Starting phenix.real_space_refine on Mon May 19 14:25:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jd5_36176/05_2025/8jd5_36176_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jd5_36176/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jd5_36176/05_2025/8jd5_36176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jd5_36176/05_2025/8jd5_36176.map" model { file = "/net/cci-nas-00/data/ceres_data/8jd5_36176/05_2025/8jd5_36176_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jd5_36176/05_2025/8jd5_36176_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 13} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 7} 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, 'ASN:plan1': 1, 'ASP:plan': 9} 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: {'GLN:plan1': 5, 'GLU:plan': 6, 'ARG:plan': 11, 'ASN:plan1': 4, 'ASP:plan': 10} 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, 'GLU:plan': 3, 'ARG:plan': 2, '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: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} 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: 11.95, per 1000 atoms: 0.66 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: 4.69 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.29 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: 7.00 Time building geometry restraints manager: 5.48 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: 2.210 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: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 44.940 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.870 ------------------------------------------------------------------------------- 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 : 9.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (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 TRP 0.012 0.001 TRP 4 717 HIS 0.005 0.000 HIS B 183 PHE 0.030 0.001 PHE A 189 TYR 0.017 0.001 TYR H 235 ARG 0.003 0.000 ARG 2 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 2) link_NAG-ASN : angle 2.02808 ( 6) hydrogen bonds : bond 0.28296 ( 685) hydrogen bonds : angle 8.01743 ( 1965) SS BOND : bond 0.00252 ( 18) SS BOND : angle 2.75881 ( 36) covalent geometry : bond 0.00483 (18448) covalent geometry : angle 0.63908 (25153) *********************** 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 : 1.733 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: 0.3172 time to fit residues: 131.8243 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 : 1.791 ------------------------------------------------------------------------------- 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 199 optimal weight: 0.2980 chunk 178 optimal weight: 0.0970 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 120 optimal weight: 0.0670 chunk 95 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 112 optimal weight: 0.5980 chunk 137 optimal weight: 0.4980 chunk 214 optimal weight: 0.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 541 HIS A 188 HIS A 204 GLN H 179 GLN H 183 GLN H 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.203023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.179943 restraints weight = 23792.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.178477 restraints weight = 39635.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.179936 restraints weight = 32777.201| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18468 Z= 0.126 Angle : 0.600 8.137 25195 Z= 0.307 Chirality : 0.043 0.252 2911 Planarity : 0.004 0.055 3179 Dihedral : 7.690 73.771 3025 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.95 % Allowed : 8.34 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2361 helix: 0.68 (0.18), residues: 802 sheet: 0.01 (0.28), residues: 367 loop : -1.55 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 211 HIS 0.016 0.001 HIS 4 541 PHE 0.022 0.001 PHE A 336 TYR 0.025 0.001 TYR 4 667 ARG 0.009 0.001 ARG B 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 2) link_NAG-ASN : angle 1.63224 ( 6) hydrogen bonds : bond 0.05236 ( 685) hydrogen bonds : angle 5.21748 ( 1965) SS BOND : bond 0.00339 ( 18) SS BOND : angle 1.19797 ( 36) covalent geometry : bond 0.00267 (18448) covalent geometry : angle 0.59809 (25153) *********************** 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 262 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 245 time to evaluate : 1.721 Fit side-chains revert: symmetry clash REVERT: 4 449 TYR cc_start: 0.8158 (m-80) cc_final: 0.7702 (m-80) REVERT: 4 499 LEU cc_start: 0.7503 (tp) cc_final: 0.7294 (tp) REVERT: 4 634 PHE cc_start: 0.8172 (t80) cc_final: 0.7858 (t80) REVERT: 4 642 LEU cc_start: 0.8160 (tt) cc_final: 0.7735 (mm) REVERT: A 303 ILE cc_start: 0.7313 (tt) cc_final: 0.7054 (tt) REVERT: A 324 THR cc_start: 0.7963 (p) cc_final: 0.7313 (p) REVERT: B 22 ARG cc_start: 0.5319 (mmt180) cc_final: 0.5098 (mtt90) REVERT: B 78 LYS cc_start: 