Starting phenix.real_space_refine on Sun Aug 24 09:02:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jd5_36176/08_2025/8jd5_36176_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jd5_36176/08_2025/8jd5_36176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jd5_36176/08_2025/8jd5_36176_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jd5_36176/08_2025/8jd5_36176_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jd5_36176/08_2025/8jd5_36176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jd5_36176/08_2025/8jd5_36176.map" } resolution = 3.6 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 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= 0.001 sd= 0.933 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 1 5.49 5 S 120 5.16 5 Cl 1 4.86 5 C 11562 2.51 5 N 3070 2.21 5 O 3274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18028 Number of models: 1 Model: "" Number of chains: 8 Chain: "2" Number of atoms: 5885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5885 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 39, 'TRANS': 745} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 14, 'ARG:plan': 13, 'ASP:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 4, 'TRP:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 183 Chain: "4" Number of atoms: 5804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 5804 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 38, 'TRANS': 726} Chain breaks: 4 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 5, 'ARG:plan': 7, 'GLN:plan1': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 129 Chain: "A" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1644 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 9, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2380 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 11, 'GLN:plan1': 5, 'GLU:plan': 6, 'ASP:plan': 10, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 141 Chain: "C" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 334 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "H" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1703 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "2" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {'CLR': 3, 'HZR': 1, 'NAG': 1, 'PEF': 1} Inner-chain residues flagged as termini: ['pdbres="GLU 2 902 "'] Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "4" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Unusual residues: {'BQI': 1, 'CLR': 2, 'NAG': 1} Inner-chain residues flagged as termini: ['pdbres="GLU 41002 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.18, per 1000 atoms: 0.18 Number of scatterers: 18028 At special positions: 0 Unit cell: (112.455, 126.378, 245.259, 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 120 16.00 P 1 15.00 O 3274 8.00 N 3070 7.00 C 11562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS 2 50 " - pdb=" SG CYS 2 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 234 " - pdb=" SG CYS 2 518 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 355 " - pdb=" SG CYS 2 362 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 400 " - pdb=" SG CYS 2 407 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 500 " - pdb=" SG CYS 2 519 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 504 " - pdb=" SG CYS 2 522 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 525 " - pdb=" SG CYS 2 537 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 67 " - pdb=" SG CYS 4 109 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 249 " - pdb=" SG CYS 4 538 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 428 " - pdb=" SG CYS 4 435 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 520 " - pdb=" SG CYS 4 539 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 524 " - pdb=" SG CYS 4 542 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 545 " - pdb=" SG CYS 4 557 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 560 " - pdb=" SG CYS 4 573 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 652 " - pdb=" SG CYS 4 746 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG 2 905 " - " ASN 2 203 " " NAG 41003 " - " ASN 4 454 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 782.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4442 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 25 sheets defined 38.7% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain '2' and resid 58 through 74 removed outlier: 3.604A pdb=" N LEU 2 66 " --> pdb=" O LEU 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 94 through 102 Processing helix chain '2' and resid 103 through 107 removed outlier: 3.623A pdb=" N ARG 2 107 " --> pdb=" O ASP 2 104 " (cutoff:3.500A) Processing helix chain '2' and resid 144 through 158 removed outlier: 3.550A pdb=" N LEU 2 154 " --> pdb=" O GLN 2 150 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE 2 158 " --> pdb=" O LEU 2 154 " (cutoff:3.500A) Processing helix chain '2' and resid 191 through 202 Processing helix chain '2' and resid 216 through 231 Processing helix chain '2' and resid 246 through 258 removed outlier: 3.587A pdb=" N GLU 2 251 " --> pdb=" O ARG 2 247 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL 2 254 " --> pdb=" O PHE 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 271 through 284 removed outlier: 3.792A pdb=" N ARG 2 276 " --> pdb=" O SER 2 272 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU 2 277 " --> pdb=" O GLU 2 273 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU 2 278 " --> pdb=" O ASP 2 274 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG 2 284 " --> pdb=" O ALA 2 280 " (cutoff:3.500A) Processing helix chain '2' and resid 324 through 333 removed outlier: 3.539A pdb=" N SER 2 329 " --> pdb=" O SER 2 325 " (cutoff:3.500A) Processing helix chain '2' and resid 344 through 352 removed outlier: 3.618A pdb=" N GLU 2 350 " --> pdb=" O ARG 2 346 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN 2 351 " --> pdb=" O GLU 2 347 " (cutoff:3.500A) Processing helix chain '2' and resid 377 through 400 removed outlier: 3.899A pdb=" N MET 2 388 " --> pdb=" O ALA 2 384 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA 2 391 " --> pdb=" O ALA 2 387 " (cutoff:3.500A) Processing helix chain '2' and resid 414 through 423 removed outlier: 3.595A pdb=" N LYS 2 420 " --> pdb=" O ARG 2 416 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP 2 421 " --> pdb=" O ARG 2 417 " (cutoff:3.500A) Processing helix chain '2' and resid 485 through 493 removed outlier: 3.880A pdb=" N SER 2 489 " --> pdb=" O PRO 2 486 " (cutoff:3.500A) Proline residue: 2 490 - end of helix removed outlier: 4.165A pdb=" N GLY 2 493 " --> pdb=" O PRO 2 490 " (cutoff:3.500A) Processing helix chain '2' and resid 565 through 568 Processing helix chain '2' and resid 569 through 592 Processing helix chain '2' and resid 597 through 601 removed outlier: 3.868A pdb=" N SER 2 601 " --> pdb=" O VAL 2 598 " (cutoff:3.500A) Processing helix chain '2' and resid 602 through 621 removed outlier: 3.517A pdb=" N TYR 2 607 " --> pdb=" O ARG 2 603 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE 2 608 " --> pdb=" O GLU 2 604 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE 2 621 " --> pdb=" O TYR 2 617 " (cutoff:3.500A) Processing helix chain '2' and resid 622 through 624 No H-bonds generated for 'chain '2' and resid 622 through 624' Processing helix chain '2' and resid 628 through 662 removed outlier: 3.946A pdb=" N LEU 2 634 " --> pdb=" O ALA 2 630 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG 2 636 " --> pdb=" O CYS 2 632 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU 