Starting phenix.real_space_refine on Thu Jul 31 23:11:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tan_41138/07_2025/8tan_41138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tan_41138/07_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_41138/07_2025/8tan_41138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tan_41138/07_2025/8tan_41138.map" model { file = "/net/cci-nas-00/data/ceres_data/8tan_41138/07_2025/8tan_41138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tan_41138/07_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.45, per 1000 atoms: 0.61 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: 4.69 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: 2.02 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: 5.69 Time building geometry restraints manager: 4.73 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: 0.590 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.940 Find NCS groups from input model: 0.560 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.130 ------------------------------------------------------------------------------- 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 : 1.631 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: 0.3360 time to fit residues: 215.5208 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 : 1.849 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.127068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.101991 restraints weight = 30410.987| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.69 r_work: 0.3598 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- 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 : 1.536 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: 0.8758 (m-40) cc_final: 0.8349 (t0) REVERT: A 373 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8465 (mtmm) REVERT: A 429 ILE cc_start: 0.7880 (pt) cc_final: 0.7664 (mt) REVERT: A 477 ILE cc_start: 0.9004 (tt) cc_final: 0.8706 (mm) REVERT: A 494 THR cc_start: 0.8842 (p) cc_final: 0.8592 (p) REVERT: A 558 MET cc_start: 0.7578 (ttm) cc_final: 0.6752 (ttm) REVERT: A 586 ASP cc_start: 0.8670 (p0) cc_final: 0.8114 (p0) REVERT: A 602 ASN cc_start: 0.8979 (m-40) cc_final: 0.8723 (m-40) REVERT: A 617 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7230 (ttm170) REVERT: A 642 LYS cc_start: 0.8902 (mttt) cc_final: 0.8688 (mmtt) REVERT: A 643 TYR cc_start: 0.8072 (p90) cc_final: 0.7555 (p90) REVERT: A 704 VAL cc_start: 0.8775 (m) cc_final: 0.8514 (p) REVERT: A 754 ASN cc_start: 0.8074 (m-40) cc_final: 0.7726 (p0) REVERT: A 820 LEU cc_start: 0.9292 (mt) cc_final: 0.9038 (mm) REVERT: A 822 TRP cc_start: 0.7864 (p90) cc_final: 0.7277 (p90) REVERT: A 848 GLU cc_start: 0.7830 (tp30) cc_final: 0.7518 (tp30) REVERT: A 850 VAL cc_start: 0.8590 (t) cc_final: 0.8378 (t) REVERT: B 79 TRP cc_start: 0.7918 (t60) cc_final: 0.7590 (t60) REVERT: B 156 MET cc_start: 0.7579 (mmm) cc_final: 0.7059 (mtp) REVERT: B 174 ARG cc_start: 0.6611 (ptt90) cc_final: 0.5222 (ptt90) REVERT: B 388 TYR cc_start: 0.6513 (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: 0.8796 (mtm) cc_final: 0.8447 (mtp) REVERT: B 476 ILE cc_start: 0.9053 (mt) cc_final: 0.8776 (mt) REVERT: B 572 LEU cc_start: 0.8669 (tp) cc_final: 0.8391 (tt) REVERT: B 686 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8399 (mt-10) REVERT: B 824 GLU cc_start: 0.8327 (tt0) cc_final: 0.8057 (tp30) REVERT: B 835 TYR cc_start: 0.8286 (m-80) cc_final: 0.7607 (m-80) REVERT: B 857 LYS cc_start: 0.9365 (tttt) cc_final: 0.9103 (ttmm) outliers start: 54 outliers final: 23 residues processed: 294 average time/residue: 0.2860 time to fit residues: 122.1135 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 : 1.591 ------------------------------------------------------------------------------- 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: 3.9990 chunk 156 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 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 = 0.4127 r_free = 0.4127 target = 0.125727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.100535 restraints weight = 