0.7394 (mmmt) cc_final: 0.7040 (mmtm) REVERT: H 95 TYR cc_start: 0.7563 (m-80) cc_final: 0.7264 (m-80) outliers start: 17 outliers final: 8 residues processed: 253 average time/residue: 0.3327 time to fit residues: 124.6659 Evaluate side-chains 207 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 522 LEU Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 296 VAL 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 88 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 230 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 153 ASN ** 2 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 283 GLN 2 374 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.183829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.158590 restraints weight = 24067.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.156925 restraints weight = 41373.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.157974 restraints weight = 43342.712| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 18468 Z= 0.277 Angle : 0.734 9.646 25195 Z= 0.377 Chirality : 0.047 0.224 2911 Planarity : 0.005 0.058 3179 Dihedral : 6.484 51.727 3020 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.69 % Allowed : 11.19 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.17), residues: 2361 helix: 0.40 (0.18), residues: 825 sheet: -0.46 (0.27), residues: 386 loop : -1.59 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 2 297 HIS 0.009 0.001 HIS B 54 PHE 0.025 0.002 PHE B 278 TYR 0.035 0.002 TYR 4 667 ARG 0.010 0.001 ARG B 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 2) link_NAG-ASN : angle 2.86086 ( 6) hydrogen bonds : bond 0.05355 ( 685) hydrogen bonds : angle 5.05878 ( 1965) SS BOND : bond 0.00351 ( 18) SS BOND : angle 1.45736 ( 36) covalent geometry : bond 0.00667 (18448) covalent geometry : angle 0.73146 (25153) *********************** 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 262 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 2.058 Fit side-chains revert: symmetry clash REVERT: 4 642 LEU cc_start: 0.8177 (tt) cc_final: 0.7686 (mm) REVERT: A 20 ASP cc_start: 0.7899 (t70) cc_final: 0.7622 (t70) REVERT: A 324 THR cc_start: 0.8345 (p) cc_final: 0.7929 (p) REVERT: B 22 ARG cc_start: 0.5177 (mmt180) cc_final: 0.4975 (mtt90) outliers start: 48 outliers final: 34 residues processed: 250 average time/residue: 0.2909 time to fit residues: 111.1904 Evaluate side-chains 222 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 153 ASN Chi-restraints excluded: chain 2 residue 205 THR Chi-restraints excluded: chain 2 residue 226 LEU 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 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 539 CYS Chi-restraints excluded: chain 4 residue 597 VAL 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 332 VAL 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 159 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 66 optimal weight: 10.0000 chunk 232 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.184836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.160202 restraints weight = 23984.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.159201 restraints weight = 45937.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.160278 restraints weight = 45050.890| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18468 Z= 0.188 Angle : 0.630 9.289 25195 Z= 0.322 Chirality : 0.044 0.277 2911 Planarity : 0.004 0.058 3179 Dihedral : 6.012 57.765 3020 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.52 % Allowed : 14.72 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.17), residues: 2361 helix: 0.53 (0.18), residues: 814 sheet: -0.50 (0.26), residues: 396 loop : -1.61 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 4 583 HIS 0.007 0.001 HIS B 183 PHE 0.023 0.002 PHE B 241 TYR 0.032 0.002 TYR 4 667 ARG 0.005 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 2) link_NAG-ASN : angle 2.81440 ( 6) hydrogen bonds : bond 0.04397 ( 685) hydrogen bonds : angle 4.70848 ( 1965) SS BOND : bond 0.00219 ( 18) SS BOND : angle 1.56224 ( 36) covalent geometry : bond 0.00444 (18448) covalent geometry : angle 0.62597 (25153) *********************** 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 250 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 1.910 Fit side-chains revert: symmetry clash REVERT: 4 449 TYR cc_start: 0.8294 (m-80) cc_final: 0.7810 (m-80) REVERT: 4 529 ARG cc_start: 0.5412 (OUTLIER) cc_final: 0.4896 (tmt170) REVERT: B 22 ARG cc_start: 0.5386 (mmt180) cc_final: 0.5114 (mtt90) outliers start: 45 outliers final: 34 residues processed: 232 average time/residue: 0.2954 time to fit residues: 105.2209 Evaluate side-chains 222 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 519 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 113 THR Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 529 ARG 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 702 ILE Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain 4 residue 829 SER Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 225 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 214 optimal weight: 10.0000 chunk 149 optimal weight: 0.0270 chunk 87 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 202 optimal weight: 0.1980 chunk 221 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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** 4 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.187104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.161916 restraints weight = 24064.