2 637 " --> pdb=" O THR 2 633 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE 2 643 " --> pdb=" O LEU 2 639 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR 2 647 " --> pdb=" O PHE 2 643 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU 2 650 " --> pdb=" O CYS 2 646 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU 2 651 " --> pdb=" O TYR 2 647 " (cutoff:3.500A) Processing helix chain '2' and resid 675 through 701 removed outlier: 3.670A pdb=" N VAL 2 680 " --> pdb=" O PRO 2 676 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA 2 681 " --> pdb=" O ALA 2 677 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU 2 686 " --> pdb=" O ILE 2 682 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN 2 690 " --> pdb=" O LEU 2 686 " (cutoff:3.500A) Processing helix chain '2' and resid 728 through 747 removed outlier: 3.982A pdb=" N LEU 2 732 " --> pdb=" O MET 2 728 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU 2 741 " --> pdb=" O LEU 2 737 " (cutoff:3.500A) Processing helix chain '2' and resid 753 through 757 removed outlier: 3.802A pdb=" N PHE 2 756 " --> pdb=" O PRO 2 753 " (cutoff:3.500A) Processing helix chain '2' and resid 758 through 783 removed outlier: 3.970A pdb=" N CYS 2 770 " --> pdb=" O MET 2 766 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU 2 777 " --> pdb=" O TRP 2 773 " (cutoff:3.500A) Proline residue: 2 778 - end of helix Processing helix chain '2' and resid 786 through 818 removed outlier: 3.680A pdb=" N THR 2 792 " --> pdb=" O ARG 2 788 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET 2 794 " --> pdb=" O GLN 2 790 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL 2 798 " --> pdb=" O MET 2 794 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER 2 799 " --> pdb=" O CYS 2 795 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA 2 811 " --> pdb=" O GLY 2 807 " (cutoff:3.500A) Proline residue: 2 812 - end of helix removed outlier: 3.723A pdb=" N ILE 2 816 " --> pdb=" O PRO 2 812 " (cutoff:3.500A) Processing helix chain '4' and resid 75 through 90 removed outlier: 3.919A pdb=" N ALA 4 81 " --> pdb=" O HIS 4 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET 4 82 " --> pdb=" O ARG 4 78 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN 4 90 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 120 removed outlier: 3.694A pdb=" N LEU 4 116 " --> pdb=" O ASP 4 112 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU 4 117 " --> pdb=" O THR 4 113 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN 4 118 " --> pdb=" O HIS 4 114 " (cutoff:3.500A) Processing helix chain '4' and resid 158 through 170 removed outlier: 4.050A pdb=" N ILE 4 168 " --> pdb=" O MET 4 164 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG 4 170 " --> pdb=" O ALA 4 166 " (cutoff:3.500A) Processing helix chain '4' and resid 184 through 188 Processing helix chain '4' and resid 201 through 216 removed outlier: 3.801A pdb=" N GLN 4 205 " --> pdb=" O SER 4 201 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN 4 207 " --> pdb=" O THR 4 203 " (cutoff:3.500A) Processing helix chain '4' and resid 230 through 246 removed outlier: 3.647A pdb=" N ALA 4 237 " --> pdb=" O SER 4 233 " (cutoff:3.500A) Processing helix chain '4' and resid 261 through 275 removed outlier: 4.144A pdb=" N PHE 4 265 " --> pdb=" O LYS 4 261 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP 4 266 " --> pdb=" O ALA 4 262 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR 4 275 " --> pdb=" O ARG 4 271 " (cutoff:3.500A) Processing helix chain '4' and resid 286 through 300 removed outlier: 4.096A pdb=" N ARG 4 291 " --> pdb=" O GLU 4 287 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG 4 292 " --> pdb=" O ASP 4 288 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG 4 298 " --> pdb=" O LEU 4 294 " (cutoff:3.500A) Processing helix chain '4' and resid 312 through 315 removed outlier: 3.635A pdb=" N GLY 4 315 " --> pdb=" O ASP 4 312 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 312 through 315' Processing helix chain '4' and resid 318 through 322 Processing helix chain '4' and resid 341 through 349 removed outlier: 3.535A pdb=" N ASP 4 345 " --> pdb=" O VAL 4 341 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG 4 346 " --> pdb=" O ARG 4 342 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR 4 347 " --> pdb=" O GLY 4 343 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER 4 349 " --> pdb=" O ASP 4 345 " (cutoff:3.500A) Processing helix chain '4' and resid 360 through 372 removed outlier: 4.341A pdb=" N GLU 4 364 " --> pdb=" O ILE 4 360 " (cutoff:3.500A) Processing helix chain '4' and resid 394 through 398 removed outlier: 3.888A pdb=" N SER 4 398 " --> pdb=" O GLY 4 395 " (cutoff:3.500A) Processing helix chain '4' and resid 405 through 428 removed outlier: 3.654A pdb=" N VAL 4 409 " --> pdb=" O LYS 4 405 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL 4 413 " --> pdb=" O VAL 4 409 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR 4 414 " --> pdb=" O ILE 4 410 " (cutoff:3.500A) Processing helix chain '4' and resid 435 through 439 Processing helix chain '4' and resid 442 through 452 removed outlier: 3.754A pdb=" N LYS 4 448 " --> pdb=" O THR 4 444 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR 4 449 " --> pdb=" O GLN 4 445 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN 4 452 " --> pdb=" O LYS 4 448 " (cutoff:3.500A) Processing helix chain '4' and resid 585 through 588 Processing helix chain '4' and resid 589 through 612 Processing helix chain '4' and resid 617 through 621 Processing helix chain '4' and resid 626 through 644 removed outlier: 3.586A pdb=" N LEU 4 630 " --> pdb=" O SER 4 626 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR 4 640 " --> pdb=" O CYS 4 636 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE 4 641 " --> pdb=" O TYR 4 637 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE 4 644 " --> pdb=" O THR 4 640 " (cutoff:3.500A) Processing helix chain '4' and resid 648 through 687 removed outlier: 3.608A pdb=" N ARG 4 656 " --> pdb=" O CYS 4 652 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE 4 657 " --> pdb=" O SER 4 653 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET 4 663 " --> pdb=" O LEU 4 659 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER 4 666 " --> pdb=" O GLY 4 662 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA 4 669 " --> pdb=" O ILE 4 665 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU 4 670 " --> pdb=" O SER 4 666 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG 4 686 " --> pdb=" O GLU 4 682 " (cutoff:3.500A) Processing helix chain '4' and resid 695 through 721 removed outlier: 3.527A pdb=" N LEU 4 700 " --> pdb=" O PRO 4 696 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA 4 701 " --> pdb=" O ALA 4 697 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE 4 702 " --> pdb=" O SER 4 698 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU 4 706 " --> pdb=" O ILE 4 702 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE 4 707 " --> pdb=" O THR 4 703 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN 4 710 " --> pdb=" O LEU 4 706 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N CYS 4 715 " --> pdb=" O LEU 4 711 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL 4 716 " --> pdb=" O LEU 4 712 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP 4 717 " --> pdb=" O GLY 4 713 " (cutoff:3.500A) Processing helix chain '4' and resid 749 through 774 removed outlier: 3.931A pdb=" N SER 4 760 " --> pdb=" O LEU 4 756 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR 4 766 " --> pdb=" O