30779.535| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.70 r_work: 0.3590 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14226 Z= 0.174 Angle : 0.730 10.846 19339 Z= 0.373 Chirality : 0.050 0.269 2118 Planarity : 0.004 0.048 2475 Dihedral : 9.006 62.845 2268 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.77 % Rotamer: Outliers : 3.31 % Allowed : 15.23 % Favored : 81.46 % 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 0.017 0.002 PHE C 61 TYR 0.018 0.002 TYR A 391 ARG 0.013 0.001 ARG A 565 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 14) link_NAG-ASN : angle 3.46225 ( 42) link_BETA1-4 : bond 0.02036 ( 4) link_BETA1-4 : angle 4.75276 ( 12) hydrogen bonds : bond 0.04054 ( 346) hydrogen bonds : angle 6.66415 ( 894) SS BOND : bond 0.00547 ( 37) SS BOND : angle 1.58406 ( 74) covalent geometry : bond 0.00383 (14171) covalent geometry : angle 0.69731 (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 272 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 1.546 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: 0.8466 (OUTLIER) cc_final: 0.8029 (ttp) REVERT: A 384 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7806 (mp) REVERT: A 461 ASP cc_start: 0.8120 (m-30) cc_final: 0.7697 (m-30) REVERT: A 494 THR cc_start: 0.8837 (p) cc_final: 0.8609 (p) REVERT: A 586 ASP cc_start: 0.8725 (p0) cc_final: 0.8217 (p0) REVERT: A 602 ASN cc_start: 0.8944 (m-40) cc_final: 0.8695 (m-40) REVERT: A 617 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7272 (ttm170) REVERT: A 642 LYS cc_start: 0.8942 (mttt) cc_final: 0.8732 (mmtt) REVERT: A 643 TYR cc_start: 0.8071 (p90) cc_final: 0.7536 (p90) REVERT: A 681 LYS cc_start: 0.8843 (mttp) cc_final: 0.8610 (mptt) REVERT: A 704 VAL cc_start: 0.8775 (m) cc_final: 0.8494 (p) REVERT: A 820 LEU cc_start: 0.9288 (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: 0.7993 (tp30) cc_final: 0.7677 (tp30) REVERT: B 156 MET cc_start: 0.7587 (mmm) cc_final: 0.7027 (mtt) REVERT: B 174 ARG cc_start: 0.6643 (ptt90) cc_final: 0.5171 (ptt90) REVERT: B 270 ASP cc_start: 0.7868 (t0) cc_final: 0.7622 (t0) REVERT: B 309 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8240 (tttm) REVERT: B 388 TYR cc_start: 0.6540 (m-80) cc_final: 0.6020 (m-80) REVERT: B 415 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7895 (ptmt) REVERT: B 416 MET cc_start: 0.8552 (mtm) cc_final: 0.8294 (mtp) REVERT: B 477 ILE cc_start: 0.9359 (mt) cc_final: 0.9145 (mp) REVERT: B 572 LEU cc_start: 0.8738 (tp) cc_final: 0.8391 (tt) REVERT: B 686 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8406 (mt-10) REVERT: B 835 TYR cc_start: 0.8390 (m-80) cc_final: 0.7879 (m-80) REVERT: B 855 TYR cc_start: 0.8028 (t80) cc_final: 0.7434 (t80) REVERT: B 857 LYS cc_start: 0.9368 (tttt) cc_final: 0.9061 (ttmm) outliers start: 50 outliers final: 31 residues processed: 255 average time/residue: 0.2689 time to fit residues: 99.7326 Evaluate side-chains 232 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 107 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.126150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.101262 restraints weight = 30460.089| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 3.64 r_work: 0.3593 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14226 Z= 0.148 Angle : 0.712 10.958 19339 Z= 0.361 Chirality : 0.049 0.260 2118 Planarity : 0.004 0.046 2475 Dihedral : 8.376 59.943 2264 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.77 % Rotamer: Outliers : 3.77 % Allowed : 16.69 % Favored : 79.54 % 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: -1.48 (0.20), residues: 1674 helix: -1.48 (0.36), residues: 183 sheet: -0.55 (0.28), residues: 327 loop : -1.05 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 822 HIS 0.015 0.001 HIS A 563 PHE 0.014 0.001 PHE A 694 TYR 0.017 0.002 TYR A 391 ARG 0.010 0.001 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00725 ( 14) link_NAG-ASN : angle 3.41433 ( 42) link_BETA1-4 : bond 0.01982 ( 4) link_BETA1-4 : angle 4.65467 ( 12) hydrogen bonds : bond 0.03749 ( 346) hydrogen bonds : angle 6.49035 ( 894) SS BOND : bond 