Starting phenix.real_space_refine on Tue Feb 20 12:27:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f57_31460/02_2024/7f57_31460_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f57_31460/02_2024/7f57_31460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f57_31460/02_2024/7f57_31460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f57_31460/02_2024/7f57_31460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f57_31460/02_2024/7f57_31460_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f57_31460/02_2024/7f57_31460_neut.pdb" } resolution = 3.8 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= 0.008 sd= 0.088 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: 4 Type Number sf(0) Gaussians S 157 5.16 5 C 17847 2.51 5 N 4605 2.21 5 O 5254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "A GLU 853": "OE1" <-> "OE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 625": "OE1" <-> "OE2" Residue "B GLU 665": "OE1" <-> "OE2" Residue "B GLU 723": "OE1" <-> "OE2" Residue "B GLU 806": "OE1" <-> "OE2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C GLU 524": "OE1" <-> "OE2" Residue "C GLU 743": "OE1" <-> "OE2" Residue "C GLU 806": "OE1" <-> "OE2" Residue "C GLU 841": "OE1" <-> "OE2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D ARG 431": "NH1" <-> "NH2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D GLU 441": "OE1" <-> "OE2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "D GLU 504": "OE1" <-> "OE2" Residue "D PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 663": "NH1" <-> "NH2" Residue "D GLU 806": "OE1" <-> "OE2" Residue "D GLU 811": "OE1" <-> "OE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E GLU 148": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27863 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6614 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 33, 'TRANS': 801} Chain: "B" Number of atoms: 6611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6611 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 801} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 6611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6611 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 801} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 6467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6467 Classifications: {'peptide': 818} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 784} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1172 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 10, 'TRANS': 134} Chain breaks: 1 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 14.47, per 1000 atoms: 0.52 Number of scatterers: 27863 At special positions: 0 Unit cell: (138.6, 139.92, 205.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 157 16.00 O 5254 8.00 N 4605 7.00 C 17847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.38 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.05 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.24 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS E 72 " distance=2.37 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A1001 " - " ASN A 423 " " NAG A1002 " - " ASN A 430 " " NAG A1003 " - " ASN A 751 " " NAG A1004 " - " ASN A 412 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 412 " " NAG C1001 " - " ASN C 412 " " NAG C1002 " - " ASN C 430 " " NAG C1003 " - " ASN C 751 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " " NAG F 1 " - " ASN A 275 " " NAG G 1 " - " ASN A 378 " " NAG H 1 " - " ASN B 378 " " NAG I 1 " - " ASN C 275 " " NAG J 1 " - " ASN C 378 " " NAG K 1 " - " ASN D 378 " Time building additional restraints: 11.45 Conformation dependent library (CDL) restraints added in 4.7 seconds 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 41 sheets defined 45.6% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.547A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.252A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 210 through 222 removed outlier: 4.676A pdb=" N LEU A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.837A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 4.263A pdb=" N SER A 272 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 273' Processing helix chain 'A' and resid 286 through 302 removed outlier: 3.793A pdb=" N GLN A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.693A pdb=" N GLY A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 335 removed outlier: 3.594A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.843A pdb=" N PHE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.578A pdb=" N GLU A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.501A pdb=" N ARG A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.557A pdb=" N TRP A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.791A pdb=" N GLY A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 664 removed outlier: 3.578A pdb=" N ILE A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 637 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.786A pdb=" N LEU A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 699 through 713 removed outlier: 3.517A pdb=" N PHE A 708 " --> pdb=" O LYS A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 731 Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.790A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.866A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 821 through 850 removed outlier: 3.730A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 830 " --> pdb=" O VAL A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 867 removed outlier: 3.688A pdb=" N ARG A 866 " --> pdb=" O VAL A 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.586A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 Processing helix chain 'B' and resid 179 through 185 removed outlier: 4.240A