Starting phenix.real_space_refine on Sun Jul 21 09:22:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tan_41138/07_2024/8tan_41138.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tan_41138/07_2024/8tan_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tan_41138/07_2024/8tan_41138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tan_41138/07_2024/8tan_41138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tan_41138/07_2024/8tan_41138.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tan_41138/07_2024/8tan_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 Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 835": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13853 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6674 Classifications: {'peptide': 831} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 783} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 6530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6530 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 765} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 400 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain breaks: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.55, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 5.16 Conformation dependent library (CDL) restraints added in 2.5 seconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3186 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 34 sheets defined 16.4% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 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: 5.04 Time building geometry restraints manager: 5.72 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: 99.36 - 106.31: 446 106.31 - 113.27: 7481 113.27 - 120.22: 5107 120.22 - 127.18: 6011 127.18 - 134.13: 166 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 2.440 nonbonded pdb=" O PRO A 584 " pdb=" ND2 ASN A 789 " model vdw 2.202 2.520 nonbonded pdb=" OE2 GLU B 26 " pdb=" NE ARG B 245 " model vdw 2.254 2.520 nonbonded pdb=" O ASP B 215 " pdb=" OG1 THR B 216 " model vdw 2.294 2.440 nonbonded pdb=" O SER A 313 " pdb=" OG SER A 316 " model vdw 2.321 2.440 ... (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 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: 0.420 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.920 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.510 ------------------------------------------------------------------------------- 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 14171 Z= 0.240 Angle : 0.772 8.551 19211 Z= 0.430 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 *********************** 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 fitting. rotamer outliers: 33 poor density : 434 time to evaluate : 1.640 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: 0.2938 time to fit residues: 186.4250 Evaluate side-chains 257 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 242 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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: 1.9990 chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 86 optimal weight: 0.3980 chunk 68 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 30.0000 chunk 98 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 827 ASN A 876 GLN B 338 ASN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14171 Z= 0.243 Angle : 0.726 8.158 19211 Z= 0.381 Chirality : 0.051 0.254 2118 Planarity : 0.005 0.049 2475 Dihedral : 9.890 69.794 2283 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.83 % Favored : 92.11 % Rotamer: Outliers : 3.84 % Allowed : 13.58 % Favored : 82.58 % 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: -1.58 (0.20), residues: 1674 helix: -1.85 (0.34), residues: 191 sheet: -0.59 (0.28), residues: 331 loop : -1.07 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 618 HIS 0.008 0.001 HIS B 699 PHE 0.014 0.002 PHE B 90 TYR 0.025 0.002 TYR A 628 ARG 0.007 0.001 ARG B 104 *********************** 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 321 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 263 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8674 (m-40) cc_final: 0.8380 (t0) REVERT: A 248 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8418 (p0) REVERT: A 373 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8341 (mtmm) REVERT: A 412 LYS cc_start: 0.8530 (tmtt) cc_final: 0.8165 (tmtt) REVERT: A 477 ILE cc_start: 