0.00391 ( 37) SS BOND : angle 1.27581 ( 74) covalent geometry : bond 0.00327 (14171) covalent geometry : angle 0.68222 (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 266 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 1.513 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: 0.8431 (OUTLIER) cc_final: 0.8015 (ttp) REVERT: A 385 GLU cc_start: 0.7824 (pm20) cc_final: 0.7596 (pm20) REVERT: A 461 ASP cc_start: 0.8065 (m-30) cc_final: 0.7743 (m-30) REVERT: A 494 THR cc_start: 0.8834 (p) cc_final: 0.8616 (p) REVERT: A 586 ASP cc_start: 0.8728 (p0) cc_final: 0.8272 (p0) REVERT: A 602 ASN cc_start: 0.8934 (m-40) cc_final: 0.8680 (m-40) REVERT: A 617 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7372 (ttm170) REVERT: A 643 TYR cc_start: 0.8023 (p90) cc_final: 0.7472 (p90) REVERT: A 704 VAL cc_start: 0.8784 (m) cc_final: 0.8498 (p) REVERT: A 833 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8483 (pt) REVERT: A 848 GLU cc_start: 0.8036 (tp30) cc_final: 0.7704 (tp30) REVERT: B 156 MET cc_start: 0.7568 (mmm) cc_final: 0.7127 (mmp) REVERT: B 174 ARG cc_start: 0.6460 (ptt90) cc_final: 0.5179 (ptt90) REVERT: B 270 ASP cc_start: 0.7848 (t0) cc_final: 0.7551 (t0) REVERT: B 388 TYR cc_start: 0.6587 (m-80) cc_final: 0.6078 (m-80) REVERT: B 415 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7937 (ptmt) REVERT: B 416 MET cc_start: 0.8459 (mtm) cc_final: 0.8213 (mtp) REVERT: B 686 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8395 (mt-10) REVERT: B 789 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8212 (t0) REVERT: B 857 LYS cc_start: 0.9373 (tttt) cc_final: 0.9122 (ttmm) REVERT: B 885 SER cc_start: 0.9151 (t) cc_final: 0.8900 (p) outliers start: 57 outliers final: 30 residues processed: 247 average time/residue: 0.2630 time to fit residues: 93.9421 Evaluate side-chains 233 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 40 optimal weight: 0.4980 chunk 132 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.126462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.100731 restraints weight = 30873.073| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.71 r_work: 0.3563 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14226 Z= 0.200 Angle : 0.718 11.763 19339 Z= 0.363 Chirality : 0.049 0.271 2118 Planarity : 0.004 0.041 2475 Dihedral : 8.163 59.851 2262 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.47 % Favored : 92.47 % Rotamer: Outliers : 3.71 % Allowed : 17.28 % Favored : 79.01 % 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: -1.46 (0.20), residues: 1674 helix: -1.36 (0.36), residues: 183 sheet: -0.51 (0.29), residues: 315 loop : -1.07 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 618 HIS 0.009 0.001 HIS B 699 PHE 0.022 0.002 PHE C 61 TYR 0.029 0.002 TYR A 835 ARG 0.007 0.000 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 14) link_NAG-ASN : angle 3.43498 ( 42) link_BETA1-4 : bond 0.01778 ( 4) link_BETA1-4 : angle 4.67745 ( 12) hydrogen bonds : bond 0.03618 ( 346) hydrogen bonds : angle 6.43216 ( 894) SS BOND : bond 0.00485 ( 37) SS BOND : angle 1.38086 ( 74) covalent geometry : bond 0.00448 (14171) covalent geometry : angle 0.68713 (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: 56 poor density : 209 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ARG cc_start: 0.8223 (mtm110) cc_final: 0.7644 (mtp-110) REVERT: A 319 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8202 (ttp) REVERT: A 461 ASP cc_start: 0.8169 (m-30) cc_final: 0.7810 (m-30) REVERT: A 494 THR cc_start: 0.8874 (p) cc_final: 0.8640 (p) REVERT: A 586 ASP cc_start: 0.8785 (p0) cc_final: 0.8364 (p0) REVERT: A 602 ASN cc_start: 0.9054 (m-40) cc_final: 0.8745 (m-40) REVERT: A 617 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7462 (tpp80) REVERT: A 643 TYR cc_start: 0.8096 (p90) cc_final: 0.7635 (p90) REVERT: A 704 VAL cc_start: 0.8827 (m) cc_final: 0.8530 (p) REVERT: A 754 ASN cc_start: 0.8276 (m-40) cc_final: 0.7865 (p0) REVERT: A 848 GLU cc_start: 0.8219 (tp30) cc_final: 0.7776 (tp30) REVERT: A 857 LYS cc_start: 0.8899 (mttp) cc_final: 0.8685 (mttp) REVERT: B 156 MET