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.159652 restraints weight = 42711.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.160978 restraints weight = 44055.936| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3340 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= 0.131 Angle : 0.568 8.699 25195 Z= 0.292 Chirality : 0.042 0.226 2911 Planarity : 0.004 0.056 3179 Dihedral : 5.709 59.739 3020 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.97 % Allowed : 15.61 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.17), residues: 2361 helix: 0.75 (0.19), residues: 810 sheet: -0.46 (0.26), residues: 396 loop : -1.55 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 4 583 HIS 0.005 0.001 HIS B 183 PHE 0.023 0.001 PHE B 241 TYR 0.028 0.001 TYR 4 667 ARG 0.006 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 2) link_NAG-ASN : angle 2.58411 ( 6) hydrogen bonds : bond 0.03823 ( 685) hydrogen bonds : angle 4.45833 ( 1965) SS BOND : bond 0.00197 ( 18) SS BOND : angle 1.36190 ( 36) covalent geometry : bond 0.00302 (18448) covalent geometry : angle 0.56497 (25153) *********************** 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 255 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 202 time to evaluate : 1.765 Fit side-chains revert: symmetry clash REVERT: 4 449 TYR cc_start: 0.8357 (m-80) cc_final: 0.7867 (m-80) REVERT: 4 464 THR cc_start: 0.9385 (m) cc_final: 0.9053 (p) REVERT: 4 479 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: A 243 MET cc_start: 0.7405 (ttp) cc_final: 0.7031 (ttp) REVERT: B 22 ARG cc_start: 0.5229 (mmt180) cc_final: 0.4988 (mtt90) REVERT: B 78 LYS cc_start: 0.8068 (mmmt) cc_final: 0.7751 (mmtm) outliers start: 53 outliers final: 33 residues processed: 237 average time/residue: 0.3028 time to fit residues: 111.6608 Evaluate side-chains 225 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 379 MET 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 57 VAL 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 658 PHE Chi-restraints excluded: chain 4 residue 717 TRP 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 195 HIS Chi-restraints excluded: chain A residue 206 SER 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 70 LEU 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 223 THR Chi-restraints excluded: chain B residue 317 CYS 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 190 optimal weight: 1.9990 chunk 183 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 139 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.185504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.157890 restraints weight = 23735.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.156628 restraints weight = 38180.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157952 restraints weight = 42094.474| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3516 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= 0.136 Angle : 0.575 9.993 25195 Z= 0.293 Chirality : 0.042 0.207 2911 Planarity : 0.004 0.056 3179 Dihedral : 5.620 59.296 3020 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.41 % Allowed : 15.89 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.17), residues: 2361 helix: 0.86 (0.19), residues: 809 sheet: -0.50 (0.26), residues: 397 loop : -1.53 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 4 583 HIS 0.005 0.001 HIS B 183 PHE 0.022 0.001 PHE B 241 TYR 0.028 0.001 TYR 4 667 ARG 0.007 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 2) link_NAG-ASN : angle 2.48723 ( 6) hydrogen bonds : bond 0.03689 ( 685) hydrogen bonds : angle 4.34958 ( 1965) SS BOND : bond 0.00206 ( 18) SS BOND : angle 1.46359 ( 36) covalent geometry : bond 0.00316 (18448) covalent geometry : angle 0.57168 (25153) *********************** 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 258 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 197 time to evaluate : 2.027 Fit side-chains revert: symmetry clash REVERT: 4 449 TYR cc_start: 0.8385 (m-80) cc_final: 0.7876 (m-80) REVERT: 4 464 THR cc_start: 0.9305 (m) cc_final: 0.9077 (p) REVERT: 4 479 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: B 78 LYS cc_start: 0.8116 (mmmt) cc_final: 0.7783 (mmtm) outliers start: 61 outliers final: 46 residues processed: 239 average time/residue: 0.3014 