Starting phenix.real_space_refine on Sun Mar 17 08:43:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/03_2024/8jd6_36177_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/03_2024/8jd6_36177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/03_2024/8jd6_36177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/03_2024/8jd6_36177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/03_2024/8jd6_36177_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/03_2024/8jd6_36177_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.899 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 114 5.16 5 Cl 1 4.86 5 C 10941 2.51 5 N 2938 2.21 5 O 3196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S ASP 48": "OD1" <-> "OD2" Residue "S ASP 92": "OD1" <-> "OD2" Residue "S PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 368": "OD1" <-> "OD2" Residue "S TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 69": "OE1" <-> "OE2" Residue "R PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 368": "OD1" <-> "OD2" Residue "R PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 109": "OD1" <-> "OD2" Residue "D ASP 137": "OD1" <-> "OD2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 231": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17192 Number of models: 1 Model: "" Number of chains: 8 Chain: "S" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5700 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 36, 'TRANS': 724} Chain breaks: 4 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 260 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 196 Chain: "R" Number of atoms: 5779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5779 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 38, 'TRANS': 735} Chain breaks: 4 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 407 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "D" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1730 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 114 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2188 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 296} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 90 Chain: "A" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1643 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 97 Chain: "S" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'BK0': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 9.49, per 1000 atoms: 0.55 Number of scatterers: 17192 At special positions: 0 Unit cell: (98.23, 128.535, 231.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 114 16.00 P 2 15.00 O 3196 8.00 N 2938 7.00 C 10941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS S 249 " - pdb=" SG CYS S 538 " distance=2.03 Simple disulfide: pdb=" SG CYS S 372 " - pdb=" SG CYS S 388 " distance=2.03 Simple disulfide: pdb=" SG CYS S 428 " - pdb=" SG CYS S 435 " distance=2.03 Simple disulfide: pdb=" SG CYS S 520 " - pdb=" SG CYS S 539 " distance=2.03 Simple disulfide: pdb=" SG CYS S 524 " - pdb=" SG CYS S 542 " distance=2.03 Simple disulfide: pdb=" SG CYS S 545 " - pdb=" SG CYS S 557 " distance=2.03 Simple disulfide: pdb=" SG CYS S 560 " - pdb=" SG CYS S 573 " distance=2.03 Simple disulfide: pdb=" SG CYS S 652 " - pdb=" SG CYS S 746 " distance=2.03 Simple disulfide: pdb=" SG CYS R 67 " - pdb=" SG CYS R 109 " distance=2.03 Simple disulfide: pdb=" SG CYS R 249 " - pdb=" SG CYS R 538 " distance=2.03 Simple disulfide: pdb=" SG CYS R 428 " - pdb=" SG CYS R 435 " distance=2.03 Simple disulfide: pdb=" SG CYS R 520 " - pdb=" SG CYS R 539 " distance=2.03 Simple disulfide: pdb=" SG CYS R 524 " - pdb=" SG CYS R 542 " distance=2.03 Simple disulfide: pdb=" SG CYS R 545 " - pdb=" SG CYS R 557 " distance=2.03 Simple disulfide: pdb=" SG CYS R 560 " - pdb=" SG CYS R 573 " distance=2.03 Simple disulfide: pdb=" SG CYS R 652 " - pdb=" SG CYS R 746 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 229 " 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 Time building additional restraints: 7.29 Conformation dependent library (CDL) restraints added in 3.1 seconds 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4294 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 22 sheets defined 33.9% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'S' and resid 75 through 91 Processing helix chain 'S' and resid 112 through 125 removed outlier: 5.149A pdb=" N ALA S 125 " --> pdb=" O THR S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 171 removed outlier: 3.660A pdb=" N MET S 164 " --> pdb=" O SER S 160 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE S 168 " --> pdb=" O MET S 164 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU S 171 " --> pdb=" O ASN S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 184 through 186 No H-bonds generated for 'chain 'S' and resid 184 through 186' Processing helix chain 'S' and resid 202 through 215 Processing helix chain 'S' and resid 229 through 244 Processing helix chain 'S' and resid 265 through 273 removed outlier: 3.591A pdb=" N ILE S 269 " --> pdb=" O PHE S 265 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 300 removed outlier: 3.611A pdb=" N ARG S 292 " --> pdb=" O ASP S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 312 through 314 No H-bonds generated for 'chain 'S' and resid 312 through 314' Processing helix chain 'S' and resid 342 through 350 removed outlier: 3.670A pdb=" N SER S 350 " --> pdb=" O ARG S 346 " (cutoff:3.500A) Processing helix chain 'S' and resid 360 through 369 removed outlier: 3.682A pdb=" N ALA S 363 " --> pdb=" O ILE S 360 " (cutoff:3.500A) Processing helix chain 'S' and resid 406 through 426 Processing helix chain 'S' and resid 436 through 439 No H-bonds generated for 'chain 'S' and resid 436 through 439' Processing helix chain 'S' and resid 443 through 451 Processing helix chain 'S' and resid 503 through 505 No H-bonds generated for 'chain 'S' and resid 503 through 505' Processing helix chain 'S' and resid 589 through 611 Processing helix chain 'S' and resid 624 through 643 Processing helix chain 'S' and resid 649 through 682 removed outlier: 3.588A pdb=" N SER S 666 " --> pdb=" O GLY S 662 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR S 667 " --> pdb=" O MET S 663 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU S 670 " --> pdb=" O SER S 666 " (cutoff:3.500A) Processing helix chain 'S' and resid 696 through 719 removed outlier: 4.078A pdb=" N VAL S 719 " --> pdb=" O CYS S 715 " (cutoff:3.500A) Processing helix chain 'S' and resid 750 through 774 removed outlier: 4.279A pdb=" N LEU S 756 " --> pdb=" O SER S 752 " (cutoff:3.500A) Processing helix chain 'S' and resid 785 through 807 removed outlier: 3.637A pdb=" N ILE S 802 " --> pdb=" O TRP S 798 " (cutoff:3.500A) Proline residue: S 803 - end of helix Processing helix chain 'S' and resid 818 through 837 removed outlier: 3.750A pdb=" N LEU S 822 " --> pdb=" O GLN S 818 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR S 823 " --> pdb=" O THR S 819 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER S 833 " --> pdb=" O SER S 829 " (cutoff:3.500A) Processing helix chain 'S' and resid 839 through 847 Processing helix chain 'R' and resid 75 through 91 Processing helix chain 'R' and resid 112 through 