LEU 4 762 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS 4 767 " --> pdb=" O LEU 4 763 " (cutoff:3.500A) Processing helix chain '4' and resid 780 through 783 Processing helix chain '4' and resid 784 through 800 removed outlier: 3.647A pdb=" N TYR 4 792 " --> pdb=" O GLY 4 788 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL 4 797 " --> pdb=" O THR 4 793 " (cutoff:3.500A) Processing helix chain '4' and resid 801 through 806 Processing helix chain '4' and resid 819 through 847 removed outlier: 4.062A pdb=" N THR 4 823 " --> pdb=" O THR 4 819 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL 4 824 " --> pdb=" O THR 4 820 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER 4 833 " --> pdb=" O SER 4 829 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET 4 836 " --> pdb=" O VAL 4 832 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET 4 839 " --> pdb=" O GLY 4 835 " (cutoff:3.500A) Proline residue: 4 840 - end of helix Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.881A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.987A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 241 through 256 removed outlier: 3.599A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.181A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.510A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 4.148A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.895A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR B 29 " --> pdb=" O CYS B 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 25 removed outlier: 3.710A pdb=" N LEU C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.710A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain '2' and resid 87 through 90 removed outlier: 7.060A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL 2 33 " --> pdb=" O ILE 2 136 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLY 2 138 " --> pdb=" O VAL 2 33 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N ILE 2 163 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL 2 139 " --> pdb=" O ILE 2 163 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLN 2 162 " --> pdb=" O ALA 2 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 41 through 43 Processing sheet with id=AA3, first strand: chain '2' and resid 234 through 235 removed outlier: 8.980A pdb=" N GLU 2 239 " --> pdb=" O VAL 2 207 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR 2 209 " --> pdb=" O GLU 2 239 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL 2 241 " --> pdb=" O THR 2 209 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA 2 211 " --> pdb=" O VAL 2 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 234 through 235 removed outlier: 7.303A pdb=" N TYR 2 206 " --> pdb=" O VAL 2 265 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL 2 267 " --> pdb=" O TYR 2 206 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER 2 208 " --> pdb=" O VAL 2 267 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE 2 269 " --> pdb=" O SER 2 208 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL 2 210 " --> pdb=" O PHE 2 269 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TRP 2 291 " --> pdb=" O ILE 2 315 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE 2 317 " --> pdb=" O TRP 2 291 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA 2 293 " --> pdb=" O ILE 2 317 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N LEU 2 319 " --> pdb=" O ALA 2 293 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALA 2 314 " --> pdb=" O TYR 2 458 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR 2 453 " --> pdb=" O TRP 2 474 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY 2 472 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR 2 457 " --> pdb=" O LYS 2 470 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS 2 470 " --> pdb=" O THR 2 457 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU 2 459 " --> pdb=" O TYR 2 468 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N TYR 2 468 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 428 through 429 Processing sheet with id=AA6, first strand: chain '2' and resid 509 through 511 Processing sheet with id=AA7, first strand: chain '4' and resid 101 through 107 removed outlier: 6.620A pdb=" N ILE 4 49 " --> pdb=" O GLY 4 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ARG 4 104 " --> pdb=" O ILE 4 49 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU 4 51 " --> pdb=" O ARG 4 104 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU 4 106 " --> pdb=" O LEU 4 51 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY 4 53 " --> pdb=" O LEU 4 106 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR 4 50 " --> pdb=" O VAL 4 150 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY 4 152 " --> pdb=" O THR 4 50 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ILE 4 177 " --> pdb=" O VAL 4 151 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL 4 153 " --> pdb=" O ILE 4 177 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN 4 176 " --> pdb=" O SER 4 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '4' and resid 249 through 256 removed outlier: 7.829A pdb=" N VAL 4 221 " --> pdb=" O ALA 4 251 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N SER 4 253 " --> pdb=" O VAL 4 221 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR 4 223 " --> pdb=" O SER 4 253 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS 4 255 " --> pdb=" O THR 4 223 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA 4 225 " --> pdb=" O LYS 4 255 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR 4 220 " --> pdb=" O ALA 4 280 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE 4 282 " --> pdb=" O TYR 4 220 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER 4 222 " --> pdb=" O ILE 4 282 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE 4 284 " --> pdb=" O SER 4 222 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL 4 224 " --> pdb=" O PHE 4 284 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE 4 334 " --> pdb=" O GLY 4 310 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR 4 475 " --> pdb=" O SER 4 494 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N SER 4 494 " --> pdb=" O TYR 4 475 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE 4 477 " --> pdb=" O ILE 4 492 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN 4 481 " --> pdb=" O GLU 4 488 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU 4 488 " --> pdb=" O GLN 4 481 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '4' and resid 455 through 456 removed outlier: 3.629A pdb=" N PHE 4 455 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '4' and resid 531 through 533 Processing sheet with id=AB2, first strand: chain '4' and resid 564 through 566 Processing sheet with id=AB3, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.648A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 36 through 39 removed outlier: 5.471A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.958A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.176A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.724A pdb=" N THR B 159 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 207 through 209 Processing sheet with id=AB9, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.517A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 284 through 286 removed outlier: 7.511A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 315 through 320 removed outlier: 