Starting phenix.real_space_refine on Sat Feb 17 08:07:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/02_2024/8jd5_36176_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/02_2024/8jd5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/02_2024/8jd5_36176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/02_2024/8jd5_36176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/02_2024/8jd5_36176_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/02_2024/8jd5_36176_neut_updated.pdb" } 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 Residue "2 GLU 273": "OE1" <-> "OE2" Residue "4 ASP 288": "OD1" <-> "OD2" Residue "4 TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 902": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 9.83, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG 2 905 " - " ASN 2 203 " " NAG 41003 " - " ASN 4 454 " Time building additional restraints: 6.79 Conformation dependent library (CDL) restraints added in 3.4 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... running ksdssp... Secondary structure from input PDB file: 62 helices and 22 sheets defined 34.2% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain '2' and resid 59 through 73 removed outlier: 3.604A pdb=" N LEU 2 66 " --> pdb=" O LEU 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 95 through 106 removed outlier: 3.944A pdb=" N LEU 2 103 " --> pdb=" O LEU 2 99 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL 2 106 " --> pdb=" O ALA 2 102 " (cutoff:3.500A) Processing helix chain '2' and resid 145 through 157 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) Processing helix chain '2' and resid 192 through 201 Processing helix chain '2' and resid 217 through 230 Processing helix chain '2' and resid 247 through 259 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 272 through 283 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) Processing helix chain '2' and resid 325 through 332 removed outlier: 3.539A pdb=" N SER 2 329 " --> pdb=" O SER 2 325 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 351 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 378 through 399 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 415 through 422 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 490 through 492 No H-bonds generated for 'chain '2' and resid 490 through 492' Processing helix chain '2' and resid 566 through 568 No H-bonds generated for 'chain '2' and resid 566 through 568' Processing helix chain '2' and resid 570 through 591 Processing helix chain '2' and resid 603 through 623 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) removed outlier: 4.090A pdb=" N ILE 2 622 " --> pdb=" O CYS 2 618 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE 2 623 " --> pdb=" O MET 2 619 " (cutoff:3.500A) Processing helix chain '2' and resid 629 through 661 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 676 through 700 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 729 through 747 removed outlier: 3.542A pdb=" N LEU 2 741 " --> pdb=" O LEU 2 737 " (cutoff:3.500A) Processing helix chain '2' and resid 754 through 756 No H-bonds generated for 'chain '2' and resid 754 through 756' Processing helix chain '2' and resid 759 through 782 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 787 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 76 through 89 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) Processing helix chain '4' and resid 112 through 121 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) removed outlier: 4.520A pdb=" N THR 4 121 " --> pdb=" O GLU 4 117 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 169 removed outlier: 4.050A pdb=" N ILE 4 168 " --> pdb=" O MET 4 164 " (cutoff:3.500A) Processing helix chain '4' and resid 185 through 187 No H-bonds generated for 'chain '4' and resid 185 through 187' Processing helix chain '4' and resid 202 through 215 removed outlier: 3.594A pdb=" N GLN 4 207 " --> pdb=" O THR 4 203 " (cutoff:3.500A) Processing helix chain '4' and resid 231 through 245 removed outlier: 3.647A pdb=" N ALA 4 237 " --> pdb=" O SER 4 233 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 274 removed outlier: 4.140A pdb=" N ASP 4 266 " --> pdb=" O ALA 4 262 " (cutoff:3.500A) Processing helix chain '4' and resid 287 through 299 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 314 No H-bonds generated for 'chain '4' and resid 312 through 314' Processing helix chain '4' and resid 319 through 321 No H-bonds generated for 'chain '4' and resid 319 through 321' Processing helix chain '4' and resid 342 through 348 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) Processing helix chain '4' and resid 361 through 371 Processing helix chain '4' and resid 395 through 397 No H-bonds generated for 'chain '4' and resid 395 through 397' Processing helix chain '4' and resid 404 through 427 removed outlier: 3.608A pdb=" N GLN 4 407 " --> pdb=" O GLY 4 404 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP 4 411 " --> pdb=" O PHE 4 408 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA 4 412 " --> pdb=" O VAL 4 409 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL 4 413 " --> pdb=" O ILE 4 410 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU 4 427 " --> pdb=" O HIS 4 424 " (cutoff:3.500A) Processing helix chain '4' and resid 436 through 438 No H-bonds generated for 'chain '4' and resid 436 through 438' Processing helix chain '4' and resid 443 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 586 through 588 No H-bonds generated for 'chain '4' and resid 586 through 588' Processing helix chain '4' and resid 590 through 611 Processing helix chain '4' and resid 618 through 