126 Processing helix chain 'R' and resid 159 through 169 removed outlier: 3.633A pdb=" N ASN R 167 " --> pdb=" O ILE R 163 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE R 168 " --> pdb=" O MET R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 187 Processing helix chain 'R' and resid 202 through 215 Processing helix chain 'R' and resid 231 through 243 Processing helix chain 'R' and resid 264 through 274 Processing helix chain 'R' and resid 287 through 300 Processing helix chain 'R' and resid 342 through 350 removed outlier: 3.521A pdb=" N SER R 350 " --> pdb=" O ARG R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 366 removed outlier: 3.742A pdb=" N GLU R 364 " --> pdb=" O ILE R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 427 Processing helix chain 'R' and resid 436 through 438 No H-bonds generated for 'chain 'R' and resid 436 through 438' Processing helix chain 'R' and resid 443 through 451 Processing helix chain 'R' and resid 503 through 505 No H-bonds generated for 'chain 'R' and resid 503 through 505' Processing helix chain 'R' and resid 589 through 611 removed outlier: 3.626A pdb=" N GLY R 598 " --> pdb=" O LEU R 594 " (cutoff:3.500A) Processing helix chain 'R' and resid 616 through 619 No H-bonds generated for 'chain 'R' and resid 616 through 619' Processing helix chain 'R' and resid 624 through 644 removed outlier: 4.626A pdb=" N VAL R 628 " --> pdb=" O GLU R 624 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU R 629 " --> pdb=" O LEU R 625 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR R 640 " --> pdb=" O CYS R 636 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE R 641 " --> pdb=" O TYR R 637 " (cutoff:3.500A) Processing helix chain 'R' and resid 649 through 685 removed outlier: 3.893A pdb=" N SER R 664 " --> pdb=" O GLY R 660 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER R 666 " --> pdb=" O GLY R 662 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR R 667 " --> pdb=" O MET R 663 " (cutoff:3.500A) Processing helix chain 'R' and resid 696 through 720 removed outlier: 3.714A pdb=" N GLN R 710 " --> pdb=" O LEU R 706 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY R 713 " --> pdb=" O LEU R 709 " (cutoff:3.500A) Processing helix chain 'R' and resid 750 through 773 Processing helix chain 'R' and resid 785 through 807 Proline residue: R 803 - end of helix Processing helix chain 'R' and resid 814 through 846 removed outlier: 3.533A pdb=" N THR R 819 " --> pdb=" O LEU R 815 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR R 820 " --> pdb=" O TYR R 816 " (cutoff:3.500A) Proline residue: R 840 - end of helix Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.595A pdb=" N ILE A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 215' Processing helix chain 'A' and resid 242 through 253 removed outlier: 3.786A pdb=" N SER A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 4.022A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 307 removed outlier: 3.542A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 352 removed outlier: 3.963A pdb=" N ASP A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 338 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N CYS A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 352 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'S' and resid 53 through 55 Processing sheet with id= B, first strand: chain 'S' and resid 253 through 256 removed outlier: 6.899A pdb=" N THR S 223 " --> pdb=" O VAL S 254 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE S 256 " --> pdb=" O THR S 223 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA S 225 " --> pdb=" O ILE S 256 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE S 307 " --> pdb=" O VAL S 281 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE S 283 " --> pdb=" O PHE S 307 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N MET S 309 " --> pdb=" O ILE S 283 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'S' and resid 331 through 336 removed outlier: 7.671A pdb=" N GLN S 479 " --> pdb=" O VAL S 491 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL S 491 " --> pdb=" O GLN S 479 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 530 through 532 Processing sheet with id= E, first strand: chain 'R' and resid 43 through 45 removed outlier: 3.717A pdb=" N ALA R 103 " --> pdb=" O ILE R 45 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE R 49 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ARG R 104 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU R 51 " --> pdb=" O ARG R 104 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU R 106 " --> pdb=" O LEU R 51 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY R 53 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY R 152 " --> pdb=" O GLY R 52 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N LEU R 54 " --> pdb=" O GLY R 152 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE R 154 " --> pdb=" O LEU R 54 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'R' and resid 176 through 178 Processing sheet with id= G, first strand: chain 'R' and resid 253 through 256 removed outlier: 9.148A pdb=" N VAL R 254 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR R 223 " --> pdb=" O VAL R 254 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE R 256 " --> pdb=" O THR R 223 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ALA R 225 " --> pdb=" O ILE R 256 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA R 280 " --> pdb=" O SER R 222 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL R 224 " --> pdb=" O ALA R 280 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE R 282 " --> pdb=" O VAL R 224 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER R 226 " --> pdb=" O ILE R 282 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N PHE R 307 " --> pdb=" O VAL R 281 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE R 283 " --> pdb=" O PHE R 307 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N MET R 309 " --> pdb=" O ILE R 283 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'R' and resid 331 through 336 removed outlier: 3.559A pdb=" N ALA R 331 " --> pdb=" O TYR R 480 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLN R 479 " --> pdb=" O VAL R 491 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL R 491 " --> pdb=" O GLN R 479 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLN R 481 " --> pdb=" O TYR R 489 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N TYR R 489 " --> pdb=" O GLN R 481 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 530 through 532 Processing sheet with id= J, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.603A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 33 through 35 removed outlier: 3.689A pdb=" N HIS D 35 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL D 97 " --> pdb=" O HIS D 35 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= M, first strand: chain 'D' and resid 174 through 176 Processing sheet with id= N, first strand: chain 'D' and resid 177 through 179 Processing sheet with id= O, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.496A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= Q, first strand: chain 'B' and resid 198 through 201 removed outlier: 3.890A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 251 through 254 removed outlier: 3.618A pdb=" N ALA B 242 " --> pdb=" O CYS B 233 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.590A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.104A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 120 through 125 removed outlier: 3.768A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 319 through 323 removed outlier: 7.660A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 187 " --> pdb=" O MET A 198 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.57 Time building geometry restraints manager: 7.