4.094A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.579A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.750A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.750A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.701A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER H 208 " --> pdb=" O ALA H 211 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER H 204 " --> pdb=" O THR H 215 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 194 through 195 removed outlier: 6.763A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR H 175 " --> pdb=" O MET H 230 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 1965 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: 3.09 Time building geometry restraints manager: 1.89 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: 2857 1.31 - 1.44: 5100 1.44 - 1.57: 10323 1.57 - 1.70: 7 1.70 - 1.83: 161 Bond restraints: 18448 Sorted by residual: bond pdb=" C18 HZR 2 901 " pdb=" C19 HZR 2 901 " ideal model delta sigma weight residual 1.353 1.524 -0.171 2.00e-02 2.50e+03 7.32e+01 bond pdb=" C19 HZR 2 901 " pdb=" N20 HZR 2 901 " ideal model delta sigma weight residual 1.353 1.487 -0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" C10 PEF 2 904 " pdb=" O2 PEF 2 904 " ideal model delta sigma weight residual 1.330 1.452 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C03 HZR 2 901 " pdb=" C05 HZR 2 901 " ideal model delta sigma weight residual 1.377 1.494 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C02 HZR 2 901 " pdb=" N20 HZR 2 901 " ideal model delta sigma weight residual 1.388 1.487 -0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 18443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 24984 3.09 - 6.18: 151 6.18 - 9.28: 14 9.28 - 12.37: 3 12.37 - 15.46: 1 Bond angle restraints: 25153 Sorted by residual: angle pdb=" C PRO 2 496 " pdb=" N ALA 2 497 " pdb=" CA ALA 2 497 " ideal model delta sigma weight residual 123.03 113.22 9.81 1.79e+00 3.12e-01 3.00e+01 angle pdb=" O3P PEF 2 904 " pdb=" P PEF 2 904 " pdb=" O4P PEF 2 904 " ideal model delta sigma weight residual 93.96 109.42 -15.46 3.00e+00 1.11e-01 2.66e+01 angle pdb=" C PRO 2 261 " pdb=" N SER 2 262 " pdb=" CA SER 2 262 " ideal model delta sigma weight residual 122.65 114.49 8.16 1.60e+00 3.91e-01 2.60e+01 angle pdb=" N LYS 2 260 " pdb=" CA LYS 2 260 " pdb=" C LYS 2 260 " ideal model delta sigma weight residual 108.76 101.60 7.16 1.44e+00 4.82e-01 2.47e+01 angle pdb=" C ARG 2 499 " pdb=" CA ARG 2 499 " pdb=" CB ARG 2 499 " ideal model delta sigma weight residual 109.37 118.41 -9.04 1.83e+00 2.99e-01 2.44e+01 ... (remaining 25148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.28: 10624 24.28 - 48.57: 438 48.57 - 72.85: 53 72.85 - 97.13: 27 97.13 - 121.42: 16 Dihedral angle restraints: 11158 sinusoidal: 4260 harmonic: 6898 Sorted by residual: dihedral pdb=" CB CYS 2 525 " pdb=" SG CYS 2 525 " pdb=" SG CYS 2 537 " pdb=" CB CYS 2 537 " ideal model delta sinusoidal sigma weight residual 93.00 -177.75 -89.25 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS 4 652 " pdb=" SG CYS 4 652 " pdb=" SG CYS 4 746 " pdb=" CB CYS 4 746 " ideal model delta sinusoidal sigma weight residual 93.00 177.57 -84.57 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" CB CYS 4 520 " pdb=" SG CYS 4 520 " pdb=" SG CYS 4 539 " pdb=" CB CYS 4 539 " ideal model delta sinusoidal sigma weight residual 93.00 175.39 -82.39 1 1.00e+01 1.00e-02 8.33e+01 ... (remaining 11155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2616 0.071 - 0.143: 268 0.143 - 0.214: 23 0.214 - 0.285: 2 0.285 - 0.357: 2 Chirality restraints: 2911 Sorted by residual: chirality pdb=" CA ASP B 186 " pdb=" N ASP B 186 " pdb=" C ASP B 186 " pdb=" CB ASP B 186 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C2 PEF 2 904 " pdb=" C1 PEF 2 904 " pdb=" C3 PEF 2 904 " pdb=" O2 PEF 2 904 " both_signs ideal model delta sigma weight residual False -2.35 -2.68 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA GLU 2 502 " pdb=" N GLU 2 502 " pdb=" C GLU 2 502 " pdb=" CB GLU 2 502 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2908 not shown) Planarity restraints: 3181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 184 " -0.026 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C THR B 184 " 0.085 2.00e-02 2.50e+03 pdb=" O THR B 184 " -0.031 2.00e-02 2.50e+03 pdb=" N GLY B 185 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU 2 258 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.51e+00 pdb=" C LEU 2 258 " 0.053 2.00e-02 2.50e+03 pdb=" O LEU 2 258 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN 2 259 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 208 " -0.270 9.50e-02 1.11e+02 1.21e-01 9.02e+00 pdb=" NE ARG A 208 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 208 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 208 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 208 " -0.009 2.00e-02 2.50e+03 ... (remaining 3178 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1285 2.74 - 3.28: 18156 3.28 - 3.82: 28928 3.82 - 4.36: 33792 4.36 - 4.90: 58412 Nonbonded interactions: 140573 Sorted by model distance: nonbonded pdb=" O LEU A 268 " pdb=" OG1 THR A 324 " model vdw 2.201 3.040 nonbonded pdb=" O GLN 2 790 " pdb=" OG1 THR 2 793 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR 4 672 " pdb=" OE1 GLN 4 699 " model vdw 2.225 3.040 nonbonded pdb=" O GLY H 112 " pdb=" OG SER H 184 " model vdw 2.225 3.040 nonbonded pdb=" O PRO 2 434 " pdb=" OG1 THR 2 437 " model vdw 2.230 3.040 ... (remaining 140568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.670 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 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 : 0.005 0.171 18468 Z= 0.283 Angle : 0.648 15.462 25195 Z= 0.360 Chirality : 0.045 0.357 2911 Planarity : 0.004 0.121 3179 Dihedral : 14.128 121.417 6662 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.18 % Rotamer: Outliers : 0.39 % Allowed : 0.67 % Favored : 98.94 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.17), residues: 2361 helix: 0.69 (0.19), residues: 753 sheet: 0.16 (0.29), residues: 353 loop : -1.61 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 264 TYR 0.017 0.001 TYR H 235 PHE 0.030 0.001 PHE A 189 TRP 0.012 0.001 TRP 4 717 HIS 0.005 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00483 (18448) covalent geometry : angle 0.63908 (25153) SS BOND : bond 0.00252 ( 18) SS BOND : angle 2.75881 ( 36) hydrogen bonds : bond 0.28296 ( 685) hydrogen bonds : angle 8.01743 ( 1965) link_NAG-ASN : bond 0.00587 ( 2) link_NAG-ASN : angle 2.02808 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 275 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: 2 82 VAL cc_start: 0.8285 (t) cc_final: 0.7924 (t) REVERT: 2 174 ASP cc_start: 0.7518 (t70) cc_final: 0.7233 (t0) REVERT: 2 262 SER cc_start: 0.7248 (OUTLIER) cc_final: 0.6695 (t) REVERT: 2 442 ARG cc_start: 0.7960 (ptm-80) cc_final: 0.7675 (ptm-80) REVERT: 4 642 LEU cc_start: 0.8372 (tt) cc_final: 0.7715 (mm) REVERT: 4 729 PHE cc_start: 0.6793 (t80) cc_final: 0.6312 (t80) REVERT: A 25 GLU cc_start: 0.7334 (pp20) cc_final: 0.7060 (pt0) REVERT: A 186 GLU cc_start: 0.6675 (tt0) cc_final: 0.5727 (pp20) REVERT: A 297 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6216 (pm20) REVERT: A 324 THR cc_start: 0.8326 (p) cc_final: 0.8118 (p) REVERT: C 48 ASP cc_start: 0.6963 (t0) cc_final: 0.6104 (t70) REVERT: H 27 PHE cc_start: 0.6987 (p90) cc_final: 0.6720 (p90) REVERT: H 173 TYR cc_start: 0.8464 (m-80) cc_final: 0.8133 (m-10) outliers start: 7 outliers final: 3 residues processed: 281 average time/residue: 0.1324 time to fit residues: 55.3958 Evaluate side-chains 210 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 206 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 262 SER Chi-restraints excluded: chain 2 residue 498 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 541 HIS A 188 HIS A 204 GLN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN H 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.195231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.172137 restraints weight = 24247.