Starting phenix.real_space_refine on Mon Feb 19 17:15:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzh_23606/02_2024/7lzh_23606_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzh_23606/02_2024/7lzh_23606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzh_23606/02_2024/7lzh_23606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzh_23606/02_2024/7lzh_23606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzh_23606/02_2024/7lzh_23606_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzh_23606/02_2024/7lzh_23606_updated.pdb" } resolution = 3.57 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= 0.014 sd= 0.065 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 110 5.16 5 C 16214 2.51 5 N 4234 2.21 5 O 4748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 797": "NH1" <-> "NH2" Residue "A ARG 806": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 436": "NH1" <-> "NH2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B ARG 708": "NH1" <-> "NH2" Residue "B ARG 789": "NH1" <-> "NH2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B ARG 806": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 361": "NH1" <-> "NH2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 436": "NH1" <-> "NH2" Residue "C ARG 548": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 789": "NH1" <-> "NH2" Residue "C ARG 797": "NH1" <-> "NH2" Residue "C ARG 806": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 361": "NH1" <-> "NH2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 436": "NH1" <-> "NH2" Residue "D ARG 548": "NH1" <-> "NH2" Residue "D ARG 708": "NH1" <-> "NH2" Residue "D ARG 789": "NH1" <-> "NH2" Residue "D ARG 797": "NH1" <-> "NH2" Residue "D ARG 806": "NH1" <-> "NH2" Residue "B GLU 1001": "OE1" <-> "OE2" Residue "D GLU 1001": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25306 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 6251 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 38, 'TRANS': 759} Chain breaks: 3 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 6174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6174 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 38, 'TRANS': 749} Chain breaks: 4 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 6251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 6251 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 38, 'TRANS': 759} Chain breaks: 3 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 6174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6174 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 38, 'TRANS': 749} Chain breaks: 4 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'GSH': 1, 'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'GSH': 1, 'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} 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: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'GSH': 1, 'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'GSH': 1, 'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 13.47, per 1000 atoms: 0.53 Number of scatterers: 25306 At special positions: 0 Unit cell: (110.39, 166.83, 189.24, 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 110 16.00 O 4748 8.00 N 4234 7.00 C 16214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 841 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 841 " distance=2.03 Simple disulfide: pdb=" SG CYS C 786 " - pdb=" SG CYS C 841 " distance=2.03 Simple disulfide: pdb=" SG CYS D 786 " - pdb=" SG CYS D 841 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1002 " - " ASN A 108 " " NAG A1003 " - " ASN A 404 " " NAG B1002 " - " ASN B 108 " " NAG B1003 " - " ASN B 404 " " NAG C1002 " - " ASN C 108 " " NAG C1003 " - " ASN C 404 " " NAG D1002 " - " ASN D 108 " " NAG D1003 " - " ASN D 404 " " NAG E 1 " - " ASN A 443 " " NAG F 1 " - " ASN A 576 " " NAG G 1 " - " ASN B 443 " " NAG H 1 " - " ASN B 576 " " NAG I 1 " - " ASN C 443 " " NAG J 1 " - " ASN C 576 " " NAG K 1 " - " ASN D 443 " " NAG L 1 " - " ASN D 576 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.39 Conformation dependent library (CDL) restraints added in 4.3 seconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 24 sheets defined 37.3% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.79 Creating SS restraints... Processing helix chain 'A' and resid 74 through 88 Proline residue: A 79 - end of helix Processing helix chain 'A' and resid 92 through 95 No H-bonds generated for 'chain 'A' and resid 92 through 95' Processing helix chain 'A' and resid 111 through 123 removed outlier: 3.744A pdb=" N THR