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2790 1.31 - 1.44: 4833 1.44 - 1.57: 9775 1.57 - 1.69: 8 1.69 - 1.82: 158 Bond restraints: 17564 Sorted by residual: bond pdb=" C07 BK0 S1001 " pdb=" N09 BK0 S1001 " ideal model delta sigma weight residual 1.358 1.454 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N ASP D 74 " pdb=" CA ASP D 74 " ideal model delta sigma weight residual 1.461 1.488 -0.027 9.20e-03 1.18e+04 8.56e+00 bond pdb=" N ILE S 694 " pdb=" CA ILE S 694 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.51e+00 bond pdb=" N THR D 78 " pdb=" CA THR D 78 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.09e-02 8.42e+03 8.42e+00 bond pdb=" C10 BK0 S1001 " pdb=" N09 BK0 S1001 " ideal model delta sigma weight residual 1.397 1.455 -0.058 2.00e-02 2.50e+03 8.40e+00 ... (remaining 17559 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.18: 417 106.18 - 113.18: 9549 113.18 - 120.18: 5905 120.18 - 127.18: 7869 127.18 - 134.18: 188 Bond angle restraints: 23928 Sorted by residual: angle pdb=" C LEU A 234 " pdb=" CA LEU A 234 " pdb=" CB LEU A 234 " ideal model delta sigma weight residual 116.54 110.72 5.82 1.15e+00 7.56e-01 2.56e+01 angle pdb=" N ILE R 694 " pdb=" CA ILE R 694 " pdb=" C ILE R 694 " ideal model delta sigma weight residual 112.80 108.15 4.65 1.15e+00 7.56e-01 1.64e+01 angle pdb=" N PRO S 696 " pdb=" CA PRO S 696 " pdb=" C PRO S 696 " ideal model delta sigma weight residual 113.53 107.93 5.60 1.39e+00 5.18e-01 1.63e+01 angle pdb=" N LYS D 76 " pdb=" CA LYS D 76 " pdb=" C LYS D 76 " ideal model delta sigma weight residual 113.28 109.05 4.23 1.22e+00 6.72e-01 1.20e+01 angle pdb=" CA LEU D 79 " pdb=" C LEU D 79 " pdb=" O LEU D 79 " ideal model delta sigma weight residual 121.45 118.10 3.35 1.07e+00 8.73e-01 9.80e+00 ... (remaining 23923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9172 17.98 - 35.95: 940 35.95 - 53.93: 215 53.93 - 71.90: 29 71.90 - 89.88: 7 Dihedral angle restraints: 10363 sinusoidal: 3694 harmonic: 6669 Sorted by residual: dihedral pdb=" CB CYS S 249 " pdb=" SG CYS S 249 " pdb=" SG CYS S 538 " pdb=" CB CYS S 538 " ideal model delta sinusoidal sigma weight residual -86.00 -173.95 87.95 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS R 524 " pdb=" SG CYS R 524 " pdb=" SG CYS R 542 " pdb=" CB CYS R 542 " ideal model delta sinusoidal sigma weight residual 93.00 159.39 -66.39 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS S 372 " pdb=" SG CYS S 372 " pdb=" SG CYS S 388 " pdb=" CB CYS S 388 " ideal model delta sinusoidal sigma weight residual 93.00 41.79 51.21 1 1.00e+01 1.00e-02 3.59e+01 ... (remaining 10360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2058 0.042 - 0.083: 509 0.083 - 0.125: 182 0.125 - 0.166: 13 0.166 - 0.208: 8 Chirality restraints: 2770 Sorted by residual: chirality pdb=" CB ILE D 58 " pdb=" CA ILE D 58 " pdb=" CG1 ILE D 58 " pdb=" CG2 ILE D 58 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE R 677 " pdb=" N ILE R 677 " pdb=" C ILE R 677 " pdb=" CB ILE R 677 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CA ILE R 694 " pdb=" N ILE R 694 " pdb=" C ILE R 694 " pdb=" CB ILE R 694 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 2767 not shown) Planarity restraints: 3062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 679 " -0.193 9.50e-02 1.11e+02 8.66e-02 4.60e+00 pdb=" NE ARG R 679 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG R 679 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG R 679 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 679 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 231 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" CG ASP A 231 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP A 231 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP A 231 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET R 839 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO R 840 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO R 840 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 840 " 0.021 5.00e-02 4.00e+02 ... (remaining 3059 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2131 2.75 - 3.29: 17396 3.29 - 3.83: 29517 3.83 - 4.36: 33065 4.36 - 4.90: 57291 Nonbonded interactions: 139400 Sorted by model distance: nonbonded pdb=" OG SER D 193 " pdb=" O GLY D 205 " model vdw 2.218 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.225 2.440 nonbonded pdb=" OG1 THR R 734 " pdb=" O ALA R 740 " model vdw 2.268 2.440 nonbonded pdb=" OG SER D 106 " pdb=" OD2 ASP D 109 " model vdw 2.278 2.440 nonbonded pdb=" O GLN R 118 " pdb=" OG1 THR R 121 " model vdw 2.281 2.440 ... (remaining 139395 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 'R' and (resid 41 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 126 or resid 148 through 172 or (r \ esid 173 and (name N or name CA or name C or name O or name CB )) or resid 174 t \ hrough 266 or (resid 267 and (name N or name CA or name C or name O or name CB ) \ ) or resid 268 through 276 or (resid 277 through 280 and (name N or name CA or n \ ame C or name O or name CB )) or resid 281 through 294 or (resid 295 through 297 \ and (name N or name CA or name C or name O or name CB )) or resid 298 through 3 \ 00 or (resid 301 and (name N or name CA or name C or name O or name CB )) or res \ id 302 through 321 or (resid 322 through 326 and (name N or name CA or name C or \ name O or name CB )) or resid 327 through 373 or resid 386 through 425 or (resi \ d 426 and (name N or name CA or name C or name O or name CB )) or resid 427 thro \ ugh 441 or (resid 442 and (name N or name CA or name C or name O or name CB )) o \ r resid 443 through 466 or (resid 467 and (name N or name CA or name C or name O \ or name CB )) or resid 468 through 473 or (resid 474 and (name N or name CA or \ name C or name O or name CB )) or resid 475 through 487 or (resid 488 and (name \ N or name CA or name C or name O or name CB )) or resid 489 through 503 or (resi \ d 504 and (name N or name CA or name C or name O or name CB )) or resid 505 thro \ ugh 550 or (resid 551 through 556 and (name N or name CA or name C or name O or \ name CB )) or resid 557 through 582 or (resid 583 and (name N or name CA or name \ C or name O or name CB )) or resid 584 through 618 or (resid 619 through 620 an \ d (name N or name CA or name C or name O or name CB )) or resid 621 through 648 \ or (resid 649 and (name N or name CA or name C or name O or name CB )) or resid \ 650 through 654 or (resid 655 and (name N or name CA or name C or name O or name \ CB )) or resid 656 through 681 or (resid 682 and (name N or name