pdb=" N ILE B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.657A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 269 through 273 removed outlier: 4.142A pdb=" N GLY B 273 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.657A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 335 removed outlier: 3.627A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.512A pdb=" N GLU B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 removed outlier: 3.583A pdb=" N GLY B 419 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 500 through 506 removed outlier: 4.223A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 527 removed outlier: 4.076A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 removed outlier: 3.825A pdb=" N PHE B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 584 removed outlier: 4.088A pdb=" N TRP B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 580 " --> pdb=" O CYS B 576 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 581 " --> pdb=" O VAL B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 620 removed outlier: 3.804A pdb=" N LEU B 619 " --> pdb=" O GLY B 615 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET B 620 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 662 removed outlier: 4.554A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 637 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 644 " --> pdb=" O TRP B 640 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 662 " --> pdb=" O PHE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.975A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 695 Processing helix chain 'B' and resid 701 through 712 Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.633A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 747 removed outlier: 3.905A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 788 removed outlier: 3.793A pdb=" N ALA B 781 " --> pdb=" O LYS B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 3.692A pdb=" N TRP B 798 " --> pdb=" O MET B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 821 removed outlier: 3.775A pdb=" N ILE B 820 " --> pdb=" O GLY B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 849 removed outlier: 3.609A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 830 " --> pdb=" O VAL B 826 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 836 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 849 " --> pdb=" O LYS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 867 Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.557A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 126 removed outlier: 4.594A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 Processing helix chain 'C' and resid 180 through 190 removed outlier: 5.246A pdb=" N GLU C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 231 through 245 removed outlier: 4.028A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 301 Processing helix chain 'C' and resid 317 through 335 removed outlier: 3.961A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.535A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 462 through 475 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 562 through 583 removed outlier: 3.551A pdb=" N LEU C 569 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 Processing helix chain 'C' and resid 630 through 665 removed outlier: 3.566A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 665 " --> pdb=" O VAL C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 677 removed outlier: 3.965A pdb=" N GLN C 677 " --> pdb=" O ASP C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 697 removed outlier: 4.168A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 696 " --> pdb=" O THR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 713 removed outlier: 3.600A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 removed outlier: 3.745A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 747 Processing helix chain 'C' and resid 773 through 789 removed outlier: 3.727A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE C 780 " --> pdb=" O ASP C 776 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA C 781 " --> pdb=" O LYS C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 800 Processing helix chain 'C' and resid 801 through 803 No H-bonds generated for 'chain 'C' and resid 801 through 803' Processing helix chain 'C' and resid 824 through 848 removed outlier: 4.316A pdb=" N SER C 846 " --> pdb=" O PHE C 842 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS C 847 " --> pdb=" O LEU C 843 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 867 removed outlier: 3.594A pdb=" N ARG C 866 " --> pdb=" O VAL C 862 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET C 867 " --> pdb=" O GLU C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.891A pdb=" N ASN D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN D 67 " --> pdb=" O THR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 102 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.882A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 3.564A pdb=" N LEU D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 190 removed outlier: 4.377A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLU D 187 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.900A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.649A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 335 removed outlier: 3.775A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.589A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'D' and resid 461 through 475 removed outlier: 3.586A pdb=" N LEU D 466 " --> pdb=" O TYR D 462 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 removed outlier: 4.304A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 560 through 584 removed outlier: 