620 No H-bonds generated for 'chain '4' and resid 618 through 620' Processing helix chain '4' and resid 627 through 643 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) Processing helix chain '4' and resid 649 through 686 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 696 through 720 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 750 through 775 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) removed outlier: 4.141A pdb=" N ARG 4 775 " --> pdb=" O ALA 4 771 " (cutoff:3.500A) Processing helix chain '4' and resid 781 through 783 No H-bonds generated for 'chain '4' and resid 781 through 783' Processing helix chain '4' and resid 785 through 799 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 802 through 807 Processing helix chain '4' and resid 820 through 846 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 31 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 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.987A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 209 through 215' Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.599A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 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 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 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) Processing helix chain 'A' and resid 331 through 351 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 28 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) Processing helix chain 'C' and resid 10 through 26 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) removed outlier: 3.969A pdb=" N ASP C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing sheet with id= A, first strand: chain '2' and resid 87 through 90 removed outlier: 3.667A pdb=" N GLY 2 36 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE 2 38 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLY 2 141 " --> pdb=" O PRO 2 161 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE 2 163 " --> pdb=" O GLY 2 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 239 through 241 removed outlier: 6.603A pdb=" N VAL 2 265 " --> pdb=" O SER 2 208 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL 2 210 " --> pdb=" O VAL 2 265 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL 2 267 " --> pdb=" O VAL 2 210 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N SER 2 212 " --> pdb=" O VAL 2 267 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE 2 269 " --> pdb=" O SER 2 212 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR 2 290 " --> pdb=" O ALA 2 266 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU 2 268 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL 2 292 " --> pdb=" O LEU 2 268 " (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= C, first strand: chain '2' and resid 509 through 511 Processing sheet with id= D, 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: 7.013A pdb=" N GLY 4 52 " --> pdb=" O VAL 4 151 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL 4 153 " --> pdb=" O GLY 4 52 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU 4 54 " --> pdb=" O VAL 4 153 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '4' and resid 253 through 256 removed outlier: 9.308A pdb=" N VAL 4 254 " --> pdb=" O VAL 4 221 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR 4 223 " --> pdb=" O VAL 4 254 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ILE 4 256 " --> pdb=" O THR 4 223 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA 4 225 " --> pdb=" O ILE 4 256 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ALA 4 280 " --> pdb=" O SER 4 222 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N VAL 4 224 " --> pdb=" O ALA 4 280 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE 4 282 " --> pdb=" O VAL 4 224 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER 4 226 " --> pdb=" O ILE 4 282 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N PHE 4 284 " --> pdb=" O SER 4 226 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE 4 307 " --> pdb=" O VAL 4 281 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE 4 283 " --> pdb=" O PHE 4 307 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET 4 309 " --> pdb=" O ILE 4 283 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain '4' and resid 332 through 336 removed outlier: 3.592A pdb=" N GLY 4 493 " --> pdb=" O ILE 4 477 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN 4 479 " --> pdb=" O VAL 4 491 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL 4 491 " --> pdb=" O GLN 4 479 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN 4 481 " --> pdb=" O TYR 4 489 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TYR 4 489 " --> pdb=" O GLN 4 481 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '4' and resid 454 through 456 removed outlier: 3.629A pdb=" N PHE 4 455 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '4' and resid 531 through 533 Processing sheet with id= I, first strand: chain '4' and resid 564 through 566 Processing sheet with id= J, first strand: chain 'A' and resid 36 through 39 removed outlier: 7.921A pdb=" N ALA A 220 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N LEU A 39 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 222 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER A 263 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE A 223 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 265 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL A 225 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A 267 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 185 through 191 Processing sheet with id= L, first strand: chain 'B' and resid 91 