A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.531A pdb=" N SER A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 191 removed outlier: 3.606A pdb=" N ALA A 185 " --> pdb=" O MET A 181 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.643A pdb=" N ASN A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.845A pdb=" N SER A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 271 removed outlier: 3.679A pdb=" N VAL A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 302 through 305 No H-bonds generated for 'chain 'A' and resid 302 through 305' Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 341 through 362 removed outlier: 3.762A pdb=" N VAL A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 350 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.737A pdb=" N ILE A 400 " --> pdb=" O PHE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 521 through 531 removed outlier: 3.725A pdb=" N GLU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 560 removed outlier: 3.878A pdb=" N GLU A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 580 No H-bonds generated for 'chain 'A' and resid 577 through 580' Processing helix chain 'A' and resid 605 through 611 Proline residue: A 611 - end of helix Processing helix chain 'A' and resid 614 through 634 removed outlier: 3.640A pdb=" N ALA A 618 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 621 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 631 " --> pdb=" O VAL A 627 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 674 through 700 removed outlier: 3.520A pdb=" N ILE A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 699 " --> pdb=" O SER A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 717 removed outlier: 3.697A pdb=" N THR A 717 " --> pdb=" O ASP A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 734 Processing helix chain 'A' and resid 753 through 756 No H-bonds generated for 'chain 'A' and resid 753 through 756' Processing helix chain 'A' and resid 774 through 783 removed outlier: 4.100A pdb=" N VAL A 779 " --> pdb=" O PRO A 775 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 823 removed outlier: 3.647A pdb=" N THR A 816 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 829 No H-bonds generated for 'chain 'A' and resid 826 through 829' Processing helix chain 'A' and resid 831 through 834 No H-bonds generated for 'chain 'A' and resid 831 through 834' Processing helix chain 'A' and resid 861 through 885 removed outlier: 3.571A pdb=" N PHE A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 90 Proline residue: B 79 - end of helix removed outlier: 3.669A pdb=" N ASN B 89 " --> pdb=" O MET B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.692A pdb=" N THR B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 177 through 191 removed outlier: 3.562A pdb=" N MET B 181 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N HIS B 182 " --> pdb=" O PHE B 179 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE B 184 " --> pdb=" O MET B 181 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP B 186 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU B 188 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 189 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 190 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.526A pdb=" N GLY B 209 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.922A pdb=" N SER B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 removed outlier: 3.573A pdb=" N SER B 268 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 269 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS B 271 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 No H-bonds generated for 'chain 'B' and resid 302 through 305' Processing helix chain 'B' and resid 320 through 332 removed outlier: 3.609A pdb=" N ASN B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 362 removed outlier: 3.809A pdb=" N VAL B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP B 350 " --> pdb=" O TYR B 346 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 3.540A pdb=" N ILE B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 400 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 401 " --> pdb=" O MET B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 455 removed outlier: 3.538A pdb=" N LEU B 455 " --> pdb=" O PRO B 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 455' Processing helix chain 'B' and resid 521 through 530 removed outlier: 3.527A pdb=" N ALA B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 560 removed outlier: 3.602A pdb=" N ASN B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 