4.259A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 620 Processing helix chain 'D' and resid 630 through 665 removed outlier: 4.337A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 647 " --> pdb=" O PHE D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 675 removed outlier: 3.691A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 695 Processing helix chain 'D' and resid 701 through 712 removed outlier: 4.095A pdb=" N MET D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.502A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 731 " --> pdb=" O ARG D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.707A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG D 748 " --> pdb=" O PHE D 744 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN D 749 " --> pdb=" O VAL D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 788 removed outlier: 3.818A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 788 " --> pdb=" O GLN D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 Processing helix chain 'D' and resid 816 through 821 Processing helix chain 'D' and resid 821 through 850 removed outlier: 3.911A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 372 removed outlier: 4.334A pdb=" N VAL E 368 " --> pdb=" O ILE E 364 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 80 removed outlier: 5.975A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP A 79 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N LEU A 107 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLY A 39 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 176 removed outlier: 6.815A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 228 removed outlier: 4.353A pdb=" N PHE A 279 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.836A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 432 through 437 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA7, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA8, first strand: chain 'A' and resid 534 through 536 removed outlier: 4.158A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 736 through 738 removed outlier: 3.973A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.116A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AB3, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.173A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.692A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AB6, first strand: chain 'B' and resid 389 through 395 removed outlier: 3.734A pdb=" N GLY B 403 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER B 393 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LYS B 401 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS B 395 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB8, first strand: chain 'B' and resid 513 through 514 Processing sheet with id=AB9, first strand: chain 'B' and resid 534 through 535 removed outlier: 4.203A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 735 through 738 Processing sheet with id=AC2, first strand: chain 'B' and resid 684 through 685 removed outlier: 6.879A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 74 through 81 removed outlier: 5.025A pdb=" N HIS C 34 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR C 77 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N LEU C 107 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY C 39 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 198 through 203 removed outlier: 3.647A pdb=" N LYS C 200 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 174 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR C 176 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 277 through 280 removed outlier: 3.956A pdb=" N GLY C 403 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER C 393 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS C 401 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 368 through 370 removed outlier: 4.017A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 478 through 482 removed outlier: 3.955A pdb=" N LEU C 512 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 444 through 446 Processing sheet with id=AC9, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AD1, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.662A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 764 " --> pdb=" O MET C 534 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 737 through 738 removed outlier: 4.103A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 755 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 35 through 38 removed outlier: 5.909A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 41 through 43 removed outlier: 5.954A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 106 through 107 removed outlier: 6.409A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.125A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL D 226 " --> pdb=" O HIS D 253 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N PHE D 279 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE D 256 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY D 403 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER D 393 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LYS D 401 " --> pdb=" O SER D 393 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS D 395 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP D 406 " --> pdb=" O GLY D 410 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 369 through 370 Processing sheet with id=AD8, first strand: chain 'D' and resid 433 through 435 removed outlier: 6.105A pdb=" N GLU D 479 " --> pdb=" O VAL D 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AE1, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AE2, first strand: chain 'D' and resid 717 through 718 removed outlier: 6.737A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N