through 94 removed outlier: 4.012A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 121 through 125 removed outlier: 3.660A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 156 through 159 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) Processing sheet with id= O, first strand: chain 'B' and resid 207 through 209 Processing sheet with id= P, first strand: chain 'B' and resid 250 through 254 removed outlier: 3.517A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 284 through 286 removed outlier: 3.616A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 336 through 339 removed outlier: 4.086A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 20 through 23 removed outlier: 3.579A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 93 through 99 removed outlier: 4.061A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 155 through 160 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= V, first strand: chain 'H' and resid 174 through 179 removed outlier: 3.586A pdb=" N TYR H 175 " --> pdb=" O MET H 230 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.27 Time building geometry restraints manager: 7.39 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: 96.83 - 104.34: 274 104.34 - 111.84: 8997 111.84 - 119.35: 6278 119.35 - 126.85: 9348 126.85 - 134.36: 256 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: 1300 2.74 - 3.28: 18228 3.28 - 3.82: 29047 3.82 - 4.36: 33984 4.36 - 4.90: 58446 Nonbonded interactions: 141005 Sorted by model distance: nonbonded pdb=" O LEU A 268 " pdb=" OG1 THR A 324 " model vdw 2.201 2.440 nonbonded pdb=" O GLN 2 790 " pdb=" OG1 THR 2 793 " model vdw 2.215 2.440 nonbonded pdb=" OG1 THR 4 672 " pdb=" OE1 GLN 4 699 " model vdw 2.225 2.440 nonbonded pdb=" O GLY H 112 " pdb=" OG SER H 184 " model vdw 2.225 2.440 nonbonded pdb=" O PRO 2 434 " pdb=" OG1 THR 2 437 " model vdw 2.230 2.440 ... (remaining 141000 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.800 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 48.220 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.240 ------------------------------------------------------------------------------- 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 18448 Z= 0.323 Angle : 0.639 15.462 25153 Z= 0.357 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 275 time to evaluate : 2.079 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: 0.3280 time to fit residues: 135.9417 Evaluate side-chains 210 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 206 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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: 0.3980 chunk 178 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 0.0030 chunk 95 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 112 optimal weight: 0.5980 chunk 137 optimal weight: 0.0870 chunk 214 optimal weight: 2.9990 overall best weight: 0.3368 ------------------------------------------------------------------------------- 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 A 255 ASN H 179 GLN H 183 GLN H 194 ASN H 231 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18448 Z= 0.176 Angle : 0.565 8.307 25153 Z= 0.288 Chirality : 0.042 0.223 2911 Planarity : 0.004 0.056 3179 Dihedral : 8.015 78.095 3025 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.23 % Allowed : 7.83 % Favored : 90.93 % 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: -0.70 (0.17), residues: 2361 helix: 0.81 (0.18), residues: 782 sheet: 0.13 (0.29), residues: 356 loop : -1.54 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 211 HIS 0.015 0.001 HIS 4 541 PHE 0.024 0.001 PHE A 336 TYR 0.021 0.001 TYR 4 667 ARG 0.009 0.000 ARG B 134 *********************** 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 261 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 239 time to evaluate : 2.005 Fit side-chains revert: symmetry clash REVERT: 2 101 GLN cc_start: 0.7422 (mt0) cc_final: 0.7158 (mt0) REVERT: 2 174 ASP cc_start: 0.7606 (t70) cc_final: 0.7286 (t0) REVERT: 2 262 SER cc_start: 0.6923 (OUTLIER) cc_final: 0.6674 (t) REVERT: 2 442 ARG cc_start: 0.8021 (ptm-80) cc_final: 0.7707 (ptm-80) REVERT: 2 747 PHE cc_start: 0.8010 (t80) cc_final: 0.7709 (t80) REVERT: 4 243 ARG cc_start: 0.6859 (mtp-110) cc_final: 0.6536 (ttp80) REVERT: 4 449 TYR cc_start: 0.7771 (m-80) cc_final: 0.7366 (m-80) REVERT: 4 634 PHE cc_start: 0.7916 (t80) cc_final: 0.7650 (t80) REVERT: 4 642 LEU cc_start: 0.8322 (tt) cc_final: 0.7586 (mm) REVERT: 4 729 PHE cc_start: 0.6875 (t80) cc_final: 0.6329 (t80) REVERT: 4 738 ARG cc_start: 0.4872 (mmt180) cc_final: 0.3883 (mpp80) REVERT: 4 764 MET cc_start: 0.6131 (tpp) cc_final: 0.5811 (tpp) REVERT: A 24 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7627 (ttp80) REVERT: A 186 GLU cc_start: 0.7231 (tt0) cc_final: 0.6989 (tt0) REVERT: A 197 LYS cc_start: 0.7289 (mttp) cc_final: 0.6979 (ttmm) REVERT: A 255 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7507 (m-40) REVERT: A 308 GLU cc_start: 0.7536 (mp0) cc_final: 0.7300 (mp0) REVERT: A 324 THR cc_start: 0.8439 (p) cc_final: 0.7992 (p) REVERT: B 78 LYS cc_start: 0.7358 (mmmt) cc_final: 0.7023 (mmtm) REVERT: H 95 TYR cc_start: 0.7162 (m-80) cc_final: 0.6741 (m-80) REVERT: H 173 TYR cc_start: 0.8474 (m-80) cc_final: 0.8082 (m-10) REVERT: H 231 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.6958 (pp30) outliers start: 22 outliers final: 11 residues processed: 249 average time/residue: 0.3258 time to fit residues: 120.1891 Evaluate side-chains 220 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 262 SER Chi-restraints excluded: chain 2 residue 379 MET Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 46 