580 removed outlier: 3.945A pdb=" N TYR B 580 " --> pdb=" O ASN B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 633 removed outlier: 3.898A pdb=" N TRP B 617 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA B 618 " --> pdb=" O GLU B 615 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL B 619 " --> pdb=" O MET B 616 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY B 621 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 622 " --> pdb=" O VAL B 619 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 623 " --> pdb=" O THR B 620 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 624 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 627 " --> pdb=" O PHE B 624 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 633 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 655 removed outlier: 3.629A pdb=" N PHE B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 700 removed outlier: 4.027A pdb=" N LEU B 678 " --> pdb=" O GLY B 674 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B 679 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 698 " --> pdb=" O ALA B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 704 No H-bonds generated for 'chain 'B' and resid 702 through 704' Processing helix chain 'B' and resid 713 through 716 No H-bonds generated for 'chain 'B' and resid 713 through 716' Processing helix chain 'B' and resid 731 through 734 No H-bonds generated for 'chain 'B' and resid 731 through 734' Processing helix chain 'B' and resid 752 through 759 removed outlier: 3.539A pdb=" N ALA B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU B 758 " --> pdb=" O TYR B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 783 removed outlier: 4.257A pdb=" N VAL B 779 " --> pdb=" O PRO B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 823 removed outlier: 3.673A pdb=" N ASP B 813 " --> pdb=" O LEU B 810 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET B 814 " --> pdb=" O ALA B 811 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 816 " --> pdb=" O ASP B 813 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 817 " --> pdb=" O MET B 814 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 819 " --> pdb=" O THR B 816 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU B 823 " --> pdb=" O GLN B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 834 Processing helix chain 'B' and resid 860 through 885 removed outlier: 3.589A pdb=" N ILE B 864 " --> pdb=" O GLY B 860 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS B 869 " --> pdb=" O CYS B 865 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 874 " --> pdb=" O PHE B 870 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 885 " --> pdb=" O PHE B 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 88 Proline residue: C 79 - end of helix Processing helix chain 'C' and resid 92 through 95 No H-bonds generated for 'chain 'C' and resid 92 through 95' Processing helix chain 'C' and resid 111 through 123 removed outlier: 3.745A pdb=" N THR C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.530A pdb=" N SER C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 191 removed outlier: 3.605A pdb=" N ALA C 185 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.642A pdb=" N ASN C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 211 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.845A pdb=" N SER C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 271 removed outlier: 3.679A pdb=" N VAL C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 302 through 305 No H-bonds generated for 'chain 'C' and resid 302 through 305' Processing helix chain 'C' and resid 320 through 332 Processing helix chain 'C' and resid 341 through 362 removed outlier: 3.762A pdb=" N VAL C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 361 " --> pdb=" O ASP C 357 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 362 " --> pdb=" O VAL C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 removed outlier: 3.738A pdb=" N ILE C 400 " --> pdb=" O PHE C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 456 No H-bonds generated for 'chain 'C' and resid 454 through 456' Processing helix chain 'C' and resid 521 through 531 removed outlier: 3.724A pdb=" N GLU C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU C 531 " --> pdb=" O ALA C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 560 removed outlier: 3.878A pdb=" N GLU C 558 " --> pdb=" O ASN C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 580 No H-bonds generated for 'chain 'C' and resid 577 through 580' Processing helix chain 