cc_start: 0.7559 (mmm) cc_final: 0.7091 (mmm) REVERT: B 174 ARG cc_start: 0.6443 (ptt90) cc_final: 0.5141 (ptt90) REVERT: B 270 ASP cc_start: 0.7949 (t0) cc_final: 0.7606 (t0) REVERT: B 374 ASN cc_start: 0.8850 (m110) cc_final: 0.8221 (t0) REVERT: B 388 TYR cc_start: 0.6767 (m-80) cc_final: 0.6075 (m-80) REVERT: B 415 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7980 (ttpt) REVERT: B 416 MET cc_start: 0.8621 (mtm) cc_final: 0.8380 (mtp) REVERT: B 686 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8422 (mt-10) REVERT: B 789 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8246 (t0) REVERT: B 835 TYR cc_start: 0.8238 (m-80) cc_final: 0.7770 (m-80) REVERT: B 857 LYS cc_start: 0.9384 (tttt) cc_final: 0.9146 (ttmm) outliers start: 56 outliers final: 39 residues processed: 246 average time/residue: 0.2721 time to fit residues: 96.4856 Evaluate side-chains 234 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 1.527 ------------------------------------------------------------------------------- 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 289 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 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 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 178 THR Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 154 optimal weight: 8.9990 chunk 7 optimal weight: 0.4980 chunk 23 optimal weight: 0.0030 chunk 49 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 148 optimal weight: 0.3980 chunk 158 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 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 = 0.122882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.097444 restraints weight = 30972.841| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.70 r_work: 0.3457 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14226 Z= 0.217 Angle : 0.724 11.025 19339 Z= 0.367 Chirality : 0.050 0.256 2118 Planarity : 0.005 0.066 2475 Dihedral : 8.102 58.700 2262 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.42 % Favored : 91.52 % Rotamer: Outliers : 3.91 % Allowed : 17.48 % Favored : 78.61 % 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: -1.13 (0.38), residues: 176 sheet: -0.54 (0.29), residues: 321 loop : -1.06 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 618 HIS 0.007 0.001 HIS B 699 PHE 0.024 0.002 PHE C 61 TYR 0.020 0.002 TYR A 391 ARG 0.009 0.001 ARG A 104 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 14) link_NAG-ASN : angle 3.44800 ( 42) link_BETA1-4 : bond 0.01822 ( 4) link_BETA1-4 : angle 4.63278 ( 12) hydrogen bonds : bond 0.03540 ( 346) hydrogen bonds : angle 6.38090 ( 894) SS BOND : bond 0.00528 ( 37) SS BOND : angle 1.39184 ( 74) covalent geometry : bond 0.00486 (14171) covalent geometry : angle 0.69340 (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 260 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 201 time to evaluate : 2.215 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: 0.8555 (OUTLIER) cc_final: 0.8255 (ttp) REVERT: A 412 LYS cc_start: 0.8602 (tmtt) cc_final: 0.8370 (tptp) REVERT: A 461 ASP cc_start: 0.8403 (m-30) cc_final: 0.7871 (m-30) REVERT: A 494 THR cc_start: 0.8894 (p) cc_final: 0.8642 (p) REVERT: A 586 ASP cc_start: 0.8748 (p0) cc_final: 0.8353 (p0) REVERT: A 602 ASN cc_start: 0.9061 (m-40) cc_final: 0.8695 (m-40) REVERT: A 643 TYR cc_start: 0.8111 (p90) cc_final: 0.7589 (p90) REVERT: A 704 VAL cc_start: 0.8761 (m) cc_final: 0.8440 (p) REVERT: A 822 TRP cc_start: 0.8205 (p90) cc_final: 0.7457 (p90) REVERT: A 848 GLU cc_start: 0.8237 (tp30) cc_final: 0.7783 (tp30) REVERT: A 857 LYS cc_start: 0.8930 (mttp) cc_final: 0.8701 (mttp) REVERT: B 156 MET cc_start: 0.7492 (mmm) cc_final: 0.7214 (mmt) REVERT: B 174 ARG cc_start: 0.6394 (ptt90) cc_final: 0.5012 (ptt90) REVERT: B 270 ASP cc_start: 0.8062 (t0) cc_final: 0.7678 (t0) REVERT: B 336 ARG cc_start: 0.8383 (tpp80) cc_final: 0.8029 (ttp-170) REVERT: B 374 ASN cc_start: 0.8933 (m110) cc_final: 0.8287 (t0) REVERT: B 388 TYR cc_start: 0.6888 (m-80) cc_final: 0.5735 (m-80) REVERT: B 393 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8364 (mt) REVERT: B 415 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7804 (ptmt) REVERT: B 416 MET cc_start: 0.8572 (mtm) cc_final: 0.8211 (mtp) REVERT: B 789 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8209 (t0) REVERT: B 835 TYR cc_start: 0.8237 (m-80) cc_final: 0.7791 (m-80) REVERT: B 857 LYS cc_start: 0.9487 (tttt) cc_final: 0.9224 (ttmm) outliers start: 59 outliers final: 37 residues processed: 243 average time/residue: 0.3567 time to fit residues: 129.6815 Evaluate side-chains 228 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 1.730 ------------------------------------------------------------------------------- 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 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 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 168 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 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 393 LEU Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 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 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: 3.9990 chunk 119 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 148 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 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 = 0.4045 r_free = 0.4045 target = 0.123464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.098115 restraints weight = 30829.914| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.70 r_work: 0.3473 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14226 Z= 0.171 Angle : 0.704 12.668 19339 Z= 0.353 Chirality : 0.049 0.251 2118 Planarity : 0.005 0.064 2475 Dihedral : 7.758 59.326 2258 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.71 % Favored : 92.23 % Rotamer: Outliers : 3.58 % Allowed : 18.28 % Favored : 78.15 % 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: -1.42 (0.20), residues: 1674 helix: -1.16 (0.38), residues: 176 sheet: -0.52 (0.29), residues: 318 loop : -1.06 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 618 HIS 0.005 0.001 HIS B 699 PHE 0.021 0.001 PHE C 61 TYR 0.018 0.002 TYR A 391 ARG 0.011 0.001 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 14) link_NAG-ASN : angle 3.35167 ( 42) link_BETA1-4 : bond 0.01708 ( 4) link_BETA1-4 : angle 4.45964 ( 12) hydrogen bonds : bond 0.03382 ( 346) hydrogen bonds : angle 6.32769 ( 894) SS BOND : bond 0.00417 ( 37) SS BOND : angle 1.24892 ( 74) covalent geometry : bond 0.00384 (14171) covalent geometry : angle 0.67566 (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 253 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 1.552 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: A 319 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8271 (ttp) REVERT: A 412 LYS cc_start: 0.8592 (tmtt) cc_final: 0.8365 (tptp) REVERT: A 461 ASP cc_start: 0.8394 (m-30) cc_final: 0.7913 (m-30) REVERT: A 494 THR cc_start: 0.8937 (p) cc_final: 0.8692 (p) REVERT: A 586 ASP cc_start: 0.8754 (p0) cc_final: 0.8380 (p0) REVERT: A 600 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8748 (ptpt) REVERT: A 602 ASN cc_start: 0.9053 (m-40) cc_final: 0.8698 (m-40) REVERT: A 643 TYR cc_start: 0.8115 (p90) cc_final: 0.7587 (p90) REVERT: A 687 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8572 (tm-30) REVERT: A 704 VAL cc_start: 0.8757 (m) cc_final: 0.8442 (p) REVERT: A 822 TRP cc_start: 0.8224 (p90) cc_final: 0.7013 (p90) REVERT: A 848 GLU cc_start: 0.8295 (tp30) cc_final: 0.7834 (tp30) REVERT: B 39 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7444 (t0) REVERT: B 156 MET cc_start: 0.7519 (mmm) cc_final: 0.7230 (mmt) REVERT: B 270 ASP cc_start: 0.8139 (t0) cc_final: 0.7799 (t0) REVERT: B 336 ARG cc_start: 0.8416 (tpp80) cc_final: 0.8051 (ttp-170) REVERT: B 374 ASN cc_start: 0.8917 (m110) cc_final: 0.8285 (t0) REVERT: B 388 TYR cc_start: 0.6862 (m-80) cc_final: 0.6386 (m-80) REVERT: B 416 MET cc_start: 0.8559 (mtm) cc_final: 0.8301 (mtp) REVERT: B 789 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8246 (t0) REVERT: B 835 TYR cc_start: 0.8162 (m-80) cc_final: 0.7806 (m-80) REVERT: B 857 LYS cc_start: 0.9485 (tttt) cc_final: 0.9259 (ttmm) outliers start: 54 outliers final: 41 residues processed: 236 average time/residue: 0.2574 time to fit residues: 89.2676 Evaluate side-chains 234 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 392 VAL Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 39 ASP 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 367 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 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 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: 0.2980 chunk 121 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 ASN ** 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 = 0.4070 r_free = 0.4070 target = 0.125277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.100130 restraints weight = 30606.275| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.73 r_work: 0.3510 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14226 Z= 0.127 Angle : 0.696 14.468 19339 Z= 0.346 Chirality : 0.048 0.252 2118 Planarity : 0.004 0.042 2475 Dihedral : 7.461 59.004 2258 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.11 % Favored : 92.83 % Rotamer: Outliers : 3.11 % Allowed : 19.47 % Favored : 77.42 % 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: -1.32 (0.20), residues: 1674 helix: -0.70 (0.41), residues: 162 sheet: -0.54 (0.29), residues: 322 loop : -1.03 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 79 HIS 0.004 0.001 HIS B 699 PHE 0.019 0.001 PHE C 61 TYR 0.015 0.001 TYR B 835 ARG 0.010 0.001 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 14) link_NAG-ASN : angle 3.26437 ( 42) link_BETA1-4 : bond 0.01828 ( 4) link_BETA1-4 : angle 4.28905 ( 12) hydrogen bonds : bond 0.03330 ( 346) hydrogen bonds : angle 6.34385 ( 894) SS BOND : bond 0.00609 ( 37) SS BOND : angle 1.09909 ( 74) covalent geometry : bond 0.00277 (14171) covalent geometry : angle 0.66909 (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 253 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 4.068 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: A 319 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8280 (ttp) REVERT: A 412 LYS cc_start: 0.8559 (tmtt) cc_final: 0.8348 (tptp) REVERT: A 461 ASP cc_start: 0.8323 (m-30) cc_final: 0.7819 (m-30) REVERT: A 494 THR cc_start: 0.8904 (p) cc_final: 0.8681 (p) REVERT: A 586 ASP cc_start: 0.8737 (p0) cc_final: 0.8345 (p0) REVERT: A 600 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8682 (ptpt) REVERT: A 602 ASN cc_start: 0.8983 (m-40) cc_final: 0.8627 (m-40) REVERT: A 643 TYR cc_start: 0.8086 (p90) cc_final: 0.7552 (p90) REVERT: A 704 VAL cc_start: 0.8740 (m) cc_final: 0.8434 (p) REVERT: A 822 TRP cc_start: 0.8228 (p90) cc_final: 0.7035 (p90) REVERT: A 848 GLU cc_start: 0.8348 (tp30) cc_final: 0.7854 (tp30) REVERT: B 39 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7427 (t0) REVERT: B 81 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8017 (mp) REVERT: B 156 MET cc_start: 0.7394 (mmm) cc_final: 0.7124 (mmt) REVERT: B 270 ASP cc_start: 0.8254 (t0) cc_final: 0.7955 (t0) REVERT: B 336 ARG cc_start: 0.8427 (tpp80) cc_final: 0.8085 (ttp-170) REVERT: B 343 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8559 (mp0) REVERT: B 374 ASN cc_start: 0.8903 (m110) cc_final: 0.8275 (t0) REVERT: B 477 ILE cc_start: 0.9520 (mt) cc_final: 0.9309 (mp) REVERT: B 857 LYS cc_start: 0.9482 (tttt) cc_final: 0.9262 (ttmm) REVERT: B 885 SER cc_start: 0.9126 (t) cc_final: 0.8850 (p) REVERT: C 60 LYS cc_start: 0.8758 (tttt) cc_final: 0.8543 (tttp) outliers start: 47 outliers final: 36 residues processed: 239 average time/residue: 0.3983 time to fit residues: 141.2245 Evaluate side-chains 230 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 392 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 600 LYS 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 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 39 ASP 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 339 ASN Chi-restraints excluded: chain B residue 348 MET 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 704 VAL 