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.170245 restraints weight = 40689.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.170858 restraints weight = 40369.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.170259 restraints weight = 29313.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.170708 restraints weight = 25836.886| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18468 Z= 0.178 Angle : 0.659 9.389 25195 Z= 0.338 Chirality : 0.045 0.233 2911 Planarity : 0.005 0.055 3179 Dihedral : 7.768 71.238 3025 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.23 % Allowed : 8.56 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.17), residues: 2361 helix: 0.49 (0.18), residues: 808 sheet: -0.23 (0.27), residues: 404 loop : -1.53 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 134 TYR 0.029 0.002 TYR 4 667 PHE 0.021 0.002 PHE A 336 TRP 0.018 0.002 TRP 2 297 HIS 0.015 0.001 HIS 4 541 Details of bonding type rmsd covalent geometry : bond 0.00408 (18448) covalent geometry : angle 0.65676 (25153) SS BOND : bond 0.00364 ( 18) SS BOND : angle 1.30515 ( 36) hydrogen bonds : bond 0.05024 ( 685) hydrogen bonds : angle 5.17165 ( 1965) link_NAG-ASN : bond 0.00467 ( 2) link_NAG-ASN : angle 1.87811 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: 4 449 TYR cc_start: 0.8273 (m-80) cc_final: 0.7807 (m-80) REVERT: 4 634 PHE cc_start: 0.8266 (t80) cc_final: 0.7971 (t80) REVERT: 4 642 LEU cc_start: 0.8041 (tt) cc_final: 0.7620 (mm) REVERT: A 186 GLU cc_start: 0.6989 (tt0) cc_final: 0.6731 (tm-30) REVERT: A 324 THR cc_start: 0.8093 (p) cc_final: 0.7401 (p) REVERT: B 22 ARG cc_start: 0.5432 (mmt180) cc_final: 0.5160 (mtt90) REVERT: B 78 LYS cc_start: 0.7848 (mmmt) cc_final: 0.7465 (mmtm) REVERT: C 48 ASP cc_start: 0.6350 (t70) cc_final: 0.6075 (t70) REVERT: H 95 TYR cc_start: 0.7699 (m-80) cc_final: 0.7409 (m-80) outliers start: 22 outliers final: 14 residues processed: 245 average time/residue: 0.1365 time to fit residues: 49.1879 Evaluate side-chains 207 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 379 MET Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 46 ASP Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 250 ILE Chi-restraints excluded: chain 4 residue 293 VAL Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 9 optimal weight: 0.0770 chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 283 GLN 2 374 GLN ** 2 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 331 ASN B 340 ASN H 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.181267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.155869 restraints weight = 24048.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154676 restraints weight = 41657.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155631 restraints weight = 35917.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.156751 restraints weight = 24044.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.156924 restraints weight = 22574.735| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 18468 Z= 0.272 Angle : 0.723 10.190 25195 Z= 0.372 Chirality : 0.047 0.228 2911 Planarity : 0.005 0.062 3179 Dihedral : 6.572 64.124 3020 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.19 % Allowed : 11.36 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.17), residues: 2361 helix: 0.36 (0.18), residues: 816 sheet: -0.56 (0.26), residues: 402 loop : -1.63 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.037 0.002 TYR 4 667 PHE 0.022 0.002 PHE B 180 TRP 0.020 0.002 TRP 2 297 HIS 0.010 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00645 (18448) covalent geometry : angle 0.71964 (25153) SS BOND : bond 0.00360 ( 18) SS BOND : angle 1.63940 ( 36) hydrogen bonds : bond 0.05473 ( 685) hydrogen bonds : angle 5.00563 ( 1965) link_NAG-ASN : bond 0.00190 ( 2) link_NAG-ASN : angle 3.08288 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 214 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: 2 221 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7440 (mm) REVERT: A 20 ASP cc_start: 0.7870 (t70) cc_final: 0.7642 (t70) REVERT: A 324 THR cc_start: 0.8404 (p) cc_final: 0.8103 (p) REVERT: B 332 TRP cc_start: 0.8517 (m-10) cc_final: 0.7978 (m-10) REVERT: H 95 TYR cc_start: 0.7717 (m-80) cc_final: 0.7423 (m-80) REVERT: H 159 CYS cc_start: 0.6543 (t) cc_final: 0.6262 (t) REVERT: H 229 CYS cc_start: 0.5730 (p) cc_final: 0.5246 (p) outliers start: 57 outliers final: 37 residues processed: 251 average time/residue: 0.1205 time to fit residues: 46.3000 Evaluate side-chains 219 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 49 ASP Chi-restraints excluded: chain 2 residue 205 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 226 LEU Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 598 VAL Chi-restraints excluded: chain 2 residue 771 ILE Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 49 ILE Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 168 ILE Chi-restraints excluded: chain 4 residue 250 ILE Chi-restraints excluded: chain 4 residue 293 VAL Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 539 CYS Chi-restraints excluded: chain 4 residue 597 VAL Chi-restraints excluded: chain 4 residue 657 ILE Chi-restraints excluded: chain 4 residue 658 PHE Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain H residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 198 optimal weight: 0.6980 chunk 201 optimal weight: 0.4980 chunk 213 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 192 optimal weight: 0.7980 chunk 220 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 191 GLN ** 2 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 355 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.186535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.162506 restraints weight = 24064.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.159488 restraints weight = 40987.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.160595 restraints weight = 43216.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.161054 restraints weight = 27691.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.161754 restraints weight = 23266.788| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18468 Z= 0.145 Angle : 0.595 9.400 25195 Z= 0.304 Chirality : 0.043 0.252 2911 Planarity : 0.004 0.057 3179 Dihedral : 5.901 58.974 3020 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.57 % Allowed : 15.22 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.17), residues: 2361 helix: 0.67 (0.19), residues: 810 sheet: -0.48 (0.26), residues: 398 loop : -1.59 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.030 0.001 TYR 4 667 PHE 0.018 0.001 PHE 4 693 TRP 0.015 0.001 TRP 4 583 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00334 (18448) covalent geometry : angle 0.59255 (25153) SS BOND : bond 0.00249 ( 18) SS BOND : angle 1.23888 ( 36) hydrogen bonds : bond 0.04079 ( 685) hydrogen bonds : angle 4.60431 ( 1965) link_NAG-ASN : bond 0.00381 ( 2) link_NAG-ASN : angle 2.72952 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 120 LEU cc_start: 0.8767 (tp) cc_final: 0.8548 (tp) REVERT: 4 449 TYR cc_start: 0.8320 (m-80) cc_final: 0.7858 (m-80) REVERT: 4 479 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: B 78 LYS cc_start: 0.8196 (mmmt) cc_final: 0.7851 (mmtm) REVERT: B 277 SER cc_start: 0.9105 (p) cc_final: 0.8785 (t) REVERT: B 332 TRP cc_start: 0.8412 (m-10) cc_final: 0.7854 (m-10) REVERT: H 159 CYS cc_start: 0.6509 (t) cc_final: 0.5801 (t) REVERT: H 180 ARG cc_start: 0.7716 (tpp80) cc_final: 0.7409 (tpp80) REVERT: H 229 CYS cc_start: 0.5568 (p) cc_final: 0.5222 (p) outliers start: 46 outliers final: 27 residues processed: 238 average time/residue: 0.1159 time to fit residues: 42.9416 Evaluate side-chains 218 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 49 ASP Chi-restraints excluded: chain 2 residue 190 PHE Chi-restraints excluded: chain 2 residue 226 LEU Chi-restraints excluded: chain 2 residue 379 MET Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 479 GLN Chi-restraints excluded: chain 4 residue 501 LEU Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 539 CYS Chi-restraints excluded: chain 4 residue 657 ILE Chi-restraints excluded: chain 4 residue 658 PHE Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 45 MET 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 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 98 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 170 optimal weight: 0.0770 chunk 38 optimal weight: 4.9990 chunk 219 optimal weight: 0.0870 chunk 136 optimal weight: 0.5980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.186166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.161690 restraints weight = 23856.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.161324 restraints weight = 45197.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.162356 restraints weight = 43420.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.162175 restraints weight = 27852.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.162771 restraints weight = 25820.072| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18468 Z= 0.142 Angle : 0.577 9.229 25195 Z= 0.296 Chirality : 0.042 0.230 2911 Planarity : 0.004 0.057 3179 Dihedral : 5.744 58.139 3020 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.19 % Allowed : 15.28 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.17), residues: 2361 helix: 0.81 (0.19), residues: 807 sheet: -0.46 (0.26), residues: 398 loop : -1.53 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.030 0.001 TYR 4 667 PHE 0.020 0.001 PHE 2 584 TRP 0.014 0.001 TRP 4 583 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00330 (18448) covalent geometry : angle 0.57470 (25153) SS BOND : bond 0.00166 ( 18) SS BOND : angle 1.06078 ( 36) hydrogen bonds : bond 0.03885 ( 685) hydrogen bonds : angle 4.43061 ( 1965) link_NAG-ASN : bond 0.00318 ( 2) link_NAG-ASN : angle 2.61891 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 197 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: 4 120 LEU cc_start: 0.8835 (tp) cc_final: 0.8585 (tp) REVERT: 4 449 TYR cc_start: 0.8392 (m-80) cc_final: 0.7865 (m-80) REVERT: 4 464 THR cc_start: 0.9357 (m) cc_final: 0.9028 (p) REVERT: 4 479 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: B 78 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7793 (mmtm) REVERT: B 277 SER cc_start: 0.9074 (p) cc_final: 0.8768 (t) REVERT: B 332 TRP cc_start: 0.8516 (m-10) cc_final: 0.7994 (m-10) outliers start: 57 outliers final: 43 residues processed: 238 average time/residue: 0.1055 time to fit residues: 39.4177 Evaluate side-chains 233 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 49 ASP Chi-restraints excluded: chain 2 residue 190 PHE Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 226 LEU Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 257 LEU Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 2 residue 598 VAL Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 168 ILE Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 293 VAL Chi-restraints excluded: chain 4 residue 479 GLN Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 539 CYS Chi-restraints excluded: chain 4 residue 597 VAL Chi-restraints excluded: chain 4 residue 657 ILE Chi-restraints excluded: chain 4 residue 658 PHE Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 45 MET 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 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 211 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 547 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.180319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.156021 restraints weight = 23837.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.154502 restraints weight = 42556.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.155457 restraints weight = 45231.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.155656 restraints weight = 28931.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.156613 restraints weight = 24733.838| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 18468 Z= 0.242 Angle : 0.680 10.495 25195 Z= 0.348 Chirality : 0.046 0.225 2911 Planarity : 0.005 0.061 3179 Dihedral : 6.105 57.915 3020 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.53 % Allowed : 16.06 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.17), residues: 2361 helix: 0.55 (0.18), residues: 817 sheet: -0.66 (0.26), residues: 400 loop : -1.61 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 19 TYR 0.037 0.002 TYR 4 667 PHE 0.027 0.002 PHE 2 38 TRP 0.022 0.002 TRP 4 583 HIS 0.011 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00584 (18448) covalent geometry : angle 0.67743 (25153) SS BOND : bond 0.00260 ( 18) SS BOND : angle 1.36960 ( 36) hydrogen bonds : bond 0.04401 ( 685) hydrogen bonds : angle 4.62865 ( 1965) link_NAG-ASN : bond 0.00159 ( 2) link_NAG-ASN : angle 2.60922 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 206 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: 2 301 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: 4 120 LEU cc_start: 0.8951 (tp) cc_final: 0.8689 (tp) REVERT: 4 216 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8859 (mp) REVERT: 4 449 TYR cc_start: 0.8391 (m-80) cc_final: 0.7882 (m-80) REVERT: 4 464 THR cc_start: 0.9422 (m) cc_final: 0.9118 (p) REVERT: 4 479 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: A 20 ASP cc_start: 0.7852 (t70) cc_final: 0.7584 (t70) REVERT: B 152 LEU cc_start: 0.7904 (tp) cc_final: 0.7608 (mt) REVERT: H 159 CYS cc_start: 0.6100 (t) cc_final: 0.5881 (t) REVERT: H 180 ARG cc_start: 0.7537 (tpp80) cc_final: 0.7267 (tpp80) outliers start: 63 outliers final: 49 residues processed: 251 average time/residue: 0.1143 time to fit residues: 44.2437 Evaluate side-chains 240 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 49 ASP Chi-restraints excluded: chain 2 residue 190 PHE Chi-restraints excluded: chain 2 residue 205 THR Chi-restraints excluded: chain 2 residue 226 LEU Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 257 LEU Chi-restraints excluded: chain 2 residue 301 GLU Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 518 CYS Chi-restraints excluded: chain 2 residue 598 VAL Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 2 residue 721 CYS Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 49 ILE Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 168 ILE Chi-restraints excluded: chain 4 residue 216 LEU Chi-restraints excluded: chain 4 residue 242 SER Chi-restraints excluded: chain 4 residue 248 VAL Chi-restraints excluded: chain 4 residue 293 VAL Chi-restraints excluded: chain 4 residue 392 GLU Chi-restraints excluded: chain 4 residue 479 GLN Chi-restraints excluded: chain 4 residue 501 LEU Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 539 CYS Chi-restraints excluded: chain 4 residue 597 VAL Chi-restraints excluded: chain 4 residue 657 ILE Chi-restraints excluded: chain 4 residue 658 PHE Chi-restraints excluded: chain 4 residue 702 ILE Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain 4 residue 824 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 218 optimal weight: 3.9990 chunk 226 optimal weight: 7.9990 chunk 162 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 150 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 149 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 26 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 549 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.186325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.162409 restraints weight = 24089.