'C' and resid 605 through 611 Proline residue: C 611 - end of helix Processing helix chain 'C' and resid 614 through 634 removed outlier: 3.640A pdb=" N ALA C 618 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 621 " --> pdb=" O TRP C 617 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C 625 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL C 627 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 631 " --> pdb=" O VAL C 627 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP C 632 " --> pdb=" O GLY C 628 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 633 " --> pdb=" O ALA C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 654 No H-bonds generated for 'chain 'C' and resid 652 through 654' Processing helix chain 'C' and resid 674 through 700 removed outlier: 3.520A pdb=" N ILE C 687 " --> pdb=" O PHE C 683 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER C 690 " --> pdb=" O LEU C 686 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA C 694 " --> pdb=" O SER C 690 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER C 698 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 699 " --> pdb=" O SER C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 717 removed outlier: 3.697A pdb=" N THR C 717 " --> pdb=" O ASP C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 734 Processing helix chain 'C' and resid 753 through 756 No H-bonds generated for 'chain 'C' and resid 753 through 756' Processing helix chain 'C' and resid 774 through 783 removed outlier: 4.100A pdb=" N VAL C 779 " --> pdb=" O PRO C 775 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 823 removed outlier: 3.648A pdb=" N THR C 816 " --> pdb=" O VAL C 812 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 829 No H-bonds generated for 'chain 'C' and resid 826 through 829' Processing helix chain 'C' and resid 831 through 834 No H-bonds generated for 'chain 'C' and resid 831 through 834' Processing helix chain 'C' and resid 861 through 885 removed outlier: 3.570A pdb=" N PHE C 881 " --> pdb=" O PHE C 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 90 Proline residue: D 79 - end of helix removed outlier: 3.669A pdb=" N ASN D 89 " --> pdb=" O MET D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 123 removed outlier: 3.692A pdb=" N THR D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 177 through 191 removed outlier: 3.562A pdb=" N MET D 181 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N HIS D 182 " --> pdb=" O PHE D 179 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE D 184 " --> pdb=" O MET D 181 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP D 186 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU D 188 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER D 189 " --> pdb=" O ASP D 186 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 190 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 219 removed outlier: 3.526A pdb=" N GLY D 209 " --> pdb=" O CYS D 205 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 212 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D 218 " --> pdb=" O GLY D 214 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.922A pdb=" N SER D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 272 removed outlier: 3.574A pdb=" N SER D 268 " --> pdb=" O ASN D 265 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 269 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS D 271 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 No H-bonds generated for 'chain 'D' and resid 302 through 305' Processing helix chain 'D' and resid 320 through 332 removed outlier: 3.609A pdb=" N ASN D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 362 removed outlier: 3.810A pdb=" N VAL D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP D 350 " --> pdb=" O TYR D 346 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 352 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 removed outlier: 3.540A pdb=" N ILE D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE D 400 " --> pdb=" O PHE D 396 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 401 " --> pdb=" O MET D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 455 removed outlier: 3.539A pdb=" N LEU D 455 " --> pdb=" O PRO D 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 452 through 455' Processing helix chain 'D' and resid 521 through 530 removed outlier: 3.527A pdb=" N ALA D 527 " --> pdb=" O ASP D 523 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 560 removed outlier: 3.602A pdb=" N ASN D 557 " --> pdb=" O ASP D 553 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 