time to fit residues: 109.9595 Evaluate side-chains 236 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 153 ASN 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 257 LEU Chi-restraints excluded: chain 2 residue 301 GLU 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 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 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 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 195 HIS Chi-restraints excluded: chain A residue 206 SER 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 70 LEU 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 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain H residue 159 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 166 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 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 = 0.4104 r_free = 0.4104 target = 0.178781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.153943 restraints weight = 24039.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.152780 restraints weight = 49071.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.153867 restraints weight = 46842.191| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 18468 Z= 0.291 Angle : 0.728 10.280 25195 Z= 0.375 Chirality : 0.048 0.223 2911 Planarity : 0.005 0.060 3179 Dihedral : 6.206 58.645 3020 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.47 % Favored : 91.49 % Rotamer: Outliers : 3.58 % Allowed : 16.40 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.17), residues: 2361 helix: 0.36 (0.18), residues: 811 sheet: -0.82 (0.26), residues: 405 loop : -1.65 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 2 297 HIS 0.012 0.002 HIS B 183 PHE 0.033 0.002 PHE 2 38 TYR 0.039 0.002 TYR 4 667 ARG 0.009 0.001 ARG B 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00056 ( 2) link_NAG-ASN : angle 2.59449 ( 6) hydrogen bonds : bond 0.04653 ( 685) hydrogen bonds : angle 4.77157 ( 1965) SS BOND : bond 0.00261 ( 18) SS BOND : angle 1.67929 ( 36) covalent geometry : bond 0.00698 (18448) covalent geometry : angle 0.72469 (25153) *********************** 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 262 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 198 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 301 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: 4 216 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8866 (mp) REVERT: 4 309 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.7082 (ttt) REVERT: 4 449 TYR cc_start: 0.8399 (m-80) cc_final: 0.7870 (m-80) REVERT: 4 464 THR cc_start: 0.9453 (m) cc_final: 0.9128 (p) REVERT: 4 479 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: 4 634 PHE cc_start: 0.8346 (t80) cc_final: 0.8037 (t80) REVERT: A 20 ASP cc_start: 0.7902 (t70) cc_final: 0.7629 (t70) REVERT: B 76 ASP cc_start: 0.7123 (t0) cc_final: 0.6797 (t0) REVERT: B 93 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8286 (pt) REVERT: B 152 LEU cc_start: 0.7931 (tp) cc_final: 0.7685 (mt) REVERT: C 48 ASP cc_start: 0.6511 (t0) cc_final: 0.6286 (t0) outliers start: 64 outliers final: 51 residues processed: 245 average time/residue: 0.2891 time to fit residues: 109.5326 Evaluate side-chains 237 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 309 MET 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 191 PHE Chi-restraints excluded: chain A residue 206 SER 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 102 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 165 THR 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 B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 235 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 12 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 138 optimal weight: 0.0470 chunk 172 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 153 ASN 4 549 GLN 4 613 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.183774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.159935 restraints weight = 23846.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.157169 restraints weight = 39967.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.158351 restraints weight = 41402.405| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18468 Z= 0.134 Angle : 0.606 10.069 25195 Z= 0.310 Chirality : 0.042 0.197 2911 Planarity : 0.004 0.061 3179 Dihedral : 5.816 56.278 3020 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.50 % Favored : 92.46 % Rotamer: Outliers : 3.30 % Allowed : 17.57 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.17), residues: 2361 helix: 0.66 (0.19), residues: 810 sheet: -0.69 (0.26), residues: 401 loop : -1.55 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 4 583 HIS 0.005 0.001 HIS B 183 PHE 0.026 0.001 PHE 4 693 TYR 0.031 0.001 TYR 4 667 ARG 0.006 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 2) link_NAG-ASN : angle 2.45608 ( 6) hydrogen bonds : bond 0.03777 ( 