0.8932 (tt) cc_final: 0.8677 (mm) REVERT: A 494 THR cc_start: 0.8876 (p) cc_final: 0.8613 (p) REVERT: A 558 MET cc_start: 0.7802 (ttm) cc_final: 0.7446 (ttp) REVERT: A 585 LEU cc_start: 0.8791 (mt) cc_final: 0.8574 (mt) REVERT: A 586 ASP cc_start: 0.8697 (p0) cc_final: 0.8091 (p0) REVERT: A 602 ASN cc_start: 0.8939 (m-40) cc_final: 0.8640 (m-40) REVERT: A 617 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7060 (ttm170) REVERT: A 642 LYS cc_start: 0.8958 (mttt) cc_final: 0.8648 (mmtt) REVERT: A 643 TYR cc_start: 0.7851 (p90) cc_final: 0.7336 (p90) REVERT: A 704 VAL cc_start: 0.8727 (m) cc_final: 0.8492 (p) REVERT: A 754 ASN cc_start: 0.8043 (m-40) cc_final: 0.7739 (p0) REVERT: A 820 LEU cc_start: 0.9291 (mt) cc_final: 0.9022 (mm) REVERT: A 822 TRP cc_start: 0.7807 (p90) cc_final: 0.7210 (p90) REVERT: A 848 GLU cc_start: 0.7782 (tp30) cc_final: 0.7465 (tp30) REVERT: A 850 VAL cc_start: 0.8579 (t) cc_final: 0.8357 (t) REVERT: B 36 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8740 (mtmm) REVERT: B 83 TYR cc_start: 0.8589 (t80) cc_final: 0.8207 (t80) REVERT: B 156 MET cc_start: 0.7519 (mmm) cc_final: 0.6941 (mtp) REVERT: B 270 ASP cc_start: 0.8071 (t0) cc_final: 0.7845 (t0) REVERT: B 388 TYR cc_start: 0.6350 (m-80) cc_final: 0.5935 (m-80) REVERT: B 415 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7746 (ptmt) REVERT: B 416 MET cc_start: 0.8772 (mtm) cc_final: 0.8235 (mtp) REVERT: B 432 MET cc_start: 0.8638 (ttt) cc_final: 0.8391 (tpp) REVERT: B 469 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7843 (p) REVERT: B 476 ILE cc_start: 0.9054 (mt) cc_final: 0.8741 (mt) REVERT: B 572 LEU cc_start: 0.8759 (tp) cc_final: 0.8329 (tt) REVERT: B 686 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8213 (mt-10) REVERT: B 751 ARG cc_start: 0.7706 (mtp180) cc_final: 0.7504 (mtp180) REVERT: B 824 GLU cc_start: 0.8327 (tt0) cc_final: 0.8051 (tp30) REVERT: B 835 TYR cc_start: 0.8147 (m-80) cc_final: 0.7407 (m-80) REVERT: B 857 LYS cc_start: 0.9428 (tttt) cc_final: 0.9138 (ttmm) outliers start: 58 outliers final: 27 residues processed: 298 average time/residue: 0.2622 time to fit residues: 112.3865 Evaluate side-chains 248 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 217 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 248 ASP 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 405 ASP Chi-restraints excluded: chain A residue 451 ASN 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 698 LEU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 405 ASP 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 699 HIS Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 888 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 85 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 166 optimal weight: 0.0370 chunk 136 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 HIS B 546 GLN ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN B 846 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14171 Z= 0.253 Angle : 0.684 8.929 19211 Z= 0.356 Chirality : 0.050 0.240 2118 Planarity : 0.004 0.047 2475 Dihedral : 9.055 63.199 2273 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.36 % Favored : 91.58 % Rotamer: Outliers : 4.24 % Allowed : 14.83 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.50 (0.20), residues: 1674 helix: -1.65 (0.35), residues: 188 sheet: -0.54 (0.28), residues: 331 loop : -1.04 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 618 HIS 0.009 0.001 HIS B 699 PHE 0.019 0.002 PHE C 61 TYR 0.020 0.002 TYR A 391 ARG 0.005 0.001 ARG B 376 *********************** 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 291 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 227 time to evaluate : 1.609 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 319 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8008 (ttp) REVERT: A 384 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7704 (mp) REVERT: A 494 THR cc_start: 0.8915 (p) cc_final: 0.8677 (p) REVERT: A 558 MET cc_start: 0.7507 (ttm) cc_final: 0.7239 (ttp) REVERT: A 565 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7827 (mmm-85) REVERT: A 586 ASP cc_start: 0.8708 (p0) cc_final: 0.8144 (p0) REVERT: A 602 ASN cc_start: 0.8932 (m-40) cc_final: 0.8620 (m-40) REVERT: A 617 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.7110 (ttm170) REVERT: A 629 ARG cc_start: 0.7831 (pmt-80) cc_final: 0.7628 (pmt-80) REVERT: A 642 LYS cc_start: 0.8988 (mttt) cc_final: 