CA or name C o \ r name O or name CB )) or resid 683 or (resid 692 through 694 and (name N or nam \ e CA or name C or name O or name CB )) or resid 695 through 699 or (resid 700 th \ rough 701 and (name N or name CA or name C or name O or name CB )) or resid 702 \ through 706 or (resid 707 and (name N or name CA or name C or name O or name CB \ )) or resid 708 through 711 or (resid 712 and (name N or name CA or name C or na \ me O or name CB )) or resid 713 through 723 or (resid 724 and (name N or name CA \ or name C or name O or name CB )) or resid 725 through 732 or (resid 733 and (n \ ame N or name CA or name C or name O or name CB )) or resid 734 or (resid 735 an \ d (name N or name CA or name C or name O or name CB )) or resid 736 through 743 \ or (resid 744 through 745 and (name N or name CA or name C or name O or name CB \ )) or resid 746 or (resid 747 through 749 and (name N or name CA or name C or na \ me O or name CB )) or resid 750 or (resid 751 through 752 and (name N or name CA \ or name C or name O or name CB )) or resid 753 or (resid 754 and (name N or nam \ e CA or name C or name O or name CB )) or resid 755 through 768 or (resid 769 an \ d (name N or name CA or name C or name O or name CB )) or resid 770 through 772 \ or (resid 773 and (name N or name CA or name C or name O or name CB )) or resid \ 774 through 847 or (resid 848 and (name N or name CA or name C or name O or name \ CB )) or resid 1001)) selection = (chain 'S' and (resid 41 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 70 or (resid 71 through 72 and (na \ me N or name CA or name C or name O or name CB )) or resid 73 through 278 or (re \ sid 279 through 280 and (name N or name CA or name C or name O or name CB )) or \ resid 281 through 290 or (resid 291 and (name N or name CA or name C or name O o \ r name CB )) or resid 292 through 322 or (resid 323 through 326 and (name N or n \ ame CA or name C or name O or name CB )) or resid 327 through 341 or (resid 342 \ and (name N or name CA or name C or name O or name CB )) or resid 343 through 35 \ 3 or (resid 354 and (name N or name CA or name C or name O or name CB )) or resi \ d 355 through 373 or (resid 386 through 387 and (name N or name CA or name C or \ name O or name CB )) or resid 388 through 400 or (resid 401 and (name N or name \ CA or name C or name O or name CB )) or resid 402 through 483 or resid 487 throu \ gh 521 or (resid 522 and (name N or name CA or name C or name O or name CB )) or \ resid 523 through 529 or (resid 530 and (name N or name CA or name C or name O \ or name CB )) or resid 531 or (resid 532 through 534 and (name N or name CA or n \ ame C or name O or name CB )) or resid 535 through 539 or (resid 540 and (name N \ or name CA or name C or name O or name CB )) or resid 541 through 542 or (resid \ 543 and (name N or name CA or name C or name O or name CB )) or resid 544 throu \ gh 545 or (resid 546 and (name N or name CA or name C or name O or name CB )) or \ resid 547 or (resid 548 and (name N or name CA or name C or name O or name CB ) \ ) or resid 549 or (resid 550 through 556 and (name N or name CA or name C or nam \ e O or name CB )) or resid 557 through 558 or (resid 559 and (name N or name CA \ or name C or name O or name CB )) or resid 560 through 563 or (resid 564 and (na \ me N or name CA or name C or name O or name CB )) or resid 565 through 567 or (r \ esid 568 and (name N or name CA or name C or name O or name CB )) or resid 569 o \ r (resid 570 through 571 and (name N or name CA or name C or name O or name CB ) \ ) or resid 572 through 578 or (resid 579 through 583 and (name N or name CA or n \ ame C or name O or name CB )) or resid 584 through 591 or (resid 592 and (name N \ or name CA or name C or name O or name CB )) or resid 593 through 607 or (resid \ 608 and (name N or name CA or name C or name O or name CB )) or resid 609 throu \ gh 613 or (resid 614 and (name N or name CA or name C or name O or name CB )) or \ resid 615 through 653 or (resid 654 through 655 and (name N or name CA or name \ C or name O or name CB )) or resid 656 through 715 or (resid 716 and (name N or \ name CA or name C or name O or name CB )) or resid 717 through 718 or (resid 719 \ and (name N or name CA or name C or name O or name CB )) or resid 720 through 7 \ 25 or (resid 726 and (name N or name CA or name C or name O or name CB )) or res \ id 727 or (resid 728 through 729 and (name N or name CA or name C or name O or n \ ame CB )) or resid 730 or (resid 731 and (name N or name CA or name C or name O \ or name CB )) or resid 732 through 737 or (resid 738 through 741 and (name N or \ name CA or name C or name O or name CB )) or resid 742 through 748 or (resid 749 \ and (name N or name CA or name C or name O or name CB )) or resid 750 through 7 \ 51 or (resid 752 and (name N or name CA or name C or name O or name CB )) or res \ id 753 through 760 or (resid 761 through 762 and (name N or name CA or name C or \ name O or name CB )) or resid 763 through 848 or resid 1002)) } 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: 3.730 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: 0.020 Extract box with map and model: 10.740 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 48.480 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.090 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 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 : 0.003 0.096 17564 Z= 0.187 Angle : 0.565 8.674 23928 Z= 0.329 Chirality : 0.042 0.208 2770 Planarity : 0.004 0.087 3062 Dihedral : 15.115 89.879 6015 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.93 % Favored : 94.03 % Rotamer: Outliers : 0.35 % Allowed : 18.40 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2278 helix: 1.44 (0.19), residues: 801 sheet: -0.78 (0.30), residues: 358 loop : -1.91 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 211 HIS 0.009 0.000 HIS D 167 PHE 0.017 0.001 PHE S 806 TYR 0.019 0.001 TYR D 59 ARG 0.009 0.000 ARG S 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 223 time to evaluate : 2.015 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 226 average time/residue: 0.2580 time to fit residues: 91.9843 Evaluate side-chains 207 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 204 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain B residue 93 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 323 HIS ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 818 GLN R 402 GLN R 732 GLN ** D 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17564 Z= 0.401 Angle : 0.675 10.084 23928 Z= 0.353 Chirality : 0.046 0.198 2770 Planarity : 0.004 0.049 3062 Dihedral : 5.164 78.206 2498 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.21 % Allowed : 16.78 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.18), residues: 2278 helix: 0.90 (0.18), residues: 804 sheet: -1.40 (0.29), residues: 353 loop : -1.84 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 111 HIS 0.013 0.002 HIS B 54 PHE 0.032 0.002 PHE R 681 TYR 0.026 0.002 TYR D 103 ARG 0.007 0.001 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 238 time to evaluate : 2.106 Fit side-chains revert: symmetry clash REVERT: S 112 ASP cc_start: 0.6767 (t0) cc_final: 0.6512 (t0) REVERT: S 168 ILE