VAL D 685 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET D 737 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 539 " --> pdb=" O MET D 737 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 717 through 718 removed outlier: 6.737A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N VAL D 685 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET D 737 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 539 " --> pdb=" O MET D 737 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 54 through 58 removed outlier: 3.740A pdb=" N ILE E 84 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER E 132 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU E 86 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE E 130 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 72 through 77 removed outlier: 3.607A pdb=" N PHE E 141 " --> pdb=" O CYS E 72 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET E 137 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS E 140 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP E 119 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP E 109 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU E 117 " --> pdb=" O ASP E 109 " (cutoff:3.500A) 1120 hydrogen bonds defined for protein. 3246 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: 9.54 Time building geometry restraints manager: 12.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5031 1.32 - 1.45: 7347 1.45 - 1.57: 15843 1.57 - 1.69: 2 1.69 - 1.82: 267 Bond restraints: 28490 Sorted by residual: bond pdb=" CA ASP D 260 " pdb=" C ASP D 260 " ideal model delta sigma weight residual 1.526 1.455 0.071 1.28e-02 6.10e+03 3.11e+01 bond pdb=" CA SER C 272 " pdb=" CB SER C 272 " ideal model delta sigma weight residual 1.532 1.471 0.060 1.74e-02 3.30e+03 1.21e+01 bond pdb=" N ILE A 755 " pdb=" CA ILE A 755 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" N MET A 340 " pdb=" CA MET A 340 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.23e-02 6.61e+03 1.02e+01 bond pdb=" N MET C 276 " pdb=" CA MET C 276 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.27e-02 6.20e+03 1.01e+01 ... (remaining 28485 not shown) Histogram of bond angle deviations from ideal: 95.84 - 103.50: 381 103.50 - 111.15: 11595 111.15 - 118.81: 11458 118.81 - 126.47: 14713 126.47 - 134.13: 433 Bond angle restraints: 38580 Sorted by residual: angle pdb=" C THR A 520 " pdb=" CA THR A 520 " pdb=" CB THR A 520 " ideal model delta sigma weight residual 116.54 102.66 13.88 1.15e+00 7.56e-01 1.46e+02 angle pdb=" C HIS B 350 " pdb=" CA HIS B 350 " pdb=" CB HIS B 350 " ideal model delta sigma weight residual 111.89 100.48 11.41 1.42e+00 4.96e-01 6.46e+01 angle pdb=" N ALA A 211 " pdb=" CA ALA A 211 " pdb=" C ALA A 211 " ideal model delta sigma weight residual 113.19 103.72 9.47 1.19e+00 7.06e-01 6.33e+01 angle pdb=" N ILE A 519 " pdb=" CA ILE A 519 " pdb=" C ILE A 519 " ideal model delta sigma weight residual 110.62 102.71 7.91 1.02e+00 9.61e-01 6.01e+01 angle pdb=" CA TYR A 521 " pdb=" C TYR A 521 " pdb=" O TYR A 521 " ideal model delta sigma weight residual 121.38 113.98 7.40 1.06e+00 8.90e-01 4.88e+01 ... (remaining 38575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 16217 21.32 - 42.64: 976 42.64 - 63.97: 113 63.97 - 85.29: 63 85.29 - 106.61: 27 Dihedral angle restraints: 17396 sinusoidal: 7343 harmonic: 10053 Sorted by residual: dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 347 " pdb=" CB CYS A 347 " ideal model delta sinusoidal sigma weight residual 93.00 159.31 -66.31 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS E 45 " pdb=" SG CYS E 45 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual 93.00 36.77 56.23 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CA SER C 427 " pdb=" C SER C 427 " pdb=" N LEU C 428 " pdb=" CA LEU C 428 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 17393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.934: 4378 0.934 - 1.868: 1 1.868 - 2.802: 0 2.802 - 3.736: 0 3.736 - 4.670: 1 Chirality restraints: 4380 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 2.27 -4.67 2.00e-02 2.50e+03 5.45e+04 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-02 2.50e+03 6.71e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 ... (remaining 4377 not shown) Planarity restraints: 4878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1002 " -0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG A1002 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A1002 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG A1002 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG A1002 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.346 2.00e-02 2.50e+03 2.99e-01 1.11e+03 pdb=" C7 NAG F 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.123 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.342 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG G 1 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.119 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.145 2.00e-02 2.50e+03 ... (remaining 4875 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 449 2.63 - 3.20: 27952 3.20 - 3.76: 42355 3.76 - 4.33: 57673 4.33 - 4.90: 90170 Nonbonded interactions: 218599 Sorted by model distance: nonbonded pdb=" O LEU D 482 " pdb=" CD1 LEU D 482 " model vdw 2.061 3.460 nonbonded pdb=" OD1 ASP B 177 " pdb=" N ASP B 178 " model vdw 2.151 2.520 nonbonded pdb=" O ASN A 819 " pdb=" OD1 ASN A 819 " model vdw 2.182 3.040 nonbonded pdb=" O ASP D 87 " pdb=" OG SER D 114 " model vdw 2.195 2.440 nonbonded pdb=" ND2 ASN B 123 " pdb=" OD1 ASP B 143 " model vdw 2.197 2.520 ... (remaining 218594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 142 or (resid 143 and (name N or n \ ame CA or name C or name O or name CB )) or resid 144 through 663 or (resid 