685) hydrogen bonds : angle 4.44705 ( 1965) SS BOND : bond 0.00218 ( 18) SS BOND : angle 1.52628 ( 36) covalent geometry : bond 0.00312 (18448) covalent geometry : angle 0.60296 (25153) *********************** 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 254 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 195 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 301 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: 4 449 TYR cc_start: 0.8427 (m-80) cc_final: 0.7907 (m-80) REVERT: 4 464 THR cc_start: 0.9377 (m) cc_final: 0.9149 (p) REVERT: 4 479 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: 4 529 ARG cc_start: 0.5940 (OUTLIER) cc_final: 0.5108 (tmt170) REVERT: 4 634 PHE cc_start: 0.8216 (t80) cc_final: 0.7945 (t80) REVERT: A 20 ASP cc_start: 0.7651 (t70) cc_final: 0.7438 (t70) REVERT: A 28 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7284 (mt-10) REVERT: B 183 HIS cc_start: 0.7141 (OUTLIER) cc_final: 0.6921 (t-170) REVERT: B 277 SER cc_start: 0.9023 (p) cc_final: 0.8740 (t) REVERT: C 58 GLU cc_start: 0.6992 (pm20) cc_final: 0.6668 (pm20) outliers start: 59 outliers final: 45 residues processed: 236 average time/residue: 0.2928 time to fit residues: 107.2593 Evaluate side-chains 239 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 153 ASN 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 301 GLU 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 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 49 ILE 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 248 VAL 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 529 ARG Chi-restraints excluded: chain 4 residue 539 CYS Chi-restraints excluded: chain 4 residue 581 LEU 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 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 206 SER 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 102 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 183 HIS 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 B residue 331 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 159 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 51 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 99 optimal weight: 0.0980 chunk 176 optimal weight: 0.3980 chunk 197 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 204 optimal weight: 0.0570 chunk 87 optimal weight: 4.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 153 ASN H 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.184499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.156700 restraints weight = 23751.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155343 restraints weight = 39543.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.156621 restraints weight = 40292.086| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3961 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= 0.122 Angle : 0.584 10.179 25195 Z= 0.299 Chirality : 0.042 0.198 2911 Planarity : 0.004 0.062 3179 Dihedral : 5.655 56.481 3020 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.54 % Favored : 92.42 % Rotamer: Outliers : 2.74 % Allowed : 18.47 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2361 helix: 0.82 (0.19), residues: 808 sheet: -0.61 (0.26), residues: 397 loop : -1.50 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 4 583 HIS 0.004 0.001 HIS B 183 PHE 0.029 0.001 PHE 2 584 TYR 0.026 0.001 TYR 4 667 ARG 0.007 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 2) link_NAG-ASN : angle 2.35227 ( 6) hydrogen bonds : bond 0.03534 ( 685) hydrogen bonds : angle 4.31828 ( 1965) SS BOND : bond 0.00299 ( 18) SS BOND : angle 1.46018 ( 36) covalent geometry : bond 0.00280 (18448) covalent geometry : angle 0.58073 (25153) *********************** 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 250 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 301 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7007 (mt-10) REVERT: 4 449 TYR cc_start: 0.8420 (m-80) cc_final: 0.7913 (m-80) REVERT: 4 479 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: 4 529 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.5139 (tmt170) REVERT: 4 634 PHE cc_start: 0.8240 (t80) cc_final: 0.7945 (t80) REVERT: A 20 ASP cc_start: 0.7695 (t70) cc_final: 0.7449 (t70) REVERT: A 28 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7290 (mt-10) REVERT: B 78 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7799 (mmtm) REVERT: B 205 ASP cc_start: 0.8035 (p0) cc_final: 0.7440 (p0) REVERT: B 277 SER cc_start: 0.9067 (p) cc_final: 0.8722 (t) REVERT: C 58 GLU cc_start: 0.7058 (pm20) cc_final: 0.6667 (pm20) outliers start: 49 outliers final: 40 residues processed: 233 average time/residue: 0.2924 time to fit residues: 103.8723 Evaluate side-chains 233 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 153 ASN 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 301 GLU 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 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 49 ILE Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 479 GLN Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 529 ARG 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 A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 195 HIS 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 158 VAL 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 159 CYS 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 0 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.181671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.153200 restraints weight = 24019.