ASP Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 231 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 178 optimal weight: 0.0040 chunk 145 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 283 GLN 2 374 GLN A 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18448 Z= 0.354 Angle : 0.667 9.249 25153 Z= 0.341 Chirality : 0.046 0.215 2911 Planarity : 0.005 0.059 3179 Dihedral : 6.343 50.530 3021 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.63 % Allowed : 10.97 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2361 helix: 0.45 (0.18), residues: 804 sheet: -0.42 (0.26), residues: 390 loop : -1.51 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 2 297 HIS 0.010 0.001 HIS B 54 PHE 0.024 0.002 PHE B 241 TYR 0.024 0.002 TYR 4 667 ARG 0.006 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 224 time to evaluate : 1.953 Fit side-chains revert: symmetry clash REVERT: 2 174 ASP cc_start: 0.8079 (t70) cc_final: 0.7391 (t0) REVERT: 2 195 MET cc_start: 0.7777 (mtp) cc_final: 0.7547 (mtp) REVERT: 2 530 TYR cc_start: 0.6409 (t80) cc_final: 0.6117 (t80) REVERT: 2 697 TRP cc_start: 0.4810 (t-100) cc_final: 0.4576 (t-100) REVERT: 4 190 SER cc_start: 0.9115 (m) cc_final: 0.8767 (p) REVERT: 4 270 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.8053 (ttm-80) REVERT: 4 642 LEU cc_start: 0.8218 (tt) cc_final: 0.7449 (mm) REVERT: 4 704 PHE cc_start: 0.6384 (m-80) cc_final: 0.6125 (m-80) REVERT: A 22 ASN cc_start: 0.8133 (m-40) cc_final: 0.7730 (t0) REVERT: A 24 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7741 (ttp80) REVERT: A 186 GLU cc_start: 0.7515 (tt0) cc_final: 0.6069 (tm-30) REVERT: A 197 LYS cc_start: 0.7668 (mttp) cc_final: 0.6855 (mtpp) REVERT: B 78 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7859 (mmtm) REVERT: B 210 LEU cc_start: 0.7402 (tt) cc_final: 0.7060 (tt) REVERT: B 332 TRP cc_start: 0.8657 (m-10) cc_final: 0.8138 (m-10) REVERT: H 95 TYR cc_start: 0.7443 (m-80) cc_final: 0.7056 (m-80) REVERT: H 179 GLN cc_start: 0.7726 (tp40) cc_final: 0.7390 (tp-100) outliers start: 47 outliers final: 34 residues processed: 254 average time/residue: 0.3213 time to fit residues: 121.7338 Evaluate side-chains 235 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 201 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 205 THR Chi-restraints excluded: chain 2 residue 379 MET Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 590 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 168 ILE Chi-restraints excluded: chain 4 residue 250 ILE Chi-restraints excluded: chain 4 residue 293 VAL Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 597 VAL Chi-restraints excluded: chain 4 residue 657 ILE Chi-restraints excluded: chain 4 residue 658 PHE Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain 4 residue 842 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 214 CYS 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 159 THR 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 194 ASN 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 212 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 215 optimal weight: 8.9990 chunk 228 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 204 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 191 GLN ** 2 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18448 Z= 0.301 Angle : 0.607 9.087 25153 Z= 0.309 Chirality : 0.044 0.200 2911 Planarity : 0.004 0.060 3179 Dihedral : 5.906 55.738 3020 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.74 % Allowed : 14.16 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2361 helix: 0.47 (0.18), residues: 800 sheet: -0.57 (0.26), residues: 408 loop : -1.55 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 4 583 HIS 0.007 0.001 HIS B 54 PHE 0.021 0.002 PHE B 241 TYR 0.031 0.002 TYR 4 667 ARG 0.010 0.001 ARG B 134 *********************** 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 262 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 213 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 190 SER cc_start: 0.9048 (m) cc_final: 0.8733 (p) REVERT: 4 270 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.8019 (ttm-80) REVERT: 4 449 TYR cc_start: 0.7852 (m-80) cc_final: 0.7427 (m-80) REVERT: A 22 ASN cc_start: 0.8100 (m-40) cc_final: 0.7753 (t0) REVERT: A 186 GLU cc_start: 0.7621 (tt0) cc_final: 0.7151 (tt0) REVERT: A 197 LYS cc_start: 0.7863 (mttp) cc_final: 0.7202 (mtmm) REVERT: B 78 LYS cc_start: 0.8253 (mmmt) cc_final: 0.7915 (mmtm) REVERT: B 210 LEU cc_start: 0.7423 (tt) cc_final: 0.7066 (tt) REVERT: C 20 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7932 (mptt) REVERT: H 95 TYR cc_start: 0.7680 (m-80) cc_final: 0.7291 (m-80) outliers start: 49 outliers final: 40 residues processed: 248 average time/residue: 0.3053 time to fit residues: 114.5083 Evaluate side-chains 235 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 195 time to evaluate : 2.081 ------------------------------------------------------------------------------- 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 379 MET Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 547 ASN Chi-restraints excluded: chain 2 residue 598 VAL Chi-restraints excluded: chain 2 residue 771 ILE Chi-restraints excluded: chain 2 residue 786 ASP Chi-restraints excluded: chain 2 residue 803 SER Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 168 ILE Chi-restraints excluded: chain 4 residue 293 VAL Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 539 CYS Chi-restraints excluded: chain 4 residue 657 ILE Chi-restraints excluded: chain 4 residue 658 PHE Chi-restraints excluded: chain 4 residue 702 ILE Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain 4 residue 842 