0.8722 (mmtt) REVERT: A 643 TYR cc_start: 0.7885 (p90) cc_final: 0.7320 (p90) REVERT: A 681 LYS cc_start: 0.8844 (mttp) cc_final: 0.8586 (mptt) REVERT: A 704 VAL cc_start: 0.8744 (m) cc_final: 0.8481 (p) REVERT: A 754 ASN cc_start: 0.8156 (m-40) cc_final: 0.7829 (p0) REVERT: A 820 LEU cc_start: 0.9288 (mt) cc_final: 0.9048 (mm) REVERT: A 833 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8363 (pt) REVERT: B 156 MET cc_start: 0.7596 (mmm) cc_final: 0.7141 (mmp) REVERT: B 270 ASP cc_start: 0.8113 (t0) cc_final: 0.7726 (t0) REVERT: B 309 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8173 (tttm) REVERT: B 388 TYR cc_start: 0.6375 (m-80) cc_final: 0.5789 (m-80) REVERT: B 415 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7713 (ptmt) REVERT: B 416 MET cc_start: 0.8679 (mtm) cc_final: 0.8253 (mtp) REVERT: B 477 ILE cc_start: 0.9436 (mt) cc_final: 0.9184 (mp) REVERT: B 572 LEU cc_start: 0.8852 (tp) cc_final: 0.8477 (tt) REVERT: B 686 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8211 (mt-10) REVERT: B 824 GLU cc_start: 0.8259 (tt0) cc_final: 0.7946 (tp30) REVERT: B 835 TYR cc_start: 0.8287 (m-80) cc_final: 0.7432 (m-80) REVERT: B 857 LYS cc_start: 0.9430 (tttt) cc_final: 0.9100 (ttmm) outliers start: 64 outliers final: 43 residues processed: 268 average time/residue: 0.2634 time to fit residues: 102.5878 Evaluate side-chains 247 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 199 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 237 ASN 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 312 ASP 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 405 ASP 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 776 CYS Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 520 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 677 THR 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 888 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 151 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 14171 Z= 0.522 Angle : 0.815 11.488 19211 Z= 0.419 Chirality : 0.054 0.318 2118 Planarity : 0.005 0.044 2475 Dihedral : 9.028 60.265 2269 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.74 % Favored : 90.20 % Rotamer: Outliers : 5.36 % Allowed : 16.16 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.69 (0.20), residues: 1674 helix: -1.56 (0.36), residues: 188 sheet: -0.68 (0.28), residues: 330 loop : -1.22 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 618 HIS 0.030 0.002 HIS A 563 PHE 0.026 0.002 PHE C 61 TYR 0.027 0.002 TYR A 391 ARG 0.007 0.001 ARG A 174 *********************** 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 282 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 201 time to evaluate : 1.647 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 91 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7603 (mp0) REVERT: A 170 GLU cc_start: 0.8088 (tt0) cc_final: 0.7809 (tt0) REVERT: A 319 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8077 (ttp) REVERT: A 384 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7717 (mp) REVERT: A 412 LYS cc_start: 0.8687 (tmtt) cc_final: 0.8351 (tmtt) REVERT: A 494 THR cc_start: 0.8991 (p) cc_final: 0.8768 (p) REVERT: A 499 GLU cc_start: 0.8048 (tt0) cc_final: 0.7499 (tm-30) REVERT: A 558 MET cc_start: 0.7353 (ttm) cc_final: 0.7046 (ttp) REVERT: A 600 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8656 (pttp) REVERT: A 602 ASN cc_start: 0.9143 (m-40) cc_final: 0.8738 (m-40) REVERT: A 617 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7187 (mtm-85) REVERT: A 643 TYR cc_start: 0.8078 (p90) cc_final: 0.7804 (p90) REVERT: A 689 GLU cc_start: 0.8639 (tp30) cc_final: 0.8425 (tp30) REVERT: A 754 ASN cc_start: 0.8331 (m-40) cc_final: 0.7879 (p0) REVERT: A 833 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8633 (pt) REVERT: A 847 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7732 (mtm180) REVERT: A 871 TYR cc_start: 0.8068 (m-80) cc_final: 0.7735 (m-80) REVERT: B 156 MET cc_start: 0.7671 (mmm) cc_final: 0.7176 (mmp) REVERT: B 270 ASP cc_start: 0.8348 (t0) cc_final: 0.8017 (t0) REVERT: B 374 ASN cc_start: 0.8921 (m110) cc_final: 0.8343 (t0) REVERT: B 388 TYR cc_start: 0.6712 (m-80) cc_final: 0.5403 (m-80) REVERT: B 415 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7748 (ttmt) REVERT: B 416 MET cc_start: 0.8678 (mtm) cc_final: 0.8283 (mtp) REVERT: B 835 TYR cc_start: 0.8435 (m-80) cc_final: 0.8103 (m-80) REVERT: C 9 LYS