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 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 86 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 778 HIS ** 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 = 0.4054 r_free = 0.4054 target = 0.124070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.098919 restraints weight = 30524.508| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.70 r_work: 0.3490 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14226 Z= 0.163 Angle : 0.707 13.532 19339 Z= 0.350 Chirality : 0.048 0.252 2118 Planarity : 0.004 0.045 2475 Dihedral : 7.383 58.948 2258 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.89 % Favored : 92.05 % Rotamer: Outliers : 3.11 % Allowed : 19.80 % Favored : 77.09 % 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: -1.31 (0.20), residues: 1674 helix: -0.80 (0.40), residues: 169 sheet: -0.48 (0.29), residues: 312 loop : -1.02 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 79 HIS 0.005 0.001 HIS B 699 PHE 0.020 0.001 PHE C 61 TYR 0.022 0.002 TYR A 391 ARG 0.009 0.001 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 14) link_NAG-ASN : angle 3.23114 ( 42) link_BETA1-4 : bond 0.01629 ( 4) link_BETA1-4 : angle 4.30781 ( 12) hydrogen bonds : bond 0.03331 ( 346) hydrogen bonds : angle 6.23955 ( 894) SS BOND : bond 0.00385 ( 37) SS BOND : angle 1.15888 ( 74) covalent geometry : bond 0.00371 (14171) covalent geometry : angle 0.68091 (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 242 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 1.541 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: A 430 TYR cc_start: 0.9038 (m-10) cc_final: 0.8793 (m-80) REVERT: A 461 ASP cc_start: 0.8387 (m-30) cc_final: 0.7851 (m-30) REVERT: A 494 THR cc_start: 0.9018 (p) cc_final: 0.8800 (p) REVERT: A 586 ASP cc_start: 0.8731 (p0) cc_final: 0.8366 (p0) REVERT: A 600 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8730 (ptpt) REVERT: A 602 ASN cc_start: 0.9060 (m-40) cc_final: 0.8705 (m-40) REVERT: A 643 TYR cc_start: 0.8085 (p90) cc_final: 0.7584 (p90) REVERT: A 704 VAL cc_start: 0.8782 (m) cc_final: 0.8460 (p) REVERT: A 754 ASN cc_start: 0.8260 (m-40) cc_final: 0.7797 (p0) REVERT: A 848 GLU cc_start: 0.8384 (tp30) cc_final: 0.7887 (tp30) REVERT: B 39 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7420 (t0) REVERT: B 81 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8057 (mp) REVERT: B 156 MET cc_start: 0.7443 (mmm) cc_final: 0.7142 (mmp) REVERT: B 336 ARG cc_start: 0.8545 (tpp80) cc_final: 0.8214 (ttp-170) REVERT: B 343 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8553 (mp0) REVERT: B 374 ASN cc_start: 0.8922 (m110) cc_final: 0.8322 (t0) REVERT: B 857 LYS cc_start: 0.9482 (tttt) cc_final: 0.9269 (ttmm) REVERT: C 60 LYS cc_start: 0.8801 (tttt) cc_final: 0.8374 (tttp) outliers start: 47 outliers final: 38 residues processed: 226 average time/residue: 0.2551 time to fit residues: 84.6926 Evaluate side-chains 233 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 600 LYS 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 A residue 834 MET Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 39 ASP 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 348 MET 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 583 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 704 VAL 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 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 113 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 146 optimal weight: 0.0170 chunk 4 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 623 GLN B 400 GLN B 406 HIS ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.125821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.100821 restraints weight = 30600.900| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.74 r_work: 0.3528 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14226 Z= 0.125 Angle : 0.704 16.319 19339 Z= 0.348 Chirality : 0.048 0.248 2118 Planarity : 0.004 0.041 2475 Dihedral : 7.223 59.601 2258 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.93 % Favored : 93.01 % Rotamer: Outliers : 2.58 % Allowed : 20.53 % Favored : 76.89 % 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: -1.34 (0.20), residues: 1674 helix: -0.82 (0.40), residues: 171 sheet: -0.48 (0.29), residues: 319 loop : -1.05 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 404 HIS 0.004 0.001 HIS B 699 PHE 0.016 0.001 PHE C 61 TYR 0.019 0.001 TYR A 893 ARG 0.010 0.000 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 14) link_NAG-ASN : angle 3.13092 ( 42) link_BETA1-4 : bond 0.01659 ( 4) link_BETA1-4 : angle 4.14301 ( 12) hydrogen bonds : bond 0.03290 ( 346) hydrogen bonds : angle 6.18865 ( 894) SS BOND : bond 0.00321 ( 37) SS BOND : angle 1.01846 ( 74) covalent geometry : bond 0.00279 (14171) covalent geometry : angle 0.67978 (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 245 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 1.508 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 91 GLU cc_start: 0.8035 (mp0) cc_final: 0.7704 (mp0) REVERT: A 461 ASP cc_start: 0.8340 (m-30) cc_final: 0.7879 (m-30) REVERT: A 494 THR cc_start: 0.8969 (p) cc_final: 0.8745 (p) REVERT: A 586 ASP cc_start: 0.8717 (p0) cc_final: 0.8352 (p0) REVERT: A 600 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8668 (ptpt) REVERT: A 602 ASN cc_start: 0.8973 (m-40) cc_final: 0.8639 (m-40) REVERT: A 643 TYR cc_start: 0.8027 (p90) cc_final: 0.7520 (p90) REVERT: A 848 GLU cc_start: 0.8352 (tp30) cc_final: 0.7828 (tp30) REVERT: B 39 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7444 (t0) REVERT: B 156 MET cc_start: 0.7389 (mmm) cc_final: 0.7094 (mmp) REVERT: B 336 ARG cc_start: 0.8350 (tpp80) cc_final: 0.8031 (ttp-170) REVERT: B 343 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8528 (mp0) REVERT: B 374 ASN cc_start: 0.8909 (m110) cc_final: 0.8284 (t0) REVERT: B 751 ARG cc_start: 0.8192 (ttt90) cc_final: 0.7857 (mtp85) REVERT: B 857 LYS cc_start: 0.9478 (tttt) cc_final: 0.9257 (ttmm) REVERT: B 885 SER cc_start: 0.9096 (t) cc_final: 0.8826 (p) REVERT: C 60 LYS cc_start: 0.8721 (tttt) cc_final: 0.8506 (tttp) outliers start: 39 outliers final: 32 residues processed: 233 average time/residue: 0.2628 time to fit residues: 89.8574 Evaluate side-chains 224 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 348 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 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 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 704 VAL 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 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 96 optimal weight: 0.2980 chunk 73 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** B 339 ASN B 400 GLN ** 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 = 0.4086 r_free = 0.4086 target = 0.126411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.101683 restraints weight = 30704.783| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.74 r_work: 0.3539 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14226 Z= 0.127 Angle : 0.707 16.813 19339 Z= 0.351 Chirality : 0.048 0.247 2118 Planarity : 0.004 0.040 2475 Dihedral : 7.096 59.617 2258 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.23 % Favored : 92.71 % Rotamer: Outliers : 2.58 % Allowed : 21.13 % Favored : 76.29 % 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: -1.32 (0.20), residues: 1674 helix: -0.80 (0.40), residues: 171 sheet: -0.50 (0.29), residues: 322 loop : -1.03 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 404 HIS 0.005 0.001 HIS B 699 PHE 0.020 0.001 PHE C 61 TYR 0.019 0.001 TYR A 391 ARG 0.010 0.000 ARG B 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 14) link_NAG-ASN : angle 3.10209 ( 42) link_BETA1-4 : bond 0.01635 ( 4) link_BETA1-4 : angle 4.08955 ( 12) hydrogen bonds : bond 0.03369 ( 346) hydrogen bonds : angle 6.12823 ( 894) SS BOND : bond 0.00275 ( 37) SS BOND : angle 0.98616 ( 74) covalent geometry : bond 0.00286 (14171) covalent geometry : angle 0.68439 (19211) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8760.43 seconds wall clock time: 158 minutes 20.06 seconds (9500.06 seconds total)