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 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 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR 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 215 THR Chi-restraints excluded: chain H residue 235 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 169 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 204 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18448 Z= 0.215 Angle : 0.558 8.981 25153 Z= 0.284 Chirality : 0.042 0.197 2911 Planarity : 0.004 0.059 3179 Dihedral : 5.710 57.119 3020 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.25 % Allowed : 15.28 % Favored : 81.48 % 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: -0.88 (0.17), residues: 2361 helix: 0.62 (0.19), residues: 798 sheet: -0.52 (0.26), residues: 397 loop : -1.47 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 4 583 HIS 0.005 0.001 HIS B 183 PHE 0.021 0.001 PHE B 241 TYR 0.026 0.001 TYR 4 667 ARG 0.009 0.000 ARG B 134 *********************** 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 266 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 208 time to evaluate : 1.980 Fit side-chains REVERT: 4 190 SER cc_start: 0.9053 (m) cc_final: 0.8743 (p) REVERT: 4 270 ARG cc_start: 0.8257 (ttm-80) cc_final: 0.8050 (ttm-80) REVERT: 4 449 TYR cc_start: 0.7874 (m-80) cc_final: 0.7449 (m-80) REVERT: A 22 ASN cc_start: 0.8010 (m-40) cc_final: 0.7677 (t0) REVERT: A 24 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7735 (ttp80) REVERT: A 197 LYS cc_start: 0.7891 (mttp) cc_final: 0.7125 (mtmm) REVERT: A 247 MET cc_start: 0.6615 (mmp) cc_final: 0.6358 (mmp) REVERT: A 308 GLU cc_start: 0.7877 (mp0) cc_final: 0.7669 (mp0) REVERT: B 78 LYS cc_start: 0.8229 (mmmt) cc_final: 0.7902 (mmtm) REVERT: B 210 LEU cc_start: 0.7318 (tt) cc_final: 0.6953 (tt) REVERT: H 67 ARG cc_start: 0.6830 (ttt180) cc_final: 0.6549 (ttt180) REVERT: H 95 TYR cc_start: 0.7662 (m-80) cc_final: 0.7188 (m-80) outliers start: 58 outliers final: 43 residues processed: 247 average time/residue: 0.3252 time to fit residues: 122.4031 Evaluate side-chains 238 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 195 time to evaluate : 2.154 ------------------------------------------------------------------------------- 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 379 MET Chi-restraints excluded: chain 2 residue 388 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 639 LEU Chi-restraints excluded: chain 2 residue 786 ASP Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 168 ILE Chi-restraints excluded: chain 4 residue 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 754 ILE Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain 4 residue 796 ILE Chi-restraints excluded: chain 4 residue 842 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 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 105 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER 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 76 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 119 optimal weight: 0.0040 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18448 Z= 0.254 Angle : 0.584 10.452 25153 Z= 0.296 Chirality : 0.043 0.355 2911 Planarity : 0.004 0.059 3179 Dihedral : 5.714 56.244 3020 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.92 % Allowed : 15.67 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.92 (0.17), residues: 2361 helix: 0.62 (0.19), residues: 798 sheet: -0.64 (0.26), residues: 384 loop : -1.47 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 4 583 HIS 0.006 0.001 HIS B 183 PHE 0.022 0.001 PHE 2 584 TYR 0.028 0.002 TYR 4 667 ARG 0.011 0.001 ARG B 134 *********************** 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 274 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 204 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 55 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6647 (tm-30) REVERT: 2 301 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: 4 185 ASP cc_start: 0.8500 (t0) cc_final: 0.8087 (t0) REVERT: 4 190 SER cc_start: 0.9029 (m) cc_final: 0.8724 (p) REVERT: 4 270 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.8009 (ttm-80) REVERT: 4 449 TYR cc_start: 0.7905 (m-80) cc_final: 0.7462 (m-80) REVERT: 4 479 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: A 20 ASP cc_start: 0.7615 (t70) cc_final: 0.7230 (t70) REVERT: A 22 ASN cc_start: 0.8014 (m-40) cc_final: 0.7681 (t0) REVERT: A 186 GLU cc_start: 0.7835 (tt0) cc_final: 0.6692 (tt0) REVERT: A 197 LYS cc_start: 0.7844 (mttp) cc_final: 0.7276 (mtpp) REVERT: A 247 MET cc_start: 0.6570 (mmp) cc_final: 0.6349 (mmp) REVERT: B 78 LYS cc_start: 0.8280 (mmmt) cc_final: 0.7948 (mmtm) REVERT: B 186 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6853 (m-30) REVERT: B 210 LEU cc_start: 0.7504 (tt) cc_final: 0.7147 (tt) REVERT: C 58 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6296 (mp0) REVERT: H 67 ARG cc_start: 0.6786 (ttt180) cc_final: 0.6489 (ttt180) REVERT: H 95 TYR cc_start: 0.7703 (m-80) cc_final: 0.7355 (m-80) REVERT: H 176 TRP cc_start: 0.7344 (m100) cc_final: 0.6735 (m100) outliers start: 70 outliers final: 55 residues processed: 255 average time/residue: 0.2983 time to fit residues: 116.4462 Evaluate side-chains 253 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 194 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 379 MET Chi-restraints excluded: chain 2 residue 388 MET 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 547 ASN Chi-restraints excluded: chain 2 residue 598 VAL Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 2 residue 771 ILE Chi-restraints excluded: chain 2 residue 786 ASP 