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.151532 restraints weight = 40152.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.153148 restraints weight = 34003.924| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18468 Z= 0.205 Angle : 0.653 10.280 25195 Z= 0.334 Chirality : 0.045 0.201 2911 Planarity : 0.004 0.066 3179 Dihedral : 5.876 57.986 3020 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.79 % Favored : 92.16 % Rotamer: Outliers : 2.74 % Allowed : 18.47 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2361 helix: 0.68 (0.19), residues: 812 sheet: -0.68 (0.26), residues: 401 loop : -1.52 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP 4 583 HIS 0.006 0.001 HIS A 213 PHE 0.025 0.002 PHE 4 693 TYR 0.029 0.002 TYR 4 667 ARG 0.007 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 2) link_NAG-ASN : angle 2.26159 ( 6) hydrogen bonds : bond 0.03916 ( 685) hydrogen bonds : angle 4.45171 ( 1965) SS BOND : bond 0.00193 ( 18) SS BOND : angle 1.55206 ( 36) covalent geometry : bond 0.00491 (18448) covalent geometry : angle 0.64965 (25153) ********************** 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 241 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 55 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7555 (mt-10) REVERT: 2 301 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: 2 388 MET cc_start: 0.7568 (ttm) cc_final: 0.7355 (ttm) REVERT: 2 459 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8125 (mt) REVERT: 2 619 MET cc_start: 0.7235 (tmm) cc_final: 0.6781 (ttp) REVERT: 4 449 TYR cc_start: 0.8452 (m-80) cc_final: 0.7926 (m-80) REVERT: 4 479 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: 4 529 ARG cc_start: 0.6029 (OUTLIER) cc_final: 0.5353 (tmt170) REVERT: 4 587 TRP cc_start: 0.7361 (m100) cc_final: 0.7091 (m100) REVERT: 4 634 PHE cc_start: 0.8279 (t80) cc_final: 0.7991 (t80) REVERT: A 20 ASP cc_start: 0.7768 (t70) cc_final: 0.7507 (t70) REVERT: A 28 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7283 (mt-10) REVERT: A 186 GLU cc_start: 0.7806 (tp30) cc_final: 0.7280 (tp30) outliers start: 49 outliers final: 41 residues processed: 226 average time/residue: 0.2857 time to fit residues: 98.9587 Evaluate side-chains 234 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 199 VAL 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 529 ARG 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 A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 206 SER 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 158 VAL 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 159 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 47 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.0980 chunk 100 optimal weight: 0.1980 chunk 46 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 222 optimal weight: 8.9990 chunk 219 optimal weight: 0.0010 chunk 226 optimal weight: 5.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.185996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.161315 restraints weight = 23357.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.159767 restraints weight = 36598.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.160877 restraints weight = 39017.736| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.4081 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= 0.117 Angle : 0.583 10.321 25195 Z= 0.297 Chirality : 0.042 0.200 2911 Planarity : 0.004 0.063 3179 Dihedral : 5.657 54.148 3020 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.62 % Favored : 92.33 % Rotamer: Outliers : 2.69 % Allowed : 18.63 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2361 helix: 0.90 (0.19), residues: 810 sheet: -0.60 (0.26), residues: 397 loop : -1.48 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 4 583 HIS 0.005 0.001 HIS B 183 PHE 0.027 0.001 PHE 2 584 TYR 0.025 0.001 TYR 4 667 ARG 0.007 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 2) link_NAG-ASN : angle 2.05011 ( 6) hydrogen bonds : bond 0.03393 ( 685) hydrogen bonds : angle 4.25711 ( 1965) SS BOND : bond 0.00172 ( 18) SS BOND : angle 1.37678 ( 36) covalent geometry : bond 0.00270 (18448) covalent geometry : angle 0.58034 (25153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5333.53 seconds wall clock time: 94 minutes 43.86 seconds (5683.86 seconds total)