cc_start: 0.8112 (pttt) cc_final: 0.7906 (pttt) outliers start: 81 outliers final: 56 residues processed: 257 average time/residue: 0.2485 time to fit residues: 94.0703 Evaluate side-chains 244 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 183 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 256 LEU 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 312 ASP Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 LEU 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 405 ASP Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 489 ASP 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 615 ILE 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 788 SER 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 151 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 298 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 520 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 699 HIS Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 2 optimal weight: 0.3980 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN B 846 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14171 Z= 0.193 Angle : 0.673 11.498 19211 Z= 0.346 Chirality : 0.048 0.251 2118 Planarity : 0.004 0.040 2475 Dihedral : 8.298 57.568 2267 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.30 % Allowed : 17.95 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.20), residues: 1674 helix: -1.06 (0.39), residues: 174 sheet: -0.63 (0.28), residues: 326 loop : -1.06 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 79 HIS 0.006 0.001 HIS B 699 PHE 0.021 0.001 PHE C 61 TYR 0.030 0.002 TYR A 835 ARG 0.004 0.000 ARG B 10 *********************** 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 279 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 214 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8100 (ttp) REVERT: A 384 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7450 (mp) REVERT: A 459 GLU cc_start: 0.6895 (pt0) cc_final: 0.6596 (pt0) REVERT: A 494 THR cc_start: 0.8935 (p) cc_final: 0.8696 (p) REVERT: A 558 MET cc_start: 0.7446 (ttm) cc_final: 0.7146 (ttt) REVERT: A 586 ASP cc_start: 0.8798 (p0) cc_final: 0.8339 (p0) REVERT: A 602 ASN cc_start: 0.8962 (m-40) cc_final: 0.8603 (m-40) REVERT: A 617 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7213 (tpp80) REVERT: A 643 TYR cc_start: 0.7988 (p90) cc_final: 0.7432 (p90) REVERT: A 681 LYS cc_start: 0.8954 (mttp) cc_final: 0.8662 (mptt) REVERT: A 689 GLU cc_start: 0.8639 (tp30) cc_final: 0.8327 (tp30) REVERT: A 704 VAL cc_start: 0.8697 (m) cc_final: 0.8491 (p) REVERT: A 847 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7122 (mtp180) REVERT: B 156 MET cc_start: 0.7541 (mmm) cc_final: 0.7072 (mmp) REVERT: B 270 ASP cc_start: 0.8412 (t0) cc_final: 0.8044 (t0) REVERT: B 343 GLU cc_start: 0.8522 (mp0) cc_final: 0.7997 (mp0) REVERT: B 374 ASN cc_start: 0.8897 (m110) cc_final: 0.8268 (t0) REVERT: B 388 TYR cc_start: 0.6650 (m-80) cc_final: 0.5413 (m-80) REVERT: B 415 LYS cc_start: 0.8047 (ttmt) cc_final: 0.7775 (ttpt) REVERT: B 416 MET cc_start: 0.8426 (mtm) cc_final: 0.8127 (mtp) REVERT: B 857 LYS cc_start: 0.9421 (tttt) cc_final: 0.9166 (ttmm) outliers start: 65 outliers final: 38 residues processed: 259 average time/residue: 0.2794 time to fit residues: 105.2064 Evaluate side-chains 235 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 489 ASP 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 788 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 520 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 888 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 0.9990 chunk 147 optimal weight: 0.0870 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 163 optimal weight: 0.0770 chunk 135 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 13 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 chunk 157 optimal weight: 0.0020 overall best weight: 0.