559 " --> pdb=" O LEU D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 580 removed outlier: 3.945A pdb=" N TYR D 580 " --> pdb=" O ASN D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 633 removed outlier: 3.898A pdb=" N TRP D 617 " --> pdb=" O ILE D 614 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA D 618 " --> pdb=" O GLU D 615 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL D 619 " --> pdb=" O MET D 616 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY D 621 " --> pdb=" O ALA D 618 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 622 " --> pdb=" O VAL D 619 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 623 " --> pdb=" O THR D 620 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE D 624 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL D 627 " --> pdb=" O PHE D 624 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE D 633 " --> pdb=" O MET D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 655 removed outlier: 3.629A pdb=" N PHE D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 700 removed outlier: 4.027A pdb=" N LEU D 678 " --> pdb=" O GLY D 674 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER D 698 " --> pdb=" O ALA D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 704 No H-bonds generated for 'chain 'D' and resid 702 through 704' Processing helix chain 'D' and resid 713 through 716 No H-bonds generated for 'chain 'D' and resid 713 through 716' Processing helix chain 'D' and resid 731 through 734 No H-bonds generated for 'chain 'D' and resid 731 through 734' Processing helix chain 'D' and resid 752 through 759 removed outlier: 3.539A pdb=" N ALA D 757 " --> pdb=" O GLN D 753 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU D 758 " --> pdb=" O TYR D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 783 removed outlier: 4.257A pdb=" N VAL D 779 " --> pdb=" O PRO D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 823 removed outlier: 3.673A pdb=" N ASP D 813 " --> pdb=" O LEU D 810 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET D 814 " --> pdb=" O ALA D 811 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 816 " --> pdb=" O ASP D 813 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA D 817 " --> pdb=" O MET D 814 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 819 " --> pdb=" O THR D 816 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU D 823 " --> pdb=" O GLN D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 834 Processing helix chain 'D' and resid 860 through 885 removed outlier: 3.589A pdb=" N ILE D 864 " --> pdb=" O GLY D 860 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS D 869 " --> pdb=" O CYS D 865 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR D 874 " --> pdb=" O PHE D 870 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN D 885 " --> pdb=" O PHE D 881 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 63 through 65 removed outlier: 7.014A pdb=" N ALA A 128 " --> pdb=" O GLY A 64 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 228 through 230 removed outlier: 3.651A pdb=" N VAL A 255 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 281 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL A 256 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 283 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 494 through 498 Processing sheet with id= D, first strand: chain 'A' and resid 508 through 510 Processing sheet with id= E, first strand: chain 'A' and resid 788 through 790 removed outlier: 3.730A pdb=" N ALA A 596 " --> pdb=" O ARG A 789 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 772 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 99 through 105 removed outlier: 3.680A pdb=" N ASN B 101 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 63 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA B 128 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LEU B 66 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 130 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 152 through 154 Processing sheet with id= H, first strand: chain 'B' and resid 228 through 230 removed outlier: 6.166A pdb=" N VAL B 253 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE B 199 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL B 255 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL B 201 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N HIS B 257 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 281 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL B 256 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 