664 \ and (name N or name CA or name C or name O or name CB )) or resid 665 through 85 \ 0)) selection = (chain 'B' and (resid 33 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 142 or (resid 143 and (name N or n \ ame CA or name C or name O or name CB )) or resid 144 through 850)) selection = (chain 'C' and (resid 33 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 663 or (resid 664 and (name N or n \ ame CA or name C or name O or name CB )) or resid 665 through 850)) selection = (chain 'D' and (resid 33 through 142 or (resid 143 and (name N or name CA or nam \ e C or name O or name CB )) or resid 144 through 850)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.070 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 69.520 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.160 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.007 0.116 28490 Z= 0.484 Angle : 0.992 13.878 38580 Z= 0.609 Chirality : 0.096 4.670 4380 Planarity : 0.015 0.302 4861 Dihedral : 14.798 106.609 10917 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.60 % Allowed : 1.49 % Favored : 97.91 % Cbeta Deviations : 0.09 % 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: -2.23 (0.14), residues: 3456 helix: -0.20 (0.14), residues: 1361 sheet: -2.84 (0.24), residues: 401 loop : -2.22 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 353 HIS 0.017 0.002 HIS A 253 PHE 0.022 0.002 PHE D 359 TYR 0.049 0.002 TYR C 44 ARG 0.009 0.001 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 242 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 TYR cc_start: 0.6149 (m-80) cc_final: 0.5913 (m-80) REVERT: A 836 PHE cc_start: 0.8820 (t80) cc_final: 0.8289 (t80) REVERT: A 861 MET cc_start: 0.4757 (ppp) cc_final: 0.4506 (ppp) REVERT: B 501 MET cc_start: 0.7635 (mmm) cc_final: 0.7089 (mmm) REVERT: B 794 MET cc_start: 0.9164 (mtm) cc_final: 0.8961 (mtp) REVERT: C 709 MET cc_start: 0.7936 (mpp) cc_final: 0.7590 (mpp) REVERT: D 364 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.9008 (ttmt) REVERT: D 367 HIS cc_start: 0.8355 (OUTLIER) cc_final: 0.8142 (m-70) REVERT: D 415 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: D 590 TYR cc_start: 0.7889 (t80) cc_final: 0.7332 (t80) REVERT: D 705 MET cc_start: 0.7852 (mpp) cc_final: 0.6713 (mpp) REVERT: D 770 MET cc_start: 0.8191 (mmp) cc_final: 0.7949 (mmp) REVERT: D 793 MET cc_start: 0.8507 (mpp) cc_final: 0.8026 (mpp) REVERT: D 804 CYS cc_start: 0.7287 (t) cc_final: 0.6908 (p) REVERT: D 836 PHE cc_start: 0.8687 (m-80) cc_final: 0.8445 (m-80) outliers start: 18 outliers final: 2 residues processed: 259 average time/residue: 0.3698 time to fit residues: 155.9522 Evaluate side-chains 189 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 184 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain D residue 364 LYS Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 415 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 7.9990 chunk 260 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 269 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 367 HIS ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 137 GLN ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN D 802 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28490 Z= 0.203 Angle : 0.694 11.094 38580 Z= 0.344 Chirality : 0.044 0.298 4380 Planarity : 0.005 0.066 4861 Dihedral : 9.224 68.666 4355 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.83 % Allowed : 8.03 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3456 helix: 0.67 (0.14), residues: 1417 sheet: -2.49 (0.25), residues: 395 loop : -2.08 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 798 HIS 0.011 0.001 HIS B 111 PHE 0.024 0.001 PHE D 735 TYR 0.020 0.001 TYR C 44 ARG 0.004 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.7654 (t0) cc_final: 0.7427 (t0) REVERT: A 627 MET cc_start: 0.7681 (mpp) cc_final: 0.7460 (mpp) REVERT: A 641 TRP cc_start: 0.8540 (m-10) cc_final: 0.8208 (m-10) REVERT: A 691 MET cc_start: 0.8111 (ttp) cc_final: 0.7752 (ptt) REVERT: A 836 PHE cc_start: 0.8752 (t80) cc_final: 0.8386 (t80) REVERT: B 709 MET cc_start: 0.8129 (ptp) cc_final: 0.7709 (ppp) REVERT: B 794 MET cc_start: 0.9156 (mtm) cc_final: 0.8886 (mtp) REVERT: C 620 MET cc_start: 0.8870 (mmm) cc_final: 0.8146 (mmm) REVERT: C 770 MET cc_start: 0.8378 (mpp) cc_final: 0.8175 (mmm) REVERT: D 565 MET cc_start: 0.8100 (mtp) cc_final: 0.7641 (mtm) REVERT: D 590 TYR cc_start: 0.7893 (t80) cc_final: 0.7397 (t80) REVERT: D 691 MET cc_start: 0.8372 (mtt) cc_final: 0.7922 (mtt) REVERT: D 705 MET cc_start: 0.7672 (mpp) cc_final: 0.7435 (mpp) REVERT: D 770 MET cc_start: 0.8094 (mmp) cc_final: 0.7893 (mmp) REVERT: D 804 CYS cc_start: 0.7452 (t) cc_final: 0.7033 (p) REVERT: E 129 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.5196 (mt) outliers start: 25 outliers final: 14 residues processed: 232 average time/residue: 0.3515 time to fit residues: 137.4183 Evaluate side-chains 205 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 129 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 9.9990 chunk 96 optimal weight: 0.1980 chunk 259 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 312 optimal weight: 8.9990 chunk 338 optimal weight: 0.5980 chunk 278 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28490 Z= 0.286 Angle : 0.664 10.563 38580 Z= 0.331 Chirality : 0.043 0.257 4380 Planarity : 0.004 0.051 4861 Dihedral : 7.442 53.263 4344 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.36 % Allowed : 11.22 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3456 helix: 0.86 (0.14), residues: 1425 sheet: -2.54 (0.24), residues: 402 loop : -2.04 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 613 HIS 0.011 0.001 HIS B 111 PHE 0.019 0.001 PHE D 735 TYR 0.024 0.001 TYR A 454 ARG 0.004 0.000 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 3.