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14171 Z= 0.167 Angle : 0.649 11.981 19211 Z= 0.331 Chirality : 0.048 0.253 2118 Planarity : 0.004 0.051 2475 Dihedral : 7.759 58.692 2265 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.51 % Allowed : 19.34 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1674 helix: -0.94 (0.39), residues: 175 sheet: -0.59 (0.29), residues: 318 loop : -1.00 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 79 HIS 0.008 0.001 HIS B 699 PHE 0.020 0.001 PHE C 61 TYR 0.023 0.002 TYR B 835 ARG 0.008 0.000 ARG B 376 *********************** 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 258 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 205 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TRP cc_start: 0.7883 (OUTLIER) cc_final: 0.7592 (t60) REVERT: A 319 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.8048 (ttp) REVERT: A 494 THR cc_start: 0.9014 (p) cc_final: 0.8802 (p) REVERT: A 586 ASP cc_start: 0.8732 (p0) cc_final: 0.8281 (p0) REVERT: A 602 ASN cc_start: 0.8874 (m-40) cc_final: 0.8612 (m-40) REVERT: A 643 TYR cc_start: 0.7888 (p90) cc_final: 0.7455 (p90) REVERT: A 681 LYS cc_start: 0.8875 (mttp) cc_final: 0.8608 (mptt) REVERT: A 704 VAL cc_start: 0.8636 (m) cc_final: 0.8435 (p) REVERT: A 822 TRP cc_start: 0.8156 (p90) cc_final: 0.7403 (p90) REVERT: A 847 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7045 (mtp180) REVERT: B 156 MET cc_start: 0.7482 (mmm) cc_final: 0.7010 (mmp) REVERT: B 170 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7958 (tm-30) REVERT: B 343 GLU cc_start: 0.8504 (mp0) cc_final: 0.8049 (mp0) REVERT: B 374 ASN cc_start: 0.8888 (m110) cc_final: 0.8272 (t0) REVERT: B 388 TYR cc_start: 0.6813 (m-80) cc_final: 0.6087 (m-80) REVERT: B 416 MET cc_start: 0.8490 (mtm) cc_final: 0.8258 (mtp) REVERT: B 857 LYS cc_start: 0.9406 (tttt) cc_final: 0.9206 (ttmm) REVERT: B 885 SER cc_start: 0.9182 (t) cc_final: 0.8911 (p) outliers start: 53 outliers final: 38 residues processed: 238 average time/residue: 0.2760 time to fit residues: 95.8037 Evaluate side-chains 234 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 194 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 837 ILE 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 84 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 99 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14171 Z= 0.378 Angle : 0.715 9.945 19211 Z= 0.364 Chirality : 0.050 0.261 2118 Planarity : 0.005 0.043 2475 Dihedral : 7.914 57.173 2261 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.62 % Favored : 90.32 % Rotamer: Outliers : 3.97 % Allowed : 18.87 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.21), residues: 1674 helix: -0.80 (0.40), residues: 175 sheet: -0.61 (0.28), residues: 328 loop : -1.03 (0.19), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 618 HIS 0.009 0.001 HIS B 699 PHE 0.030 0.002 PHE C 61 TYR 0.036 0.002 TYR A 430 ARG 0.009 0.001 ARG B 59 *********************** 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 249 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 189 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8146 (ttp) REVERT: A 494 THR cc_start: 0.9002 (p) cc_final: 0.8792 (p) REVERT: A 558 MET cc_start: 0.7030 (ttt) cc_final: 0.6775 (ttt) REVERT: A 586 ASP cc_start: 0.8787 (p0) cc_final: 0.8432 (p0) REVERT: A 602 ASN cc_start: 0.9062 (m-40) cc_final: 0.8704 (m-40) REVERT: A 643 TYR cc_start: 0.7970 (p90) cc_final: 0.7446 (p90) REVERT: A 689 GLU cc_start: 0.8596 (tp30) cc_final: 0.7909 (tp30) REVERT: A 704 VAL cc_start: 0.8620 (m) cc_final: 0.8406 (p) REVERT: A 822 TRP cc_start: 0.8277 (p90) cc_final: 0.7200 (p90) REVERT: A 847 ARG cc_start: 0.7983 (mtp85) cc_final: 0.7721 (mtm180) REVERT: B 156 MET cc_start: 0.7541 (mmm) cc_final: 0.7064 (mmp) REVERT: B 290 TYR cc_start: 0.6296 (m-80) cc_final: 0.5989 (m-10) REVERT: B 343 GLU cc_start: 0.8530 (mp0) cc_final: 0.8040 (mp0) REVERT: B 374 ASN cc_start: 0.8956 (m110) cc_final: 0.8373 (t0) REVERT: B 388 TYR cc_start: 0.6901 (m-80) cc_final: 0.6051 (m-80) REVERT: B 416 MET cc_start: 0.8549 (mtm) cc_final: 0.8294 (mtp) REVERT: B 857 LYS cc_start: 0.9439 (tttt) cc_final: 0.9199 (ttmm) outliers start: 60 outliers final: 48 residues processed: 228 average time/residue: 0.2579 time to fit residues: 87.1151 Evaluate side-chains 237 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 188 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 181 CYS 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 312 ASP Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 520 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 24 VAL 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 65 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 15 optimal weight: 0.3980 chunk 128 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 406 HIS ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14171 Z= 0.188 Angle : 0.651 13.905 19211 Z= 0.329 Chirality : 0.048 0.251 2118 Planarity : 0.004 0.044 2475 Dihedral : 7.601 56.832 2261 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.44 % Allowed : 19.67 % 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: -1.25 (0.21), residues: 1674 helix: -0.73 (0.41), residues: 174 sheet: -0.54 (0.29), residues: 318 loop : -0.95 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 79 HIS 0.005 0.001 HIS B 699 PHE 0.017 0.001 PHE C 61 TYR 0.018 0.001 TYR B 835 ARG 0.009 0.000 ARG B 376 *********************** 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 255 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 203 time to evaluate : 1.529 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 336 ARG cc_start: 0.7954 (mtm180) cc_final: 0.7669 (mtm180) REVERT: A 494 THR cc_start: 0.8978 (p) cc_final: 0.8736 (p) REVERT: A 558 MET cc_start: 0.7033 (ttt) cc_final: 0.6832 (ttt) REVERT: A 586 ASP cc_start: 0.8759 (p0) cc_final: 0.8377 (p0) REVERT: A 602 ASN cc_start: 0.8957 (m-40) cc_final: 0.8615 (m-40) REVERT: A 642 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7880 (mmtt) REVERT: A 643 TYR cc_start: 0.7902 (p90) cc_final: 0.7429 (p90) REVERT: A 681 LYS cc_start: 0.8936 (mttp) cc_final: 0.8641 (mptt) REVERT: A 689 GLU cc_start: 0.8598 (tp30) cc_final: 0.7856 (tp30) REVERT: A 704 VAL cc_start: 0.8583 (m) cc_final: 0.8354 (p) REVERT: A 847 ARG cc_start: 0.7929 (mtp85) cc_final: 0.7664 (mtm180) REVERT: B 39 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7707 (t70) REVERT: B 156 MET cc_start: 0.7458 (mmm) cc_final: 0.7189 (mmt) REVERT: B 170 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 343 GLU cc_start: 0.8485 (mp0) cc_final: 0.7994 (mp0) REVERT: B 374 ASN cc_start: 0.8917 (m110) cc_final: 0.8325 (t0) REVERT: B 388 TYR cc_start: 0.6920 (m-80) cc_final: 0.6117 (m-80) REVERT: B 857 LYS cc_start: 0.9408 (tttt) cc_final: 0.9208 (ttmm) REVERT: C 60 LYS cc_start: 0.8703 (tttt) cc_final: 0.8497 (tttp) outliers start: 52 outliers final: 48 residues processed: 241 average time/residue: 0.2448 time to fit residues: 87.3474 Evaluate side-chains 237 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 188 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 633 CYS Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 837 ILE 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 84 ASN Chi-restraints excluded: chain B residue 181 CYS 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 372 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 520 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 15 LEU 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 156 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14171 Z= 0.296 Angle : 0.679 16.112 19211 Z= 0.343 Chirality : 0.049 0.254 2118 Planarity : 0.004 0.042 2475 Dihedral : 7.682 56.556 2261 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 3.51 % Allowed : 20.07 % Favored : 76.42 % 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: -1.24 (0.21), residues: 1674 helix: -0.64 (0.41), residues: 175 sheet: -0.51 (0.29), residues: 320 loop : -0.96 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 404 HIS 0.006 0.001 HIS B 699 PHE 0.025 0.002 PHE C 61 TYR 0.030 0.002 TYR A 430 ARG 0.008 0.001 ARG B 376 *********************** 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 244 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 191 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 ARG cc_start: 0.7926 (mtm180) cc_final: 0.7646 (mtm180) REVERT: A 494 THR cc_start: 0.9000 (p) cc_final: 0.8772 (p) REVERT: A 586 ASP cc_start: 0.8808 (p0) cc_final: 0.8466 (p0) REVERT: A 602 ASN cc_start: 0.9029 (m-40) cc_final: 0.8681 (m-40) REVERT: A 642 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7915 (mmtt) REVERT: A 643 TYR cc_start: 0.7912 (p90) cc_final: 0.7357 (p90) REVERT: A 704 VAL cc_start: 0.8579 (m) cc_final: 0.8344 (p) REVERT: A 822 TRP cc_start: 0.8289 (p90) cc_final: 0.7442 (p90) REVERT: A 847 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7615 (mtm180) REVERT: B 39 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7784 (t70) REVERT: B 156 MET cc_start: 0.7546 (mmm) cc_final: 0.7256 (mmp) REVERT: B 170 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7932 (tm-30) REVERT: B 352 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7530 (mm-30) REVERT: B 374 ASN cc_start: 0.8941 (m110) cc_final: 0.8211 (m110) REVERT: B 388 TYR cc_start: 0.6972 (m-80) cc_final: 0.6088 (m-80) REVERT: B 857 LYS