283 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 312 through 314 Processing sheet with id= J, first strand: chain 'B' and resid 367 through 369 removed outlier: 4.446A pdb=" N THR B 367 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 494 through 498 Processing sheet with id= L, first strand: chain 'B' and resid 788 through 790 Processing sheet with id= M, first strand: chain 'C' and resid 63 through 65 removed outlier: 7.014A pdb=" N ALA C 128 " --> pdb=" O GLY C 64 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 228 through 230 removed outlier: 3.651A pdb=" N VAL C 255 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL C 281 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL C 256 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE C 283 " --> pdb=" O VAL C 256 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 494 through 498 Processing sheet with id= P, first strand: chain 'C' and resid 508 through 510 Processing sheet with id= Q, first strand: chain 'C' and resid 788 through 790 removed outlier: 3.730A pdb=" N ALA C 596 " --> pdb=" O ARG C 789 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 772 " --> pdb=" O VAL C 593 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 99 through 105 removed outlier: 3.680A pdb=" N ASN D 101 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 63 " --> pdb=" O ASN D 101 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA D 128 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LEU D 66 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE D 130 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 152 through 154 Processing sheet with id= T, first strand: chain 'D' and resid 228 through 230 removed outlier: 6.167A pdb=" N VAL D 253 " --> pdb=" O ILE D 197 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE D 199 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL D 255 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL D 201 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N HIS D 257 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL D 281 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL D 256 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE D 283 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 312 through 314 Processing sheet with id= V, first strand: chain 'D' and resid 367 through 369 removed outlier: 4.445A pdb=" N THR D 367 " --> pdb=" O ASN D 391 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 494 through 498 Processing sheet with id= X, first strand: chain 'D' and resid 788 through 790 640 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.54 Time building geometry restraints manager: 10.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4113 1.30 - 1.43: 7190 1.43 - 1.57: 14405 1.57 - 1.70: 0 1.70 - 1.83: 188 Bond restraints: 25896 Sorted by residual: bond pdb=" CD1 GSH A1004 " pdb=" N2 GSH A1004 " ideal model delta sigma weight residual 1.336 1.451 -0.115 1.20e-02 6.94e+03 9.17e+01 bond pdb=" CD1 GSH C1004 " pdb=" N2 GSH C1004 " ideal model delta sigma weight residual 1.336 1.450 -0.114 1.20e-02 6.94e+03 9.10e+01 bond pdb=" CD1 GSH B1004 " pdb=" N2 GSH B1004 " ideal model delta sigma weight residual 1.336 1.446 -0.110 1.20e-02 6.94e+03 8.43e+01 bond pdb=" CD1 GSH D1004 " pdb=" N2 GSH D1004 " ideal model delta sigma weight residual 1.336 1.446 -0.110 1.20e-02 6.94e+03 8.39e+01 bond pdb=" C2 GSH A1004 " pdb=" N3 GSH A1004 " ideal model delta sigma weight residual 1.333 1.449 -0.116 1.30e-02 5.92e+03 7.97e+01 ... (remaining 25891 not shown) Histogram of bond angle deviations from ideal: 90.75 - 99.41: 17 99.41 - 108.06: 1434 108.06 - 116.72: 16202 116.72 - 125.37: 17033 125.37 - 134.03: 530 Bond angle restraints: 35216 Sorted by residual: angle pdb=" C ASN A 108 " pdb=" CA ASN A 108 " pdb=" CB ASN A 108 " ideal model delta sigma weight residual 111.22 90.75 20.47 1.23e+00 6.61e-01 2.77e+02 angle pdb=" N VAL A 449 " pdb=" CA VAL A 449 " pdb=" C VAL A 449 " ideal model delta sigma weight residual 113.71 107.58 6.13 9.50e-01 1.11e+00 4.16e+01 angle pdb=" N VAL C 449 " pdb=" CA VAL C 449 " pdb=" C VAL C 449 " ideal model delta sigma weight residual 113.71 107.69 6.02 9.50e-01 1.11e+00 4.01e+01 angle pdb=" N ASN B 108 " pdb=" CA ASN B 108 " pdb=" C ASN B 108 " ideal model delta sigma weight residual 111.81 103.81 8.00 1.54e+00 4.22e-01 2.70e+01 angle pdb=" CG1 GSH D1004 " pdb=" CD1 GSH D1004 " pdb=" N2 GSH D1004 " ideal model delta sigma weight residual 115.92 121.06 -5.14 1.00e+00 1.00e+00 2.64e+01 ... (remaining 35211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.69: 