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 168 ILE Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 248 VAL Chi-restraints excluded: chain 4 residue 293 VAL Chi-restraints excluded: chain 4 residue 392 GLU Chi-restraints excluded: chain 4 residue 479 GLN Chi-restraints excluded: chain 4 residue 501 LEU Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 529 ARG Chi-restraints excluded: chain 4 residue 539 CYS Chi-restraints excluded: chain 4 residue 597 VAL Chi-restraints excluded: chain 4 residue 657 ILE Chi-restraints excluded: chain 4 residue 658 PHE Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain 4 residue 754 ILE Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain 4 residue 796 ILE Chi-restraints excluded: chain 4 residue 842 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 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 227 optimal weight: 0.0970 chunk 142 optimal weight: 0.4980 chunk 138 optimal weight: 0.8980 chunk 105 optimal weight: 0.0030 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18448 Z= 0.177 Angle : 0.544 9.028 25153 Z= 0.275 Chirality : 0.041 0.249 2911 Planarity : 0.004 0.058 3179 Dihedral : 5.501 58.537 3020 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.36 % Allowed : 16.84 % Favored : 79.80 % 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: -0.79 (0.17), residues: 2361 helix: 0.76 (0.19), residues: 791 sheet: -0.58 (0.26), residues: 391 loop : -1.42 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 4 583 HIS 0.004 0.001 HIS H 35 PHE 0.019 0.001 PHE B 241 TYR 0.026 0.001 TYR 4 667 ARG 0.012 0.000 ARG B 134 *********************** 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 267 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 207 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 55 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6466 (tm-30) REVERT: 2 301 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: 4 185 ASP cc_start: 0.8413 (t0) cc_final: 0.7999 (t0) REVERT: 4 190 SER cc_start: 0.9069 (m) cc_final: 0.8774 (p) REVERT: 4 270 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7978 (ttm-80) REVERT: 4 449 TYR cc_start: 0.7837 (m-80) cc_final: 0.7410 (m-80) REVERT: A 20 ASP cc_start: 0.7483 (t70) cc_final: 0.7161 (t70) REVERT: A 22 ASN cc_start: 0.7954 (m-40) cc_final: 0.7677 (t0) REVERT: A 28 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7554 (mt-10) REVERT: B 66 ASP cc_start: 0.8347 (p0) cc_final: 0.8140 (p0) REVERT: B 78 LYS cc_start: 0.8247 (mmmt) cc_final: 0.7895 (mmtm) REVERT: B 186 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: B 210 LEU cc_start: 0.7365 (tt) cc_final: 0.7015 (tt) REVERT: C 20 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8026 (mmtm) REVERT: C 58 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6190 (mp0) REVERT: H 67 ARG cc_start: 0.6754 (ttt180) cc_final: 0.6408 (ttt180) REVERT: H 95 TYR cc_start: 0.7604 (m-80) cc_final: 0.7288 (m-80) REVERT: H 176 TRP cc_start: 0.7298 (m100) cc_final: 0.6673 (m100) outliers start: 60 outliers final: 48 residues processed: 246 average time/residue: 0.3060 time to fit residues: 114.7518 Evaluate side-chains 250 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 199 time to evaluate : 1.906 ------------------------------------------------------------------------------- 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 379 MET Chi-restraints excluded: chain 2 residue 388 MET 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 786 ASP Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 392 GLU Chi-restraints excluded: chain 4 residue 501 LEU Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 529 ARG Chi-restraints excluded: chain 4 residue 539 CYS Chi-restraints excluded: chain 4 residue 597 VAL Chi-restraints excluded: chain 4 residue 657 ILE Chi-restraints excluded: chain 4 residue 658 PHE Chi-restraints excluded: chain 4 residue 717 TRP Chi-restraints excluded: chain 4 residue 754 ILE Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain 4 residue 796 ILE 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 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 105 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP 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 C residue 30 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain H residue 215 THR 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 140 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 0.0000 chunk 144 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 18448 Z= 0.411 Angle : 0.673 9.896 25153 Z= 0.343 Chirality : 0.046 0.259 2911 Planarity : 0.005 0.058 3179 Dihedral : 6.020 56.467 3020 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 3.53 % Allowed : 17.07 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.13 (0.17), residues: 2361 helix: 0.35 (0.18), residues: 803 sheet: -0.75 (0.26), residues: 397 loop : -1.53 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 4 583 HIS 0.010 0.001 HIS B 183 PHE 0.027 0.002 PHE 2 38 TYR 0.031 0.002 TYR 4 667 ARG 0.012 0.001 ARG B 134 *********************** 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 276 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 213 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 55 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6714 (tm-30) REVERT: 2 301 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: 2 520 TRP cc_start: 0.7066 (p-90) cc_final: 0.6710 (p-90) REVERT: 4 185 ASP cc_start: 0.8453 (t0) cc_final: 0.7976 (t0) REVERT: 4 190 SER cc_start: 0.9028 (m) cc_final: 0.8771 (p) REVERT: 4 270 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7994 (ttm-80) REVERT: 4 479 