B 156 MET cc_start: 0.7448 (mmm) cc_final: 0.7161 (mmt) REVERT: B 242 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7664 (mt-10) REVERT: B 336 ARG cc_start: 0.8417 (tpp80) cc_final: 0.8087 (ttp-170) REVERT: B 343 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8530 (mp0) REVERT: B 857 LYS cc_start: 0.9475 (tttt) cc_final: 0.9249 (ttmm) REVERT: C 13 ASP cc_start: 0.8607 (m-30) cc_final: 0.8392 (m-30) outliers start: 36 outliers final: 34 residues processed: 221 average time/residue: 0.2492 time to fit residues: 81.1237 Evaluate side-chains 222 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 525 ASP 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 191 LYS 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 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 845 ASP Chi-restraints excluded: chain B residue 846 GLN Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 9 LYS 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 62 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 400 GLN B 406 HIS ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.121325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.095705 restraints weight = 30895.238| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.71 r_work: 0.3437 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14226 Z= 0.258 Angle : 0.771 17.528 19339 Z= 0.384 Chirality : 0.050 0.238 2118 Planarity : 0.005 0.042 2475 Dihedral : 7.507 57.047 2258 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.26 % Favored : 90.68 % Rotamer: Outliers : 2.45 % Allowed : 20.53 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.20), residues: 1674 helix: -1.00 (0.39), residues: 177 sheet: -0.45 (0.29), residues: 311 loop : -1.11 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 404 HIS 0.006 0.001 HIS B 699 PHE 0.026 0.002 PHE C 61 TYR 0.032 0.002 TYR A 391 ARG 0.010 0.001 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 14) link_NAG-ASN : angle 3.21798 ( 42) link_BETA1-4 : bond 0.01371 ( 4) link_BETA1-4 : angle 4.40654 ( 12) hydrogen bonds : bond 0.03701 ( 346) hydrogen bonds : angle 6.26476 ( 894) SS BOND : bond 0.00632 ( 37) SS BOND : angle 1.43918 ( 74) covalent geometry : bond 0.00584 (14171) covalent geometry : angle 0.74501 (19211) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7494.59 seconds wall clock time: 130 minutes 18.24 seconds (7818.24 seconds total)