cc_start: 0.8623 (mm) cc_final: 0.8318 (mm) REVERT: S 603 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7176 (mm) REVERT: R 267 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7730 (mtmm) REVERT: B 83 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7287 (p0) REVERT: B 119 ASN cc_start: 0.8484 (m-40) cc_final: 0.8160 (m-40) REVERT: B 146 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8294 (tt) REVERT: B 225 HIS cc_start: 0.3505 (OUTLIER) cc_final: 0.2659 (t-170) REVERT: A 268 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7971 (mt) outliers start: 73 outliers final: 44 residues processed: 294 average time/residue: 0.2521 time to fit residues: 117.1062 Evaluate side-chains 250 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 200 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 256 ILE Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 568 GLU Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 644 ILE Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 736 ASP Chi-restraints excluded: chain S residue 842 VAL Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 267 LYS Chi-restraints excluded: chain R residue 350 SER Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 780 THR Chi-restraints excluded: chain R residue 820 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 311 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 208 optimal weight: 0.6980 chunk 225 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 chunk 206 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 167 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 98 ASN R 732 GLN D 167 HIS B 340 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17564 Z= 0.239 Angle : 0.551 9.637 23928 Z= 0.285 Chirality : 0.042 0.220 2770 Planarity : 0.004 0.039 3062 Dihedral : 4.863 77.898 2496 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.09 % Allowed : 19.09 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.18), residues: 2278 helix: 1.11 (0.18), residues: 803 sheet: -1.43 (0.29), residues: 364 loop : -1.88 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 176 HIS 0.005 0.001 HIS B 54 PHE 0.017 0.002 PHE R 681 TYR 0.018 0.001 TYR D 190 ARG 0.018 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 218 time to evaluate : 1.971 Fit side-chains REVERT: S 216 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7418 (mp) REVERT: S 400 TYR cc_start: 0.5461 (OUTLIER) cc_final: 0.4072 (p90) REVERT: R 334 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7213 (mp) REVERT: R 414 TYR cc_start: 0.6488 (m-10) cc_final: 0.6283 (m-80) REVERT: R 634 PHE cc_start: 0.7946 (t80) cc_final: 0.7694 (t80) REVERT: B 83 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.6907 (p0) REVERT: B 225 HIS cc_start: 0.3905 (OUTLIER) cc_final: 0.3359 (t-170) REVERT: B 278 PHE cc_start: 0.6744 (OUTLIER) cc_final: 0.5232 (m-10) REVERT: A 268 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7859 (mt) outliers start: 71 outliers final: 43 residues processed: 274 average time/residue: 0.2738 time to fit residues: 116.3946 Evaluate side-chains 243 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 193 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 400 TYR Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 842 VAL Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 350 SER Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 791 MET Chi-restraints excluded: chain R residue 834 LEU Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 311 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 17564 Z= 0.510 Angle : 0.749 11.936 23928 Z= 0.389 Chirality : 0.048 0.249 2770 Planarity : 0.005 0.059 3062 Dihedral : 5.709 73.906 2496 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.78 % Favored : 91.18 % Rotamer: Outliers : 6.34 % Allowed : 18.74 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.17), residues: 2278 helix: 0.42 (0.18), residues: 812 sheet: -1.89 (0.28), residues: 346 loop : -2.11 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 63 HIS 0.011 0.002 HIS A 322 PHE 0.031 0.003 PHE R 681 TYR 0.026 0.002 TYR D 103 ARG 0.016 0.001 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 246 time to evaluate : 1.979 Fit side-chains revert: symmetry clash REVERT: S 216 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7417 (mp) REVERT: S 217 LYS cc_start: 0.8535 (mppt) cc_final: 0.8235 (mmtp) REVERT: S 387 LYS cc_start: 0.6480 (tppt) cc_final: 0.5907 (tptt) REVERT: S 400 TYR cc_start: 0.6356 (OUTLIER) cc_final: 0.4143 (p90) REVERT: S 603 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7403 (mm) REVERT: R 270 ARG cc_start: 0.7676 (ptp90) cc_final: 0.7212 (ptp90) REVERT: R 334 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7400 (mp) REVERT: R 843 TYR cc_start: 0.7506 (t80) cc_final: 0.7281 (t80) REVERT: R 846 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7534 (pp) REVERT: D 20 LEU cc_start: 0.4766 (mp) cc_final: 0.4327 (pt) REVERT: D 183 GLN cc_start: 0.7498 (mt0) cc_final: 0.7165 (mt0) REVERT: B 83 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.6957 (p0) REVERT: B 85 TYR cc_start: 0.8195 (m-10) cc_final: 0.7927 (m-80) REVERT: B 118 ASP cc_start: 0.8404 (t0) cc_final: 0.8170 (t0) REVERT: B 215 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6864 (pp20) REVERT: B 278 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.5592 (m-80) REVERT: A 268 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8184 (mt) outliers start: 110 outliers final: 67 residues processed: 331 average time/residue: 0.2584 time to fit residues: 134.1619 Evaluate side-chains 294 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 218 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 256 ILE Chi-restraints excluded: chain S residue 340 SER Chi-restraints excluded: chain S residue 400 TYR Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 568 GLU Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 644 ILE Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 736 ASP Chi-restraints excluded: chain S residue 821 THR Chi-restraints excluded: chain S residue 842 VAL Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 639 THR Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 754 ILE Chi-restraints excluded: chain R residue 780 THR Chi-restraints excluded: chain R residue 791 MET Chi-restraints excluded: chain R residue 820 THR Chi-restraints excluded: chain R residue 846 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 184 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 91 optimal weight: 0.2980 chunk 188 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 198 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 732 GLN D 194 ASN B 259 GLN A 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17564 Z= 0.237 Angle : 0.575 10.143 23928 Z= 0.298 Chirality : 0.043 0.265 2770 Planarity : 0.004 0.044 3062 Dihedral : 5.277 76.234 2496 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.55 % Favored : 92.41 % Rotamer: Outliers : 5.07 % Allowed : 21.22 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2278 helix: 0.88 (0.18), residues: 805 sheet: -1.75 (0.29), residues: 327 loop : -2.04 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 63 HIS 0.006 0.001 HIS A 322 PHE 0.034 0.002 PHE