Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 17:28:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/07_2023/8jd6_36177_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/07_2023/8jd6_36177.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/07_2023/8jd6_36177_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/07_2023/8jd6_36177_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/07_2023/8jd6_36177_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/07_2023/8jd6_36177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/07_2023/8jd6_36177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/07_2023/8jd6_36177_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd6_36177/07_2023/8jd6_36177_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 8.37, per 1000 atoms: 0.49 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: 6.72 Conformation dependent library (CDL) restraints added in 2.4 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: 1.91 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: 5.78 Time building geometry restraints manager: 7.22 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=" 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=" N VAL R 769 " pdb=" CA VAL R 769 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.29e+00 bond pdb=" N ILE R 677 " pdb=" CA ILE R 677 " ideal model delta sigma weight residual 1.461 1.495 -0.033 1.17e-02 7.31e+03 8.13e+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: 9168 17.98 - 35.95: 941 35.95 - 53.93: 215 53.93 - 71.90: 29 71.90 - 89.88: 7 Dihedral angle restraints: 10360 sinusoidal: 3691 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 10357 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: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 11.310 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 42.860 Find NCS groups from input model: 1.230 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.640 ------------------------------------------------------------------------------- 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 0.039 17564 Z= 0.180 Angle : 0.560 8.674 23928 Z= 0.328 Chirality : 0.042 0.208 2770 Planarity : 0.004 0.087 3062 Dihedral : 15.118 89.879 6012 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 % 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 *********************** 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 : 2.047 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 226 average time/residue: 0.2685 time to fit residues: 96.0208 Evaluate side-chains 207 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 204 time to evaluate : 1.832 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1525 time to fit residues: 3.4791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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** D 232 HIS B 293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 17564 Z= 0.409 Angle : 0.688 10.067 23928 Z= 0.361 Chirality : 0.047 0.250 2770 Planarity : 0.005 0.050 3062 Dihedral : 5.166 78.127 2490 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.33 % Favored : 92.63 % Rotamer Outliers : 4.15 % 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: -1.22 (0.18), residues: 2278 helix: 0.85 (0.18), residues: 804 sheet: -1.52 (0.29), residues: 359 loop : -1.84 (0.18), residues: 1115 *********************** 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 312 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 240 time to evaluate : 1.912 Fit side-chains outliers start: 72 outliers final: 42 residues processed: 295 average time/residue: 0.2749 time to fit residues: 128.6248 Evaluate side-chains 244 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 202 time to evaluate : 2.036 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.1840 time to fit residues: 16.5279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 115 optimal weight: 0.0030 chunk 64 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 208 optimal weight: 0.3980 chunk 225 optimal weight: 0.9980 chunk 185 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 167 optimal weight: 4.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 17564 Z= 0.195 Angle : 0.535 9.294 23928 Z= 0.276 Chirality : 0.042 0.243 2770 Planarity : 0.003 0.041 3062 Dihedral : 4.841 78.545 2490 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer Outliers : 2.08 % 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: -1.04 (0.18), residues: 2278 helix: 1.15 (0.18), residues: 804 sheet: -1.41 (0.28), residues: 364 loop : -1.87 (0.18), residues: 1110 *********************** 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 261 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 225 time to evaluate : 1.770 Fit side-chains outliers start: 36 outliers final: 15 residues processed: 254 average time/residue: 0.2687 time to fit residues: 107.1144 Evaluate side-chains 214 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1531 time to fit residues: 6.8955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 17564 Z= 0.330 Angle : 0.617 12.572 23928 Z= 0.320 Chirality : 0.044 0.242 2770 Planarity : 0.004 0.045 3062 Dihedral : 5.175 76.572 2490 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 3.34 % 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: -1.31 (0.17), residues: 2278 helix: 0.87 (0.18), residues: 807 sheet: -1.60 (0.29), residues: 329 loop : -1.98 (0.18), residues: 1142 *********************** 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 288 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 230 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 30 residues processed: 276 average time/residue: 0.2683 time to fit residues: 117.3386 Evaluate side-chains 239 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 209 time to evaluate : 1.880 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1614 time to fit residues: 11.6358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 184 optimal weight: 0.6980 chunk 125 optimal weight: 0.0670 chunk 3 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 188 optimal weight: 0.2980 chunk 153 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 17564 Z= 0.205 Angle : 0.537 10.088 23928 Z= 0.280 Chirality : 0.042 0.256 2770 Planarity : 0.004 0.044 3062 Dihedral : 5.008 78.377 2490 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.80 % Favored : 93.15 % Rotamer Outliers : 1.79 % 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: -1.09 (0.18), residues: 2278 helix: 1.12 (0.19), residues: 806 sheet: -1.47 (0.29), residues: 335 loop : -1.91 (0.18), residues: 1137 *********************** 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 258 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 227 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 250 average time/residue: 0.2717 time to fit residues: 108.0513 Evaluate side-chains 213 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 199 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2047 time to fit residues: 7.5612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 221 optimal weight: 0.0980 chunk 183 optimal weight: 0.0870 chunk 102 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.0362 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 17564 Z= 0.312 Angle : 0.594 10.902 23928 Z= 0.309 Chirality : 0.044 0.263 2770 Planarity : 0.004 0.041 3062 Dihedral : 5.114 74.779 2490 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.08 % Favored : 91.88 % Rotamer Outliers : 1.67 % 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: -1.21 (0.18), residues: 2278 helix: 0.99 (0.18), residues: 812 sheet: -1.55 (0.29), residues: 332 loop : -1.96 (0.18), residues: 1134 *********************** 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 244 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 215 time to evaluate : 1.916 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 238 average time/residue: 0.2624 time to fit residues: 99.6325 Evaluate side-chains 218 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 203 time to evaluate : 1.917 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1643 time to fit residues: 7.2875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 213 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 126 optimal weight: 0.0000 chunk 161 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 186 optimal weight: 0.4980 chunk 123 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 732 GLN 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: 0.6908 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 17564 Z= 0.196 Angle : 0.544 10.565 23928 Z= 0.281 Chirality : 0.042 0.259 2770 Planarity : 0.003 0.042 3062 Dihedral : 4.967 77.798 2490 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.29 % Favored : 92.67 % Rotamer Outliers : 1.10 % 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: -1.06 (0.18), residues: 2278 helix: 1.14 (0.19), residues: 815 sheet: -1.44 (0.28), residues: 343 loop : -1.92 (0.18), residues: 1120 *********************** 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 236 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 217 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 230 average time/residue: 0.2679 time to fit residues: 98.0433 Evaluate side-chains 216 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 206 time to evaluate : 1.847 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1618 time to fit residues: 5.6914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 136 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 150 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 20 optimal weight: 0.0060 chunk 173 optimal weight: 1.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- 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 340 ASN A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 17564 Z= 0.285 Angle : 0.579 10.162 23928 Z= 0.301 Chirality : 0.043 0.257 2770 Planarity : 0.004 0.041 3062 Dihedral : 5.051 73.905 2490 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.95 % Favored : 92.01 % Rotamer Outliers : 0.75 % 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: -1.18 (0.18), residues: 2278 helix: 1.03 (0.18), residues: 814 sheet: -1.47 (0.29), residues: 342 loop : -1.99 (0.18), residues: 1122 *********************** 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 232 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 219 time to evaluate : 1.915 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 230 average time/residue: 0.2806 time to fit residues: 102.0202 Evaluate side-chains 210 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 204 time to evaluate : 1.931 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2256 time to fit residues: 4.8433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0070 chunk 192 optimal weight: 0.0980 chunk 205 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 185 optimal weight: 0.5980 chunk 194 optimal weight: 0.9980 chunk 204 optimal weight: 0.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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** A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 17564 Z= 0.208 Angle : 0.550 10.207 23928 Z= 0.285 Chirality : 0.042 0.265 2770 Planarity : 0.004 0.056 3062 Dihedral : 4.965 75.310 2490 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.37 % Favored : 92.58 % Rotamer Outliers : 0.52 % 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: 1.14 (0.19), residues: 812 sheet: -1.46 (0.29), residues: 343 loop : -1.93 (0.18), residues: 1123 *********************** 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 222 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 213 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 219 average time/residue: 0.2684 time to fit residues: 93.1157 Evaluate side-chains 210 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 204 time to evaluate : 1.965 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1788 time to fit residues: 4.6693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 132 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 chunk 228 optimal weight: 0.0870 chunk 209 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 140 optimal weight: 0.0570 chunk 111 optimal weight: 5.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- 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** A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 17564 Z= 0.184 Angle : 0.539 8.415 23928 Z= 0.279 Chirality : 0.042 0.254 2770 Planarity : 0.004 0.056 3062 Dihedral : 4.880 75.775 2490 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.68 % Favored : 92.27 % Rotamer Outliers : 0.40 % 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: -0.99 (0.18), residues: 2278 helix: 1.27 (0.19), residues: 800 sheet: -1.38 (0.29), residues: 348 loop : -1.91 (0.18), residues: 1130 ********************** 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 223 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 216 time to evaluate : 1.901 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 221 average time/residue: 0.2785 time to fit residues: 97.7895 Evaluate side-chains 210 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 205 time to evaluate : 2.231 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1719 time to fit residues: 4.2857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 144 optimal weight: 0.6980 chunk 193 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 167 optimal weight: 0.6980 chunk 26 optimal weight: 0.0060 chunk 50 optimal weight: 0.0170 chunk 181 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 186 optimal weight: 0.0170 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 overall best weight: 0.2872 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.203356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.181445 restraints weight = 21817.290| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.93 r_work: 0.3932 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 17564 Z= 0.175 Angle : 0.536 11.183 23928 Z= 0.277 Chirality : 0.042 0.254 2770 Planarity : 0.004 0.043 3062 Dihedral : 4.813 75.381 2490 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.94 % Favored : 93.02 % Rotamer Outliers : 0.40 % 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: -1.01 (0.18), residues: 2278 helix: 1.22 (0.19), residues: 815 sheet: -1.41 (0.29), residues: 353 loop : -1.93 (0.18), residues: 1110 =============================================================================== Job complete usr+sys time: 3357.03 seconds wall clock time: 62 minutes 15.29 seconds (3735.29 seconds total)