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 TRP cc_start: 0.8332 (m-10) cc_final: 0.7921 (m-10) REVERT: A 836 PHE cc_start: 0.8765 (t80) cc_final: 0.8358 (t80) REVERT: B 578 LEU cc_start: 0.8136 (tt) cc_final: 0.7906 (tp) REVERT: B 709 MET cc_start: 0.8076 (ptp) cc_final: 0.7725 (ppp) REVERT: B 794 MET cc_start: 0.9067 (mtm) cc_final: 0.8214 (mtt) REVERT: B 795 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8570 (mmmm) REVERT: C 316 MET cc_start: 0.7943 (ttt) cc_final: 0.7716 (ttt) REVERT: C 413 MET cc_start: 0.8070 (mtp) cc_final: 0.7828 (mtp) REVERT: C 705 MET cc_start: 0.8711 (tpp) cc_final: 0.8481 (tpp) REVERT: C 709 MET cc_start: 0.8116 (mpp) cc_final: 0.7785 (mpp) REVERT: C 737 MET cc_start: 0.8216 (ppp) cc_final: 0.7438 (ppp) REVERT: C 742 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8443 (mm) REVERT: D 565 MET cc_start: 0.8018 (mtp) cc_final: 0.7639 (mtm) REVERT: D 590 TYR cc_start: 0.7978 (t80) cc_final: 0.7501 (t80) REVERT: D 691 MET cc_start: 0.8310 (mtt) cc_final: 0.7964 (mtt) REVERT: D 804 CYS cc_start: 0.7720 (t) cc_final: 0.7164 (p) outliers start: 41 outliers final: 27 residues processed: 230 average time/residue: 0.3586 time to fit residues: 138.9534 Evaluate side-chains 214 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 361 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 0.2980 chunk 235 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 34 optimal weight: 0.4980 chunk 149 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 314 optimal weight: 40.0000 chunk 332 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 297 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 28490 Z= 0.297 Angle : 0.653 12.722 38580 Z= 0.325 Chirality : 0.043 0.239 4380 Planarity : 0.004 0.049 4861 Dihedral : 6.670 56.825 4344 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.69 % Allowed : 13.41 % Favored : 84.89 % 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: -1.24 (0.14), residues: 3456 helix: 0.95 (0.14), residues: 1429 sheet: -2.57 (0.23), residues: 421 loop : -2.02 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 613 HIS 0.010 0.001 HIS B 111 PHE 0.015 0.001 PHE D 735 TYR 0.025 0.001 TYR B 682 ARG 0.003 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 196 time to evaluate : 3.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 619 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8834 (tp) REVERT: A 641 TRP cc_start: 0.8293 (m-10) cc_final: 0.8001 (m-10) REVERT: A 836 PHE cc_start: 0.8774 (t80) cc_final: 0.8395 (t80) REVERT: B 50 MET cc_start: 0.8668 (tmm) cc_final: 0.8405 (ppp) REVERT: B 323 MET cc_start: 0.8926 (tpp) cc_final: 0.8516 (tpp) REVERT: B 629 LYS cc_start: 0.7413 (ptpt) cc_final: 0.6983 (tptm) REVERT: B 705 MET cc_start: 0.8730 (tpp) cc_final: 0.8440 (tpt) REVERT: B 709 MET cc_start: 0.8135 (ptp) cc_final: 0.7900 (ptm) REVERT: B 794 MET cc_start: 0.8482 (mtm) cc_final: 0.8252 (mtt) REVERT: C 413 MET cc_start: 0.8102 (mtp) cc_final: 0.7873 (mtp) REVERT: D 565 MET cc_start: 0.7882 (mtp) cc_final: 0.7459 (mtm) REVERT: D 590 TYR cc_start: 0.7934 (t80) cc_final: 0.7461 (t80) REVERT: D 691 MET cc_start: 0.8269 (mtt) cc_final: 0.7840 (mtt) REVERT: D 804 CYS cc_start: 0.7833 (t) cc_final: 0.7322 (p) outliers start: 51 outliers final: 28 residues processed: 236 average time/residue: 0.3438 time to fit residues: 137.3789 Evaluate side-chains 215 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 186 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 546 ASN Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 361 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 0.6980 chunk 188 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 247 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 chunk 283 optimal weight: 3.9990 chunk 229 optimal weight: 0.3980 chunk 0 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28490 Z= 0.172 Angle : 0.596 12.520 38580 Z= 0.295 Chirality : 0.041 0.214 4380 Planarity : 0.004 0.051 4861 Dihedral : 6.139 56.217 4344 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.30 % Favored : 94.68 % Rotamer: Outliers : 1.43 % Allowed : 14.54 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3456 helix: 1.19 (0.14), residues: 1435 sheet: -2.30 (0.24), residues: 427 loop : -1.90 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 613 HIS 0.007 0.001 HIS B 111 PHE 0.012 0.001 PHE D 735 TYR 0.023 0.001 TYR B 682 ARG 0.003 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 205 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 TRP cc_start: 0.8150 (m-10) cc_final: 0.7834 (m-10) REVERT: A 836 PHE cc_start: 0.8744 (t80) cc_final: 0.8377 (t80) REVERT: B 50 MET cc_start: 0.8618 (tmm) cc_final: 0.8348 (ppp) REVERT: B 360 MET cc_start: 0.8339 (tpt) cc_final: 0.8080 (tpt) REVERT: B 629 LYS cc_start: 0.7286 (ptpt) cc_final: 0.6923 (tptm) REVERT: B 794 MET cc_start: 0.8511 (mtm) cc_final: 0.8300 (mtt) REVERT: C 620 MET cc_start: 0.9238 (mmm) cc_final: 0.7485 (mmm) REVERT: D 565 MET cc_start: 0.7898 (mtp) cc_final: 0.7559 (mtm) REVERT: D 590 TYR cc_start: 0.7958 (t80) cc_final: 0.7523 (t80) outliers start: 43 outliers final: 21 residues processed: 238 average time/residue: 0.3841 time to fit residues: 154.0548 Evaluate side-chains 207 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 487 LYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 129 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 5.9990 chunk 299 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 195 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 332 optimal weight: 5.9990 chunk 276 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 81 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 28490 Z= 0.401 Angle : 0.705 13.551 38580 Z= 0.353 Chirality : 0.044 0.272 4380 Planarity : 0.004 0.047 4861 Dihedral : 6.324 57.071 4344 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.06 % Favored : 92.91 % Rotamer: Outliers : 1.89 % Allowed : 15.57 % Favored : 82.54 % 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: -1.17 (0.14), residues: 3456 helix: 1.05 (0.14), residues: 1432 sheet: -2.68 (0.23), residues: 431 loop : -1.96 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 353 HIS 0.010 0.001 HIS B 111 PHE 0.017 0.002 PHE E 102 TYR 0.023 0.002 TYR B 682 ARG 0.004 0.001 ARG D 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 186 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.7876 (mpp) cc_final: 0.7671 (mpp) REVERT: A 641 TRP cc_start: 0.8312 (m-10) cc_final: 0.7897 (m-10) REVERT: A 836 PHE cc_start: 0.8792 (t80) cc_final: 0.8436 (t80) REVERT: B 629 LYS cc_start: 0.7378 (ptpt) cc_final: 0.6984 (tptm) REVERT: B 737 MET cc_start: 0.8617 (ppp) cc_final: 0.8197 (ppp) REVERT: C 620 MET cc_start: 0.9383 (mmm) cc_final: 0.7636 (mmm) REVERT: C 742 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8586 (mm) REVERT: C 793 MET cc_start: 0.8807 (mtm) cc_final: 0.8514 (ptp) REVERT: D 145 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8875 (m-10) REVERT: D 565 MET cc_start: 0.7942 (mtp) cc_final: 0.7597 (mtm) REVERT: D 590 TYR cc_start: 0.7883 (t80) cc_final: 0.7403 (t80) REVERT: D 802 ASN cc_start: 0.8456 (m-40) cc_final: 0.8256 (m-40) outliers start: 57 outliers final: 42 residues processed: 234 average time/residue: 0.3517 time to fit residues: 138.7543 Evaluate side-chains 226 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 182 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 549 ASN Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 546 ASN Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 361 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 189 optimal weight: 8.9990 chunk 243 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 280 optimal weight: 0.0270 chunk 185 optimal weight: 0.9990 chunk 331 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN C 81 GLN C 346 GLN ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28490 Z= 0.185 Angle : 0.614 11.494 38580 Z= 0.303 Chirality : 0.041 0.234 4380 Planarity : 0.004 0.050 4861 Dihedral : 6.038 53.069 4344 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.53 % Favored : 94.44 % Rotamer: Outliers : 1.83 % Allowed : 16.50 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 3456 helix: 1.27 (0.14), residues: 1435 sheet: -2.30 (0.24), residues: 426 loop : -1.86 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 706 HIS 0.007 0.001 HIS B 111 PHE 0.017 0.001 PHE E 102 TYR 0.010 0.001 TYR E 92 ARG 0.003 0.000 ARG E 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 193 time to evaluate : 3.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.7885 (mpp) cc_final: 0.7683 (mpp) REVERT: A 641 TRP cc_start: 0.8105 (m-10) cc_final: 0.7709 (m-10) REVERT: A 705 MET cc_start: 0.8485 (ptp) cc_final: 0.8276 (ptp) REVERT: A 836 PHE cc_start: 0.8793 (t80) cc_final: 0.8408 (t80) REVERT: B 50 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8309 (ppp) REVERT: B 578 LEU cc_start: 0.8145 (tt) cc_final: 0.7784 (tp) REVERT: B 629 LYS cc_start: 0.7316 (ptpt) cc_final: 0.6978 (tptm) REVERT: B 737 MET cc_start: 0.8544 (ppp) cc_final: 0.8097 (ppp) REVERT: C 620 MET cc_start: 0.9221 (mmm) cc_final: 0.7597 (mmm) REVERT: C 742 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8610 (mm) REVERT: C 793 MET cc_start: 0.8738 (mtm) cc_final: 0.8430 (ptp) REVERT: C 800 ARG cc_start: 0.7383 (mmp-170) cc_final: 0.6907 (mmp80) REVERT: D 565 MET cc_start: 0.7855 (mtp) cc_final: 0.7539 (mtm) REVERT: D 590 TYR cc_start: 0.7891 (t80) cc_final: 0.7428 (t80) REVERT: E 119 ASP cc_start: 0.7527 (t70) cc_final: 0.7272 (t0) outliers start: 55 outliers final: 36 residues processed: 238 average time/residue: 0.3595 time to fit residues: 143.4223 Evaluate side-chains 223 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 185 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 144 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 163 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 260 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28490 Z= 0.165 Angle : 0.599 12.506 38580 Z= 0.295 Chirality : 0.041 0.360 4380 Planarity : 0.004 0.049 4861 Dihedral : 5.812 54.068 4344 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 1.73 % Allowed : 16.87 % Favored : 81.41 % 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: -0.74 (0.15), residues: 3456 helix: 1.33 (0.14), residues: 1446 sheet: -2.13 (0.24), residues: 425 loop : -1.79 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 138 HIS 0.005 0.001 HIS A 253 PHE 0.013 0.001 PHE E 102 TYR 0.013 0.001 TYR D 521 ARG 0.006 0.000 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 200 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8756 (mm) REVERT: A 641 TRP cc_start: 0.8020 (m-10) cc_final: 0.7515 (m-10) REVERT: A 836 PHE cc_start: 0.8806 (t80) cc_final: 0.8434 (t80) REVERT: B 50 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8349 (ppp) REVERT: B 578 LEU cc_start: 0.8056 (tt) cc_final: 0.7699 (tp) REVERT: B 629 LYS cc_start: 0.7268 (ptpt) cc_final: 0.6965 (tptm) REVERT: B 705 MET cc_start: 0.8359 (tpt) cc_final: 0.8095 (tpt) REVERT: C 620 MET cc_start: 0.9183 (mmm) cc_final: 0.8003 (mmm) REVERT: C 770 MET cc_start: 0.8292 (mpp) cc_final: 0.7984 (mmm) REVERT: D 360 MET cc_start: 0.8559 (tpp) cc_final: 0.8225 (tpp) REVERT: D 501 MET cc_start: 0.8437 (mmt) cc_final: 0.7951 (mmt) REVERT: D 590 TYR cc_start: 0.7989 (t80) cc_final: 0.7573 (t80) REVERT: D 705 MET cc_start: 0.7972 (mpp) cc_final: 0.7753 (mpp) outliers start: 52 outliers final: 41 residues processed: 242 average time/residue: 0.3617 time to fit residues: 147.2306 Evaluate side-chains 234 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 