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: 4 791 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6730 (mmp) REVERT: A 20 ASP cc_start: 0.7657 (t70) cc_final: 0.7313 (t70) REVERT: A 22 ASN cc_start: 0.8055 (m-40) cc_final: 0.7717 (t0) REVERT: A 28 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7470 (mt-10) REVERT: A 186 GLU cc_start: 0.7898 (tt0) cc_final: 0.7645 (tp30) REVERT: B 66 ASP cc_start: 0.8430 (p0) cc_final: 0.8169 (p0) REVERT: B 76 ASP cc_start: 0.7420 (t0) cc_final: 0.7007 (t0) REVERT: B 152 LEU cc_start: 0.8188 (tp) cc_final: 0.7937 (mt) REVERT: B 210 LEU cc_start: 0.7767 (tt) cc_final: 0.7523 (tt) REVERT: C 58 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: H 47 TRP cc_start: 0.8265 (t60) cc_final: 0.8054 (t60) REVERT: H 67 ARG cc_start: 0.6950 (ttt180) cc_final: 0.6653 (ttt180) REVERT: H 95 TYR cc_start: 0.7702 (m-80) cc_final: 0.7359 (m-80) REVERT: H 176 TRP cc_start: 0.7235 (m100) cc_final: 0.6668 (m100) outliers start: 63 outliers final: 54 residues processed: 255 average time/residue: 0.3197 time to fit residues: 126.7691 Evaluate side-chains 261 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 203 time to evaluate : 2.147 ------------------------------------------------------------------------------- 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 379 MET Chi-restraints excluded: chain 2 residue 388 MET 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 590 VAL Chi-restraints excluded: chain 2 residue 598 VAL Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 2 residue 771 ILE Chi-restraints excluded: chain 2 residue 786 ASP Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 168 ILE Chi-restraints excluded: chain 4 residue 242 SER Chi-restraints excluded: chain 4 residue 248 VAL Chi-restraints excluded: chain 4 residue 293 VAL Chi-restraints excluded: chain 4 residue 392 GLU Chi-restraints excluded: chain 4 residue 479 GLN Chi-restraints excluded: chain 4 residue 501 LEU Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 539 CYS Chi-restraints excluded: chain 4 residue 597 VAL Chi-restraints excluded: chain 4 residue 657 ILE Chi-restraints excluded: chain 4 residue 658 PHE Chi-restraints excluded: chain 4 residue 702 ILE Chi-restraints excluded: chain 4 residue 754 ILE Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain 4 residue 791 MET Chi-restraints excluded: chain 4 residue 842 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 182 THR 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 74 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 166 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 58 HIS ** 4 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 549 GLN 4 613 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18448 Z= 0.215 Angle : 0.590 9.969 25153 Z= 0.297 Chirality : 0.042 0.228 2911 Planarity : 0.004 0.058 3179 Dihedral : 5.787 59.002 3020 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.25 % Allowed : 18.35 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2361 helix: 0.58 (0.19), residues: 797 sheet: -0.65 (0.26), residues: 381 loop : -1.53 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 4 583 HIS 0.005 0.001 HIS B 183 PHE 0.018 0.001 PHE B 241 TYR 0.026 0.001 TYR 4 667 ARG 0.011 0.000 ARG B 134 *********************** 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 265 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 207 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 55 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6679 (tm-30) REVERT: 2 301 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: 2 520 TRP cc_start: 0.7045 (p-90) cc_final: 0.6711 (p-90) REVERT: 4 185 ASP cc_start: 0.8431 (t0) cc_final: 0.7968 (t0) REVERT: 4 190 SER cc_start: 0.9065 (m) cc_final: 0.8768 (p) REVERT: 4 270 ARG cc_start: 0.8187 (ttm-80) cc_final: 0.7962 (ttm-80) REVERT: 4 449 TYR cc_start: 0.7854 (m-80) cc_final: 0.7451 (m-80) REVERT: 4 479 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: 4 791 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6458 (mmp) REVERT: A 20 ASP cc_start: 0.7526 (t70) cc_final: 0.7184 (t70) REVERT: A 22 ASN cc_start: 0.8080 (m-40) cc_final: 0.7772 (t0) REVERT: A 28 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7417 (mt-10) REVERT: A 186 GLU cc_start: 0.7931 (tt0) cc_final: 0.7618 (tt0) REVERT: A 197 LYS cc_start: 0.8082 (mttp) cc_final: 0.7293 (mtmm) REVERT: A 243 MET cc_start: 0.6788 (ttp) cc_final: 0.6220 (ttp) REVERT: A 247 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6480 (mmm) REVERT: B 19 ARG cc_start: 0.8670 (tpm170) cc_final: 0.8360 (mtm180) REVERT: B 66 ASP cc_start: 0.8348 (p0) cc_final: 0.8109 (p0) REVERT: B 78 LYS cc_start: 0.8354 (mmmt) cc_final: 0.8013 (mmtm) REVERT: B 210 LEU cc_start: 0.7614 (tt) cc_final: 0.7335 (tt) REVERT: B 332 TRP cc_start: 0.8781 (m-10) cc_final: 0.8504 (m-10) REVERT: C 20 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8117 (mmtm) REVERT: C 58 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6367 (mp0) REVERT: H 67 ARG cc_start: 0.6879 (ttt180) cc_final: 0.6562 (ttt180) REVERT: H 176 TRP cc_start: 0.7175 (m100) cc_final: 0.6617 (m100) outliers start: 58 outliers final: 50 residues processed: 245 average time/residue: 0.2945 time to fit residues: 110.2065 Evaluate side-chains 255 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 200 time to evaluate : 1.928 ------------------------------------------------------------------------------- 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 379 MET Chi-restraints excluded: chain 2 residue 388 MET 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 786 ASP Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 49 