A 334 TYR 0.020 0.002 TYR D 190 ARG 0.009 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 233 time to evaluate : 1.999 Fit side-chains revert: symmetry clash REVERT: S 216 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7266 (mp) REVERT: S 400 TYR cc_start: 0.6217 (OUTLIER) cc_final: 0.4208 (p90) REVERT: S 603 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7207 (mm) REVERT: R 302 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7015 (tp40) REVERT: R 334 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7161 (mp) REVERT: R 474 ARG cc_start: 0.7289 (mtp-110) cc_final: 0.6998 (mtm-85) REVERT: R 836 MET cc_start: 0.8287 (ptm) cc_final: 0.8045 (ptp) REVERT: R 843 TYR cc_start: 0.7404 (t80) cc_final: 0.7187 (t80) REVERT: D 20 LEU cc_start: 0.4571 (mp) cc_final: 0.4170 (pt) REVERT: B 118 ASP cc_start: 0.8332 (t0) cc_final: 0.8102 (t0) REVERT: B 278 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.5511 (m-80) REVERT: A 268 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7963 (mt) outliers start: 88 outliers final: 57 residues processed: 302 average time/residue: 0.2694 time to fit residues: 126.8759 Evaluate side-chains 271 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 208 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 269 ILE Chi-restraints excluded: chain S residue 340 SER Chi-restraints excluded: chain S residue 400 TYR Chi-restraints excluded: chain S residue 524 CYS Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 808 THR Chi-restraints excluded: chain S residue 842 VAL Chi-restraints excluded: chain S residue 845 ILE Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 573 CYS Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 639 THR Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 340 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 74 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 221 optimal weight: 0.3980 chunk 183 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 466 ASN ** R 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN B 340 ASN A 294 ASN A 306 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17564 Z= 0.325 Angle : 0.613 10.899 23928 Z= 0.319 Chirality : 0.044 0.260 2770 Planarity : 0.004 0.049 3062 Dihedral : 5.274 72.137 2496 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.52 % Favored : 91.44 % Rotamer: Outliers : 6.00 % Allowed : 21.80 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 2278 helix: 0.81 (0.18), residues: 805 sheet: -1.85 (0.28), residues: 352 loop : -2.04 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 587 HIS 0.008 0.001 HIS A 322 PHE 0.031 0.002 PHE A 334 TYR 0.023 0.002 TYR D 103 ARG 0.006 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 217 time to evaluate : 2.040 Fit side-chains revert: symmetry clash REVERT: S 216 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7380 (mp) REVERT: S 387 LYS cc_start: 0.6466 (tppt) cc_final: 0.5875 (tptt) REVERT: S 400 TYR cc_start: 0.6379 (OUTLIER) cc_final: 0.4270 (p90) REVERT: S 503 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7498 (tp) REVERT: S 592 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7513 (mm) REVERT: S 603 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7129 (mm) REVERT: R 267 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7547 (mtmm) REVERT: R 302 GLN cc_start: 0.7417 (mm-40) cc_final: 0.7080 (tp40) REVERT: R 334 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7224 (mp) REVERT: R 407 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.7330 (tm130) REVERT: R 474 ARG cc_start: 0.7232 (mtp-110) cc_final: 0.6958 (mtm-85) REVERT: R 594 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7797 (tp) REVERT: R 846 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7488 (pp) REVERT: D 20 LEU cc_start: 0.4570 (mp) cc_final: 0.4167 (pt) REVERT: B 83 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.6914 (p0) REVERT: B 118 ASP cc_start: 0.8360 (t0) cc_final: 0.8153 (t0) REVERT: B 119 ASN cc_start: 0.8069 (m-40) cc_final: 0.7866 (m-40) REVERT: B 215 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7032 (pp20) REVERT: B 278 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.5533 (m-80) outliers start: 104 outliers final: 74 residues processed: 298 average time/residue: 0.2566 time to fit residues: 120.4649 Evaluate side-chains 295 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 208 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 269 ILE Chi-restraints excluded: chain S residue 340 SER Chi-restraints excluded: chain S residue 370 PHE Chi-restraints excluded: chain S residue 400 TYR Chi-restraints excluded: chain S residue 414 TYR Chi-restraints excluded: chain S residue 503 ILE Chi-restraints excluded: chain S residue 522 LEU Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 568 GLU Chi-restraints excluded: chain S residue 592 LEU Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 736 ASP Chi-restraints excluded: chain S residue 746 CYS Chi-restraints excluded: chain S residue 808 THR Chi-restraints excluded: chain S residue 821 THR Chi-restraints excluded: chain S residue 822 LEU Chi-restraints excluded: chain S residue 842 VAL Chi-restraints excluded: chain S residue 845 ILE Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 267 LYS Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 407 GLN Chi-restraints excluded: chain R residue 458 ILE Chi-restraints excluded: chain R residue 466 ASN Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 573 CYS Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 639 THR Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 780 THR Chi-restraints excluded: chain R residue 791 MET Chi-restraints excluded: chain R residue 820 THR Chi-restraints excluded: chain R residue 846 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 213 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 126 optimal weight: 0.0060 chunk 161 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 220 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 732 GLN A 294 ASN A 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 17564 Z= 0.327 Angle : 0.607 11.084 23928 Z= 0.317 Chirality : 0.044 0.257 2770 Planarity : 0.004 0.043 3062 Dihedral : 5.265 71.856 2496 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.30 % Favored : 91.66 % Rotamer: Outliers : 6.23 % Allowed : 21.68 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.17), residues: 2278 helix: 0.76 (0.18), residues: 804 sheet: -1.88 (0.28), residues: 350 loop : -2.07 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 587 HIS 0.009 0.001 HIS A 322 PHE 0.026 0.002 PHE A 334 TYR 0.023 0.002 TYR A 302 ARG 0.006 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 219 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 216 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7384 (mp) REVERT: S 387 LYS cc_start: 0.6628 (tppt) cc_final: 0.5997 (tptt) REVERT: S 400 TYR cc_start: 0.6396 (OUTLIER) cc_final: 0.4097 (p90) REVERT: S 506 MET cc_start: 0.7500 (mtp) cc_final: 0.7238 (mtp) REVERT: S 592 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7495 (mm) REVERT: S 603 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7082 (mm) REVERT: R 302 GLN cc_start: 0.7387 (mm-40) cc_final: 0.7176 (tm-30) REVERT: R 334 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7203 (mp) REVERT: R 407 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7329 (tm130) REVERT: R 474 ARG cc_start: 0.7213 (mtp-110) cc_final: 0.6922 (mtm-85) REVERT: R 594 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7754 (tp) REVERT: R 843 TYR cc_start: 0.7466 (t80) cc_final: 0.7256 (t80) REVERT: R 846 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7245 (pp) REVERT: R 847 PHE cc_start: 0.7501 (m-10) cc_final: 0.7216 (m-10) REVERT: D 20 LEU cc_start: 0.4595 (mp) cc_final: 0.4034 (pt) REVERT: B 83 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.6827 (p0) REVERT: B 118 ASP cc_start: 0.8421 (t0) cc_final: 0.8206 (t0) REVERT: B 119 ASN cc_start: 0.8209 (m-40) cc_final: 0.7984 (m-40) REVERT: B 215 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7051 (pp20) REVERT: B 278 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.5560 (m-80) outliers start: 108 outliers final: 82 residues processed: 305 average time/residue: 0.2499 time to fit residues: 120.7131 Evaluate side-chains 298 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 205 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 269 ILE Chi-restraints excluded: chain S residue 340 SER Chi-restraints excluded: chain S residue 370 PHE Chi-restraints excluded: chain S residue 400 TYR Chi-restraints excluded: chain S residue 522 LEU Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 592 LEU Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 746 CYS Chi-restraints excluded: chain S residue 808 THR Chi-restraints excluded: chain S residue 821 THR Chi-restraints excluded: chain S residue 822 LEU Chi-restraints excluded: chain S residue 842 VAL Chi-restraints excluded: chain S residue 845 ILE Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 407 GLN Chi-restraints excluded: chain R residue 458 ILE Chi-restraints excluded: chain R residue 466 ASN Chi-restraints excluded: chain R residue 565 ARG Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 573 CYS Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 639 THR Chi-restraints excluded: chain R residue 644 ILE Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 754 ILE Chi-restraints excluded: chain R residue 780 THR Chi-restraints excluded: chain R residue 791 MET Chi-restraints excluded: chain R residue 820 THR Chi-restraints excluded: chain R residue 846 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 176 TRP Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 136 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 150 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS R 466 ASN ** R 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17564 Z= 0.249 Angle : 0.575 10.327 23928 Z= 0.299 Chirality : 0.043 0.211 2770 Planarity : 0.004 0.043 3062 Dihedral : 5.146 72.781 2496 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.17 % Favored : 91.79 % Rotamer: Outliers : 5.59 % Allowed : 22.20 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 2278 helix: 0.86 (0.18), residues: 805 sheet: -1.82 (0.28), residues: 350 loop : -2.06 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 798 HIS 0.007 0.001 HIS A 322 PHE 0.026 0.002 PHE A 334 TYR 0.022 0.001 TYR D 190 ARG 0.006 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 219 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 216 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7372 (mp) REVERT: S 387 LYS cc_start: 0.6626 (tppt) cc_final: 0.5992 (tptt) REVERT: S 400 TYR cc_start: 0.6395 (OUTLIER) cc_final: 0.4005 (p90) REVERT: S 506 MET cc_start: 0.7527 (mtp) cc_final: 0.7319 (mtp) REVERT: S 522 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7577 (mp) REVERT: S 603 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7048 (mm) REVERT: R 302 GLN cc_start: 0.7365 (mm-40) cc_final: 0.7041 (tp40) REVERT: R 334 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7135 (mp) REVERT: R 474 ARG cc_start: 0.7196 (mtp-110) cc_final: 0.6915 (mtm-85) REVERT: R 594 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7682 (tp) REVERT: R 843 TYR cc_start: 0.7454 (t80) cc_final: 0.7193 (t80) REVERT: R 846 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7233 (pp) REVERT: R 847 PHE cc_start: 0.7494 (m-10) cc_final: 0.7233 (m-10) REVERT: D 20 LEU cc_start: 0.4668 (mp) cc_final: 0.4190 (pt) REVERT: B 83 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.6676 (p0) REVERT: B 118 ASP cc_start: 0.8402 (t0) cc_final: 0.8154 (t0) REVERT: B 119 ASN cc_start: 0.8185 (m-40) cc_final: 0.7942 (m-40) REVERT: B 215 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6818 (pp20) REVERT: B 278 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.5506 (m-80) outliers start: 97 outliers final: 76 residues processed: 299 average time/residue: 0.2521 time to fit residues: 119.2026 Evaluate side-chains 290 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 204 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 269 ILE Chi-restraints excluded: chain S residue 340 SER Chi-restraints excluded: chain S residue 400 TYR Chi-restraints excluded: chain S residue 522 LEU Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 644 ILE Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 736 ASP Chi-restraints excluded: chain S residue 746 CYS Chi-restraints excluded: chain S residue 808 THR Chi-restraints excluded: chain S residue 821 THR Chi-restraints excluded: chain S residue 822 LEU Chi-restraints excluded: chain S residue 842 VAL Chi-restraints excluded: chain S residue 845 ILE Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 458 ILE Chi-restraints excluded: chain R residue 466 ASN Chi-restraints excluded: chain R residue 565 ARG Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 573 CYS Chi-restraints excluded: chain R residue 594 LEU Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 626 SER Chi-restraints excluded: chain R residue 639 THR Chi-restraints excluded: chain R residue 712 LEU Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 754 ILE Chi-restraints excluded: chain R residue 791 MET Chi-restraints excluded: chain R residue 846 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 176 TRP Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 200 optimal weight: 1.9990 chunk 211 optimal weight: 0.0980 chunk 192 optimal weight: 0.0670 chunk 205 optimal weight: 0.0670 chunk 123 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 63 optimal weight: 0.0570 chunk 185 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 204 optimal weight: 0.5980 overall best weight: 0.1774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 189 ASN S 452 ASN R 277 ASN R 466 ASN ** R 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17564 Z= 0.166 Angle : 0.546 10.250 23928 Z= 0.283 Chirality : 0.042 0.246 2770 Planarity : 0.004 0.090 3062 Dihedral : 4.949 76.094 2496 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 4.44 % Allowed : 23.70 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), residues: 2278 helix: 1.09 (0.18), residues: 802 sheet: -1.86 (0.27), residues: 372 loop : -1.95 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 798 HIS 0.006 0.001 HIS A 322 PHE 0.024 0.001 PHE A 334 TYR 0.017 0.001 TYR D 190 ARG 0.010 0.000 ARG S 