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.162561 restraints weight = 43156.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.163359 restraints weight = 42323.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.163188 restraints weight = 28037.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.163730 restraints weight = 26409.636| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18468 Z= 0.121 Angle : 0.573 10.502 25195 Z= 0.293 Chirality : 0.041 0.198 2911 Planarity : 0.004 0.060 3179 Dihedral : 5.717 56.843 3020 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.69 % Allowed : 17.68 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.17), residues: 2361 helix: 0.92 (0.19), residues: 800 sheet: -0.54 (0.26), residues: 396 loop : -1.53 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.027 0.001 TYR 4 667 PHE 0.022 0.001 PHE 2 584 TRP 0.016 0.001 TRP 4 583 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00277 (18448) covalent geometry : angle 0.56986 (25153) SS BOND : bond 0.00190 ( 18) SS BOND : angle 1.28433 ( 36) hydrogen bonds : bond 0.03578 ( 685) hydrogen bonds : angle 4.29668 ( 1965) link_NAG-ASN : bond 0.00333 ( 2) link_NAG-ASN : angle 2.47617 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 120 LEU cc_start: 0.8922 (tp) cc_final: 0.8634 (tp) REVERT: 4 449 TYR cc_start: 0.8405 (m-80) cc_final: 0.7889 (m-80) REVERT: 4 464 THR cc_start: 0.9340 (m) cc_final: 0.9117 (p) REVERT: 4 479 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: A 20 ASP cc_start: 0.7702 (t70) cc_final: 0.7458 (t70) REVERT: A 28 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7307 (mt-10) REVERT: B 66 ASP cc_start: 0.8150 (p0) cc_final: 0.7906 (p0) REVERT: B 78 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7820 (mmtm) REVERT: B 277 SER cc_start: 0.9080 (p) cc_final: 0.8793 (t) REVERT: C 58 GLU cc_start: 0.6711 (mp0) cc_final: 0.6423 (pm20) outliers start: 48 outliers final: 38 residues processed: 239 average time/residue: 0.1207 time to fit residues: 44.4135 Evaluate side-chains 230 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 49 ASP Chi-restraints excluded: chain 2 residue 190 PHE Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 226 LEU Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 379 MET Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 598 VAL Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 2 residue 721 CYS Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 168 ILE Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 392 GLU Chi-restraints excluded: chain 4 residue 479 GLN Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 539 CYS Chi-restraints excluded: chain 4 residue 657 ILE Chi-restraints excluded: chain 4 residue 658 PHE Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 70 LEU 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 181 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain H residue 58 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 134 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 218 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 547 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.184042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.160128 restraints weight = 24028.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.160044 restraints weight = 45601.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.160938 restraints weight = 40681.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.162010 restraints weight = 27713.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.162165 restraints weight = 26286.068| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18468 Z= 0.155 Angle : 0.603 10.929 25195 Z= 0.306 Chirality : 0.042 0.197 2911 Planarity : 0.004 0.061 3179 Dihedral : 5.726 59.659 3020 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.08 % Allowed : 18.07 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.17), residues: 2361 helix: 0.92 (0.19), residues: 802 sheet: -0.55 (0.26), residues: 396 loop : -1.52 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 24 TYR 0.028 0.001 TYR 4 667 PHE 0.020 0.001 PHE 4 693 TRP 0.018 0.001 TRP 4 583 HIS 0.007 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00365 (18448) covalent geometry : angle 0.59963 (25153) SS BOND : bond 0.00148 ( 18) SS BOND : angle 1.42729 ( 36) hydrogen bonds : bond 0.03669 ( 685) hydrogen bonds : angle 4.29684 ( 1965) link_NAG-ASN : bond 0.00257 ( 2) link_NAG-ASN : angle 2.42998 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 301 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7064 (mt-10) REVERT: 2 459 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8151 (mt) REVERT: 4 120 LEU cc_start: 0.8952 (tp) cc_final: 0.8653 (tp) REVERT: 4 216 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8874 (mp) REVERT: 4 449 TYR cc_start: 0.8423 (m-80) cc_final: 0.7905 (m-80) REVERT: 4 464 THR cc_start: 0.9354 (m) cc_final: 0.9141 (p) REVERT: 4 479 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: A 20 ASP cc_start: 0.7708 (t70) cc_final: 0.7458 (t70) REVERT: A 28 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7243 (mt-10) REVERT: A 308 GLU cc_start: 0.8291 (mp0) cc_final: 0.7842 (mp0) REVERT: B 66 ASP cc_start: 0.8167 (p0) cc_final: 0.7953 (p0) REVERT: B 78 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7773 (mmtm) REVERT: C 58 GLU cc_start: 0.6774 (mp0) cc_final: 0.6502 (pm20) outliers start: 55 outliers final: 47 residues processed: 227 average time/residue: 0.1111 time to fit residues: 39.3666 Evaluate side-chains 236 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 49 ASP Chi-restraints excluded: chain 2 residue 190 PHE Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 226 LEU Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 301 GLU Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 2 residue 598 VAL Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 2 residue 721 CYS Chi-restraints excluded: chain 2 residue 771 ILE Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 49 ILE Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 168 ILE Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 216 LEU Chi-restraints excluded: chain 4 residue 242 SER Chi-restraints excluded: chain 4 residue 392 GLU Chi-restraints excluded: chain 4 residue 479 GLN Chi-restraints excluded: chain 4 residue 501 LEU Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 539 CYS Chi-restraints excluded: chain 4 residue 581 LEU Chi-restraints excluded: chain 4 residue 597 VAL Chi-restraints excluded: chain 4 residue 657 ILE Chi-restraints excluded: chain 4 residue 658 PHE Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 70 LEU 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 181 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 151 optimal weight: 0.9990 chunk 35 optimal weight: 0.0040 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 0.0170 chunk 158 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 172 optimal weight: 0.3980 chunk 31 optimal weight: 6.9990 chunk 128 optimal weight: 0.0770 chunk 78 optimal weight: 0.0060 overall best weight: 0.