ILE Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 168 ILE Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 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 529 ARG 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 754 ILE Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain 4 residue 791 MET Chi-restraints excluded: chain 4 residue 796 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 247 MET 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 220 GLN 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 C residue 30 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 144 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 199 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18448 Z= 0.353 Angle : 0.651 10.124 25153 Z= 0.329 Chirality : 0.044 0.232 2911 Planarity : 0.004 0.060 3179 Dihedral : 6.014 59.673 3020 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.02 % Allowed : 18.52 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.17), residues: 2361 helix: 0.40 (0.18), residues: 801 sheet: -0.77 (0.26), residues: 404 loop : -1.58 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 4 583 HIS 0.009 0.001 HIS B 183 PHE 0.028 0.002 PHE 2 584 TYR 0.026 0.002 TYR 4 667 ARG 0.013 0.001 ARG B 134 ********************** 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 262 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 208 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 55 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6712 (tm-30) REVERT: 2 301 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: 2 520 TRP cc_start: 0.7115 (p-90) cc_final: 0.6835 (p-90) REVERT: 4 185 ASP cc_start: 0.8478 (t0) cc_final: 0.8009 (t0) REVERT: 4 190 SER cc_start: 0.9035 (m) cc_final: 0.8773 (p) REVERT: 4 270 ARG cc_start: 0.8195 (ttm-80) cc_final: 0.7969 (ttm-80) REVERT: 4 449 TYR cc_start: 0.7842 (m-80) cc_final: 0.7473 (m-80) REVERT: 4 479 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: 4 529 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.4713 (tmt170) REVERT: 4 791 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6768 (mmp) REVERT: A 20 ASP cc_start: 0.7614 (t70) cc_final: 0.7258 (t70) REVERT: A 22 ASN cc_start: 0.8119 (m-40) cc_final: 0.7787 (t0) REVERT: A 28 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7386 (mt-10) REVERT: A 243 MET cc_start: 0.6862 (ttp) cc_final: 0.6315 (ttp) REVERT: A 247 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6427 (mmm) REVERT: A 296 TYR cc_start: 0.6487 (t80) cc_final: 0.6226 (t80) REVERT: B 66 ASP cc_start: 0.8409 (p0) cc_final: 0.8119 (p0) REVERT: B 76 ASP cc_start: 0.7457 (t0) cc_final: 0.7011 (t0) REVERT: B 78 LYS cc_start: 0.8427 (mmmt) cc_final: 0.8090 (mmtm) REVERT: B 210 LEU cc_start: 0.7755 (tt) cc_final: 0.7519 (tt) REVERT: C 20 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8171 (mmtm) REVERT: C 58 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: H 67 ARG cc_start: 0.6779 (ttt180) cc_final: 0.6494 (ttt180) REVERT: H 176 TRP cc_start: 0.7199 (m100) cc_final: 0.6624 (m100) outliers start: 54 outliers final: 46 residues processed: 243 average time/residue: 0.3215 time to fit residues: 118.3693 Evaluate side-chains 251 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 199 time to evaluate : 2.064 ------------------------------------------------------------------------------- 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 379 MET Chi-restraints excluded: chain 2 residue 388 MET 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 786 ASP Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 2 residue 828 HIS Chi-restraints excluded: chain 4 residue 49 ILE Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 4 residue 168 ILE Chi-restraints excluded: chain 4 residue 242 SER Chi-restraints excluded: chain 4 residue 392 GLU Chi-restraints excluded: chain 4 residue 479 GLN Chi-restraints excluded: chain 4 residue 501 LEU Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 529 ARG 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 754 ILE Chi-restraints excluded: chain 4 residue 767 CYS Chi-restraints excluded: chain 4 residue 791 MET Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 247 MET 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 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 58 GLU 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 57 optimal weight: 0.4980 chunk 172 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 187 optimal weight: 0.5980 chunk 78 optimal weight: 0.4980 chunk 192 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 164 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 167 ASN ** 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 = 0.4167 r_free = 0.4167 target = 0.184005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.158788 restraints weight = 23536.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.158119 restraints weight = 42350.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.159317 restraints weight = 39774.170| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18448 Z= 0.201 Angle : 0.588 10.017 25153 Z= 0.297 Chirality : 0.042 0.199 2911 Planarity : 0.004 0.058 3179 Dihedral : 5.788 58.044 3020 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.91 % Allowed : 19.08 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2361 helix: 0.59 (0.19), residues: 801 sheet: -0.67 (0.26), residues: 381 loop : -1.54 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 4 583 HIS 0.005 0.001 HIS B 183 PHE 0.018 0.001 PHE B 241 TYR 0.025 0.001 TYR 4 667 ARG 0.013 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3580.28 seconds wall clock time: 66 minutes 24.89 seconds (3984.89 seconds total)