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 228 time to evaluate : 1.954 Fit side-chains revert: symmetry clash REVERT: S 216 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7274 (mp) REVERT: S 387 LYS cc_start: 0.6329 (tppt) cc_final: 0.5746 (tptt) REVERT: S 522 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7405 (mp) REVERT: S 603 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7021 (mm) REVERT: R 302 GLN cc_start: 0.7001 (mm-40) cc_final: 0.6730 (tp40) REVERT: R 334 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7049 (mp) REVERT: R 474 ARG cc_start: 0.7179 (mtp-110) cc_final: 0.6868 (mtm-85) REVERT: R 704 PHE cc_start: 0.7164 (m-10) cc_final: 0.6600 (m-80) REVERT: R 846 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7154 (pp) REVERT: R 847 PHE cc_start: 0.7444 (m-10) cc_final: 0.7222 (m-10) REVERT: D 20 LEU cc_start: 0.4433 (mp) cc_final: 0.3947 (pt) REVERT: D 187 LEU cc_start: 0.7407 (tt) cc_final: 0.7203 (tt) REVERT: B 83 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6603 (p0) REVERT: B 118 ASP cc_start: 0.8414 (t0) cc_final: 0.8190 (t0) REVERT: B 215 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6697 (pp20) REVERT: B 278 PHE cc_start: 0.6767 (OUTLIER) cc_final: 0.5439 (m-80) REVERT: A 247 MET cc_start: 0.7761 (mmm) cc_final: 0.7464 (mtt) outliers start: 77 outliers final: 56 residues processed: 289 average time/residue: 0.2581 time to fit residues: 117.5208 Evaluate side-chains 269 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 205 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 189 ASN Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 269 ILE Chi-restraints excluded: chain S residue 340 SER Chi-restraints excluded: chain S residue 522 LEU Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 644 ILE Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 746 CYS Chi-restraints excluded: chain S residue 808 THR Chi-restraints excluded: chain S residue 821 THR Chi-restraints excluded: chain S residue 822 LEU Chi-restraints excluded: chain S residue 842 VAL Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 277 ASN Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 573 CYS Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 639 THR Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 791 MET Chi-restraints excluded: chain R residue 846 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 135 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 chunk 228 optimal weight: 0.5980 chunk 209 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 ASN ** R 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17564 Z= 0.266 Angle : 0.578 9.812 23928 Z= 0.301 Chirality : 0.043 0.191 2770 Planarity : 0.004 0.041 3062 Dihedral : 4.978 72.370 2496 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.81 % Favored : 92.14 % Rotamer: Outliers : 3.92 % Allowed : 24.05 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.18), residues: 2278 helix: 1.08 (0.18), residues: 798 sheet: -1.81 (0.27), residues: 376 loop : -1.98 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 587 HIS 0.007 0.001 HIS A 322 PHE 0.023 0.002 PHE A 334 TYR 0.019 0.001 TYR D 190 ARG 0.007 0.000 ARG B 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 208 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 216 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7368 (mp) REVERT: S 387 LYS cc_start: 0.6514 (tppt) cc_final: 0.5901 (tptt) REVERT: S 522 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7437 (mp) REVERT: S 592 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7523 (mm) REVERT: S 603 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7039 (mm) REVERT: R 302 GLN cc_start: 0.7027 (mm-40) cc_final: 0.6698 (tp40) REVERT: R 334 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7141 (mp) REVERT: R 474 ARG cc_start: 0.7193 (mtp-110) cc_final: 0.6867 (mtm-85) REVERT: R 704 PHE cc_start: 0.7205 (m-10) cc_final: 0.6668 (m-80) REVERT: R 846 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7182 (pp) REVERT: R 847 PHE cc_start: 0.7496 (m-10) cc_final: 0.7246 (m-10) REVERT: D 20 LEU cc_start: 0.4533 (mp) cc_final: 0.3989 (pt) REVERT: B 83 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7013 (p0) REVERT: B 118 ASP cc_start: 0.8418 (t0) cc_final: 0.8176 (t0) REVERT: B 215 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6758 (pp20) REVERT: B 278 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.5460 (m-80) REVERT: A 247 MET cc_start: 0.7812 (mmm) cc_final: 0.7532 (mtt) outliers start: 68 outliers final: 56 residues processed: 261 average time/residue: 0.2537 time to fit residues: 106.5086 Evaluate side-chains 271 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 206 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 71 LYS Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 254 VAL Chi-restraints excluded: chain S residue 269 ILE Chi-restraints excluded: chain S residue 522 LEU Chi-restraints excluded: chain S residue 564 MET Chi-restraints excluded: chain S residue 592 LEU Chi-restraints excluded: chain S residue 603 LEU Chi-restraints excluded: chain S residue 644 ILE Chi-restraints excluded: chain S residue 718 PHE Chi-restraints excluded: chain S residue 746 CYS Chi-restraints excluded: chain S residue 808 THR Chi-restraints excluded: chain S residue 821 THR Chi-restraints excluded: chain S residue 822 LEU Chi-restraints excluded: chain S residue 842 VAL Chi-restraints excluded: chain S residue 847 PHE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 277 ASN Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 458 ILE Chi-restraints excluded: chain R residue 567 THR Chi-restraints excluded: chain R residue 573 CYS Chi-restraints excluded: chain R residue 618 VAL Chi-restraints excluded: chain R residue 639 THR Chi-restraints excluded: chain R residue 714 ILE Chi-restraints excluded: chain R residue 754 ILE Chi-restraints excluded: chain R residue 791 MET Chi-restraints excluded: chain R residue 846 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 176 TRP Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 144 optimal weight: 2.9990 chunk 193 optimal weight: 0.0980 chunk 55 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 50 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 ASN ** R 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.198140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.173964 restraints weight = 21853.604| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.22 r_work: 0.3860 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17564 Z= 0.202 Angle : 0.553 10.012 23928 Z= 0.285 Chirality : 0.042 0.218 2770 Planarity : 0.004 0.041 3062 Dihedral : 4.932 72.652 2496 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.42 % Favored : 92.54 % Rotamer: Outliers : 3.98 % Allowed : 23.93 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.18), residues: 2278 helix: 1.12 (0.18), residues: 800 sheet: -1.92 (0.27), residues: 377 loop : -1.92 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 798 HIS 0.006 0.001 HIS A 322 PHE 0.023 0.001 PHE A 334 TYR 0.018 0.001 TYR D 190 ARG 0.009 0.000 ARG D 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3648.47 seconds wall clock time: 66 minutes 49.60 seconds (4009.60 seconds total)