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.188951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.164645 restraints weight = 23642.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.162428 restraints weight = 38119.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.163674 restraints weight = 39400.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.164043 restraints weight = 24280.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.164589 restraints weight = 22006.528| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18468 Z= 0.104 Angle : 0.563 10.453 25195 Z= 0.286 Chirality : 0.041 0.198 2911 Planarity : 0.004 0.058 3179 Dihedral : 5.468 55.670 3020 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.24 % Allowed : 18.91 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.17), residues: 2361 helix: 1.10 (0.19), residues: 802 sheet: -0.44 (0.26), residues: 378 loop : -1.48 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 24 TYR 0.020 0.001 TYR 4 667 PHE 0.024 0.001 PHE 2 584 TRP 0.015 0.001 TRP 4 583 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00226 (18448) covalent geometry : angle 0.56035 (25153) SS BOND : bond 0.00214 ( 18) SS BOND : angle 1.23837 ( 36) hydrogen bonds : bond 0.03184 ( 685) hydrogen bonds : angle 4.05839 ( 1965) link_NAG-ASN : bond 0.00434 ( 2) link_NAG-ASN : angle 2.31496 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 105 ILE cc_start: 0.8309 (pt) cc_final: 0.7850 (pt) REVERT: 4 120 LEU cc_start: 0.8907 (tp) cc_final: 0.8558 (tp) REVERT: 4 449 TYR cc_start: 0.8414 (m-80) cc_final: 0.7914 (m-80) REVERT: 4 634 PHE cc_start: 0.8193 (t80) cc_final: 0.7867 (t80) REVERT: A 28 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7251 (mt-10) REVERT: B 66 ASP cc_start: 0.8101 (p0) cc_final: 0.7886 (p0) REVERT: B 78 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7690 (mmtm) REVERT: B 277 SER cc_start: 0.9045 (p) cc_final: 0.8726 (t) REVERT: C 58 GLU cc_start: 0.6698 (mp0) cc_final: 0.6375 (pm20) REVERT: H 27 PHE cc_start: 0.7018 (p90) cc_final: 0.6813 (p90) outliers start: 40 outliers final: 33 residues processed: 244 average time/residue: 0.1143 time to fit residues: 43.4202 Evaluate side-chains 227 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 190 PHE Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 2 residue 509 VAL Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 2 residue 598 VAL Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 2 residue 721 CYS Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 392 GLU Chi-restraints excluded: chain 4 residue 501 LEU Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 539 CYS Chi-restraints excluded: chain 4 residue 581 LEU Chi-restraints excluded: chain 4 residue 658 PHE Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 103 optimal weight: 0.6980 chunk 186 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 136 optimal weight: 0.6980 chunk 121 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.184075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.157773 restraints weight = 23718.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.155863 restraints weight = 38764.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.157122 restraints weight = 40512.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.157658 restraints weight = 24960.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.158496 restraints weight = 21812.515| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18468 Z= 0.151 Angle : 0.607 10.719 25195 Z= 0.308 Chirality : 0.042 0.199 2911 Planarity : 0.004 0.060 3179 Dihedral : 5.536 58.165 3020 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.41 % Favored : 92.55 % Rotamer: Outliers : 2.13 % Allowed : 19.36 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.18), residues: 2361 helix: 1.06 (0.19), residues: 805 sheet: -0.55 (0.26), residues: 400 loop : -1.47 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 24 TYR 0.029 0.001 TYR 4 667 PHE 0.028 0.001 PHE 2 747 TRP 0.029 0.001 TRP H 47 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00358 (18448) covalent geometry : angle 0.60107 (25153) SS BOND : bond 0.00164 ( 18) SS BOND : angle 2.16805 ( 36) hydrogen bonds : bond 0.03444 ( 685) hydrogen bonds : angle 4.14249 ( 1965) link_NAG-ASN : bond 0.00259 ( 2) link_NAG-ASN : angle 2.15017 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 120 LEU cc_start: 0.8923 (tp) cc_final: 0.8593 (tp) REVERT: 4 449 TYR cc_start: 0.8428 (m-80) cc_final: 0.7925 (m-80) REVERT: 4 634 PHE cc_start: 0.8298 (t80) cc_final: 0.7951 (t80) REVERT: A 20 ASP cc_start: 0.7691 (t70) cc_final: 0.7429 (t70) REVERT: A 28 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7249 (mt-10) REVERT: B 66 ASP cc_start: 0.8219 (p0) cc_final: 0.7986 (p0) REVERT: B 78 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7725 (mmtm) REVERT: C 58 GLU cc_start: 0.6860 (mp0) cc_final: 0.6507 (pm20) outliers start: 38 outliers final: 32 residues processed: 214 average time/residue: 0.1232 time to fit residues: 41.3400 Evaluate side-chains 219 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 190 PHE Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 2 residue 509 VAL Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 2 residue 598 VAL Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 2 residue 721 CYS Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 242 SER Chi-restraints excluded: chain 4 residue 392 GLU Chi-restraints excluded: chain 4 residue 501 LEU Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 539 CYS Chi-restraints excluded: chain 4 residue 581 LEU Chi-restraints excluded: chain 4 residue 658 PHE Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 51 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 149 optimal weight: 0.0870 chunk 61 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.185431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.159187 restraints weight = 23714.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.157416 restraints weight = 38799.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.158654 restraints weight = 39403.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.159069 restraints weight = 25559.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.160169 restraints weight = 22120.924| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18468 Z= 0.124 Angle : 0.588 10.520 25195 Z= 0.299 Chirality : 0.041 0.198 2911 Planarity : 0.004 0.060 3179 Dihedral : 5.493 59.365 3020 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.29 % Favored : 92.67 % Rotamer: Outliers : 2.01 % Allowed : 19.53 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.18), residues: 2361 helix: 1.07 (0.19), residues: 811 sheet: -0.54 (0.26), residues: 399 loop : -1.43 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 24 TYR 0.024 0.001 TYR 4 667 PHE 0.029 0.001 PHE 2 584 TRP 0.030 0.001 TRP 4 583 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00289 (18448) covalent geometry : angle 0.58165 (25153) SS BOND : bond 0.00241 ( 18) SS BOND : angle 2.19741 ( 36) hydrogen bonds : bond 0.03267 ( 685) hydrogen bonds : angle 4.08151 ( 1965) link_NAG-ASN : bond 0.00331 ( 2) link_NAG-ASN : angle 1.99512 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2370.78 seconds wall clock time: 41 minutes 59.52 seconds (2519.52 seconds total)