191 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 144 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 0.9980 chunk 317 optimal weight: 0.7980 chunk 289 optimal weight: 20.0000 chunk 308 optimal weight: 20.0000 chunk 185 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 242 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 279 optimal weight: 0.0070 chunk 292 optimal weight: 6.9990 chunk 307 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28490 Z= 0.155 Angle : 0.605 12.135 38580 Z= 0.296 Chirality : 0.041 0.258 4380 Planarity : 0.004 0.051 4861 Dihedral : 5.718 54.324 4344 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 1.63 % Allowed : 17.33 % Favored : 81.04 % 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: -0.61 (0.15), residues: 3456 helix: 1.41 (0.14), residues: 1444 sheet: -1.90 (0.25), residues: 418 loop : -1.73 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 296 HIS 0.004 0.001 HIS A 253 PHE 0.016 0.001 PHE D 145 TYR 0.022 0.001 TYR E 121 ARG 0.005 0.000 ARG C 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 205 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8719 (mm) REVERT: A 210 ASP cc_start: 0.7377 (t0) cc_final: 0.7092 (t0) REVERT: A 641 TRP cc_start: 0.7994 (m-10) cc_final: 0.7203 (m-10) REVERT: A 836 PHE cc_start: 0.8805 (t80) cc_final: 0.8433 (t80) REVERT: B 50 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8331 (ppp) REVERT: B 360 MET cc_start: 0.8445 (tpt) cc_final: 0.8178 (tpt) REVERT: B 435 VAL cc_start: 0.4762 (OUTLIER) cc_final: 0.4518 (p) REVERT: B 578 LEU cc_start: 0.8028 (tt) cc_final: 0.7687 (tp) REVERT: B 629 LYS cc_start: 0.7203 (ptpt) cc_final: 0.6937 (tptm) REVERT: B 705 MET cc_start: 0.8327 (tpt) cc_final: 0.8028 (tpt) REVERT: C 620 MET cc_start: 0.9205 (mmm) cc_final: 0.7632 (mmm) REVERT: C 770 MET cc_start: 0.8252 (mpp) cc_final: 0.7981 (mmm) REVERT: D 590 TYR cc_start: 0.7968 (t80) cc_final: 0.7570 (t80) REVERT: D 705 MET cc_start: 0.7887 (mpp) cc_final: 0.7003 (mpp) outliers start: 49 outliers final: 33 residues processed: 245 average time/residue: 0.3644 time to fit residues: 149.6091 Evaluate side-chains 230 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 194 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 144 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 5.9990 chunk 326 optimal weight: 0.0030 chunk 199 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 342 optimal weight: 4.9990 chunk 315 optimal weight: 0.7980 chunk 272 optimal weight: 7.9990 chunk 28 optimal weight: 0.1980 chunk 210 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28490 Z= 0.195 Angle : 0.620 13.907 38580 Z= 0.303 Chirality : 0.041 0.301 4380 Planarity : 0.004 0.051 4861 Dihedral : 5.759 53.101 4344 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.30 % Favored : 94.68 % Rotamer: Outliers : 1.63 % Allowed : 17.40 % Favored : 80.98 % 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: -0.55 (0.15), residues: 3456 helix: 1.46 (0.14), residues: 1447 sheet: -1.92 (0.25), residues: 422 loop : -1.69 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 706 HIS 0.005 0.001 HIS A 253 PHE 0.015 0.001 PHE D 708 TYR 0.024 0.001 TYR E 121 ARG 0.004 0.000 ARG C 300 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 196 time to evaluate : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8731 (mm) REVERT: A 836 PHE cc_start: 0.8805 (t80) cc_final: 0.8428 (t80) REVERT: B 50 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8335 (ppp) REVERT: B 360 MET cc_start: 0.8429 (tpt) cc_final: 0.8103 (tpt) REVERT: B 578 LEU cc_start: 0.8051 (tt) cc_final: 0.7708 (tp) REVERT: B 705 MET cc_start: 0.8254 (tpt) cc_final: 0.7958 (tpt) REVERT: B 737 MET cc_start: 0.8814 (ppp) cc_final: 0.8430 (ppp) REVERT: C 620 MET cc_start: 0.9231 (mmm) cc_final: 0.7929 (mmm) REVERT: C 713 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6913 (tpt170) REVERT: C 742 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8629 (mm) REVERT: C 770 MET cc_start: 0.8298 (mpp) cc_final: 0.8029 (mmm) REVERT: D 501 MET cc_start: 0.8557 (mmt) cc_final: 0.8088 (mmt) REVERT: D 590 TYR cc_start: 0.7914 (t80) cc_final: 0.7509 (t80) REVERT: D 691 MET cc_start: 0.8705 (tpp) cc_final: 0.7933 (tpt) outliers start: 49 outliers final: 39 residues processed: 232 average time/residue: 0.3652 time to fit residues: 141.7965 Evaluate side-chains 233 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 713 ARG Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 144 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 6.9990 chunk 290 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 251 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 280 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.090012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.062178 restraints weight = 105154.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.061654 restraints weight = 74348.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.061875 restraints weight = 60981.000| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 28490 Z= 0.360 Angle : 0.711 12.355 38580 Z= 0.352 Chirality : 0.044 0.273 4380 Planarity : 0.004 0.048 4861 Dihedral : 6.167 53.850 4344 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.86 % Favored : 93.11 % Rotamer: Outliers : 1.73 % Allowed : 17.50 % Favored : 80.78 % 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: -0.78 (0.15), residues: 3456 helix: 1.29 (0.14), residues: 1435 sheet: -2.24 (0.24), residues: 427 loop : -1.74 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 706 HIS 0.007 0.001 HIS A 253 PHE 0.019 0.002 PHE E 102 TYR 0.021 0.002 TYR E 121 ARG 0.007 0.001 ARG A 300 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4452.39 seconds wall clock time: 83 minutes 43.33 seconds (5023.33 seconds total)