cc_start: 0.9407 (tttt) cc_final: 0.9199 (ttmm) REVERT: C 60 LYS cc_start: 0.8739 (tttt) cc_final: 0.8460 (tttp) outliers start: 53 outliers final: 46 residues processed: 227 average time/residue: 0.2527 time to fit residues: 85.1159 Evaluate side-chains 235 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 188 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 489 ASP 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 633 CYS Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 837 ILE 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 84 ASN Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 520 ASN Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 776 CYS Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 0.0570 chunk 76 optimal weight: 0.0370 chunk 111 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 13 optimal weight: 0.0170 chunk 103 optimal weight: 0.0870 chunk 82 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 ASN ** B 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14171 Z= 0.163 Angle : 0.658 16.949 19211 Z= 0.331 Chirality : 0.048 0.244 2118 Planarity : 0.004 0.040 2475 Dihedral : 7.331 57.150 2261 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.72 % Allowed : 20.93 % Favored : 76.36 % 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: -1.14 (0.21), residues: 1674 helix: -0.42 (0.42), residues: 169 sheet: -0.40 (0.29), residues: 318 loop : -0.93 (0.19), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 404 HIS 0.005 0.001 HIS A 30 PHE 0.015 0.001 PHE A 90 TYR 0.023 0.001 TYR B 835 ARG 0.010 0.000 ARG B 376 ********************** 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 247 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 THR cc_start: 0.8962 (p) cc_final: 0.8728 (p) REVERT: A 586 ASP cc_start: 0.8730 (p0) cc_final: 0.8359 (p0) REVERT: A 602 ASN cc_start: 0.8926 (m-40) cc_final: 0.8615 (m-40) REVERT: A 642 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7967 (mmtt) REVERT: A 643 TYR cc_start: 0.7855 (p90) cc_final: 0.7392 (p90) REVERT: A 681 LYS cc_start: 0.8895 (mttp) cc_final: 0.8642 (mptt) REVERT: A 847 ARG cc_start: 0.7838 (mtp85) cc_final: 0.7120 (mmm160) REVERT: B 39 ASP cc_start: 0.8092 (m-30) cc_final: 0.7641 (t0) REVERT: B 170 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7965 (tm-30) REVERT: B 374 ASN cc_start: 0.8885 (m110) cc_final: 0.8308 (t0) REVERT: B 388 TYR cc_start: 0.6846 (m-80) cc_final: 0.6030 (m-80) REVERT: B 477 ILE cc_start: 0.9453 (mt) cc_final: 0.9225 (mp) REVERT: B 506 THR cc_start: 0.8862 (p) cc_final: 0.8644 (t) REVERT: B 751 ARG cc_start: 0.7734 (mtp180) cc_final: 0.6391 (mtp85) REVERT: B 878 THR cc_start: 0.9131 (m) cc_final: 0.8862 (p) REVERT: B 885 SER cc_start: 0.9160 (t) cc_final: 0.8893 (p) outliers start: 41 outliers final: 39 residues processed: 236 average time/residue: 0.2442 time to fit residues: 85.9945 Evaluate side-chains 229 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 190 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 633 CYS Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 84 ASN 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 520 ASN 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 845 ASP Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 53 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 19 optimal weight: 0.0470 chunk 37 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 ASN ** B 442 GLN ** 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 = 0.4035 r_free = 0.4035 target = 0.122926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.097604 restraints weight = 30527.994| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.67 r_work: 0.3472 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14171 Z= 0.280 Angle : 0.681 14.596 19211 Z= 0.345 Chirality : 0.049 0.250 2118 Planarity : 0.004 0.042 2475 Dihedral : 7.400 57.906 2258 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.05 % Allowed : 21.39 % Favored : 75.56 % 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: -1.12 (0.21), residues: 1674 helix: -0.48 (0.42), residues: 175 sheet: -0.38 (0.29), residues: 318 loop : -0.91 (0.19), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP A 404 HIS 0.006 0.001 HIS B 699 PHE 0.026 0.001 PHE C 61 TYR 0.036 0.002 TYR A 430 ARG 0.008 0.000 ARG B 376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3441.84 seconds wall clock time: 61 minutes 59.24 seconds (3719.24 seconds total)