14807 20.69 - 41.39: 636 41.39 - 62.08: 97 62.08 - 82.78: 33 82.78 - 103.47: 55 Dihedral angle restraints: 15628 sinusoidal: 6430 harmonic: 9198 Sorted by residual: dihedral pdb=" C ASN A 108 " pdb=" N ASN A 108 " pdb=" CA ASN A 108 " pdb=" CB ASN A 108 " ideal model delta harmonic sigma weight residual -122.60 -98.38 -24.22 0 2.50e+00 1.60e-01 9.39e+01 dihedral pdb=" CA THR A 575 " pdb=" C THR A 575 " pdb=" N ASN A 576 " pdb=" CA ASN A 576 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA THR C 575 " pdb=" C THR C 575 " pdb=" N ASN C 576 " pdb=" CA ASN C 576 " ideal model delta harmonic sigma weight residual 180.00 151.32 28.68 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 15625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.988: 4019 0.988 - 1.976: 0 1.976 - 2.964: 0 2.964 - 3.952: 0 3.952 - 4.940: 3 Chirality restraints: 4022 Sorted by residual: chirality pdb=" C1 NAG D1002 " pdb=" ND2 ASN D 108 " pdb=" C2 NAG D1002 " pdb=" O5 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.40 2.54 -4.94 2.00e-01 2.50e+01 6.10e+02 chirality pdb=" C1 NAG B1002 " pdb=" ND2 ASN B 108 " pdb=" C2 NAG B1002 " pdb=" O5 NAG B1002 " both_signs ideal model delta sigma weight residual False -2.40 2.45 -4.85 2.00e-01 2.50e+01 5.87e+02 chirality pdb=" C1 NAG C1002 " pdb=" ND2 ASN C 108 " pdb=" C2 NAG C1002 " pdb=" O5 NAG C1002 " both_signs ideal model delta sigma weight residual False -2.40 2.06 -4.46 2.00e-01 2.50e+01 4.97e+02 ... (remaining 4019 not shown) Planarity restraints: 4504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1002 " 0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C1002 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C1002 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG C1002 " -0.537 2.00e-02 2.50e+03 pdb=" O7 NAG C1002 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1002 " -0.234 2.00e-02 2.50e+03 1.94e-01 4.72e+02 pdb=" C7 NAG B1002 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG B1002 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG B1002 " 0.321 2.00e-02 2.50e+03 pdb=" O7 NAG B1002 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1002 " 0.209 2.00e-02 2.50e+03 1.75e-01 3.81e+02 pdb=" C7 NAG D1002 " -0.053 2.00e-02 2.50e+03 pdb=" C8 NAG D1002 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG D1002 " -0.289 2.00e-02 2.50e+03 pdb=" O7 NAG D1002 " -0.015 2.00e-02 2.50e+03 ... (remaining 4501 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5409 2.77 - 3.30: 23431 3.30 - 3.83: 40755 3.83 - 4.37: 48483 4.37 - 4.90: 80613 Nonbonded interactions: 198691 Sorted by model distance: nonbonded pdb=" OH TYR B 534 " pdb=" OD2 ASP B 813 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR D 534 " pdb=" OD2 ASP D 813 " model vdw 2.232 2.440 nonbonded pdb=" OE2 GLU B 526 " pdb=" OH TYR B 540 " model vdw 2.244 2.440 nonbonded pdb=" OE2 GLU D 526 " pdb=" OH TYR D 540 " model vdw 2.244 2.440 nonbonded pdb=" OE2 GLU A 526 " pdb=" OH TYR A 540 " model vdw 2.253 2.440 ... (remaining 198686 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 56 through 842 or resid 853 through 886 or resid 1001 thro \ ugh 1004)) selection = chain 'B' selection = (chain 'C' and (resid 56 through 842 or resid 853 through 886 or resid 1001 thro \ ugh 1004)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 10.940 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 64.840 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.009 0.116 25896 Z= 0.600 Angle : 1.036 20.468 35216 Z= 0.576 Chirality : 0.145 4.940 4022 Planarity : 0.010 0.302 4488 Dihedral : 14.007 103.472 9688 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.67 % Allowed : 4.81 % Favored : 94.53 % Cbeta Deviations : 0.03 % 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: -5.49 (0.10), residues: 3136 helix: -4.20 (0.06), residues: 1386 sheet: -3.42 (0.20), residues: 420 loop : -2.85 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP C 193 HIS 0.008 0.002 HIS B 257 PHE 0.027 0.003 PHE C 612 TYR 0.037 0.003 TYR D 474 ARG 0.014 0.001 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 424 time to evaluate : 2.838 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 MET cc_start: 0.9110 (tpt) cc_final: 0.8884 (tpp) REVERT: A 422 ASN cc_start: 0.8220 (m-40) cc_final: 0.7457 (p0) REVERT: A 609 LEU cc_start: 0.8935 (mt) cc_final: 0.8607 (pt) REVERT: B 468 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7876 (ptp-110) REVERT: B 562 ASP cc_start: 0.7440 (t0) cc_final: 0.7175 (t0) REVERT: B 582 ASP cc_start: 0.8105 (m-30) cc_final: 0.7800 (p0) REVERT: B 616 MET cc_start: 0.5635 (mmt) cc_final: 0.5086 (tpp) REVERT: B 772 ASP cc_start: 0.8043 (m-30) cc_final: 0.7795 (m-30) REVERT: C 397 MET cc_start: 0.9107 (tpt) cc_final: 0.8857 (tpt) REVERT: C 403 MET cc_start: 0.7847 (tpp) cc_final: 0.7627 (tpp) REVERT: C 422 ASN cc_start: 0.8030 (m-40) cc_final: 0.7390 (p0) REVERT: C 616 MET cc_start: 0.7412 (tpp) cc_final: 0.7139 (tpt) REVERT: C 754 TYR cc_start: 0.8209 (m-10) cc_final: 0.7795 (m-10) REVERT: D 141 ILE cc_start: 0.9095 (mm) cc_final: 0.8542 (mm) REVERT: D 468 ARG cc_start: 0.8022 (ttp-110) cc_final: 0.7638 (ptp-110) REVERT: D 562 ASP cc_start: 0.7671 (t0) cc_final: 0.7451 (t0) REVERT: D 582 ASP cc_start: 0.8066 (m-30) cc_final: 0.7718 (p0) REVERT: D 616 MET cc_start: 0.4925 (mmt) cc_final: 0.4603 (mtm) REVERT: D 722 ILE cc_start: 0.8156 (mt) cc_final: 0.7881 (mp) REVERT: D 772 ASP cc_start: 0.8245 (m-30) cc_final: 0.7986 (m-30) outliers start: 18 outliers final: 4 residues processed: 436 average time/residue: 0.3939 time to fit residues: 261.5452 Evaluate side-chains 227 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 223 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain C residue 273 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 0.9990 chunk 237 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 246 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 285 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 175 GLN ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 HIS A 331 ASN A 365 ASN A 391 ASN A 466 ASN A 557 ASN A 689 ASN A 704 GLN A 725 GLN A 732 ASN A 736 ASN A 831 HIS B 89 ASN B 180 GLN B 182 HIS B 257 HIS B 307 GLN B 331 ASN B 365 ASN B 383 GLN B 391 ASN B 451 HIS B 466 ASN B 557 ASN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 HIS C 89 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 HIS C 365 ASN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 ASN C 689 ASN C 704 GLN C 725 GLN C 736 ASN C 831 HIS C 839 HIS D 89 ASN D 180 GLN D 182 HIS D 257 HIS D 307 GLN D 331 ASN D 365 ASN D 391 ASN D 466 ASN D 557 ASN ** D 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25896 Z= 0.184 Angle : 0.654 17.701 35216 Z= 0.332 Chirality : 0.054 1.185 4022 Planarity : 0.005 0.053 4488 Dihedral : 11.750 76.200 4018 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.29 % Allowed : 8.73 % Favored : 88.98 % 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: -3.94 (0.12), residues: 3136 helix: -2.78 (0.10), residues: 1368 sheet: -2.77 (0.22), residues: 410 loop : -2.17 (0.15), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 193 HIS 0.008 0.001 HIS A 839 PHE 0.021 0.002 PHE D 683 TYR 0.022 0.002 TYR D 504 ARG 0.005 0.001 ARG C 731 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 270 time to evaluate : 2.856 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 276 MET cc_start: 0.8319 (ttm) cc_final: 0.8092 (mtp) REVERT: A 305 LEU cc_start: 0.8052 (mp) cc_final: 0.7725 (mp) REVERT: A 804 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7427 (m-10) REVERT: B 286 ASP cc_start: 0.8177 (t0) cc_final: 0.7950 (t0) REVERT: B 307 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6723 (tm130) REVERT: B 468 ARG cc_start: 0.8174 (ttp-110) cc_final: 0.7881 (ptp-110) REVERT: B 562 ASP cc_start: 0.7416 (t0) cc_final: 0.7116 (t0) REVERT: B 616 MET cc_start: 0.5604 (mmt) cc_final: 0.5125 (tpp) REVERT: B 814 MET cc_start: 0.8203 (ttm) cc_final: 0.7971 (ttm) REVERT: B 858 PHE cc_start: 0.4397 (p90) cc_final: 0.4170 (p90) REVERT: C 403 MET cc_start: 0.7795 (tpp) cc_final: 0.7541 (tpp) REVERT: C 422 ASN cc_start: 0.7913 (m-40) cc_final: 0.7261 (p0) REVERT: C 553 ASP cc_start: 0.7561 (t0) cc_final: 0.7239 (t70) REVERT: C 609 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7891 (tp) REVERT: C 630 MET cc_start: 0.7635 (tpp) cc_final: 0.7390 (tmm) REVERT: C 683 PHE cc_start: 0.6846 (m-10) cc_final: 0.6578 (t80) REVERT: C 754 TYR cc_start: 0.8280 (m-10) cc_final: 0.7671 (m-80) REVERT: C 820 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7579 (tm-30) REVERT: D 307 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6705 (tm130) REVERT: D 468 ARG cc_start: 0.8015 (ttp-110) cc_final: 0.7666 (ptp-110) REVERT: D 562 ASP cc_start: 0.7642 (t0) cc_final: 0.7312 (t0) REVERT: D 582 ASP cc_start: 0.7922 (m-30) cc_final: 0.7711 (p0) REVERT: D 616 MET cc_start: 0.5109 (mmt) cc_final: 0.4323 (mpp) REVERT: D 722 ILE cc_start: 0.8158 (mt) cc_final: 0.7877 (mp) REVERT: D 725 GLN cc_start: 0.7406 (pt0) cc_final: 0.7057 (tt0) REVERT: D 772 ASP cc_start: 0.8007 (m-30) cc_final: 0.7799 (m-30) outliers start: 62 outliers final: 33 residues processed: 313 average time/residue: 0.3617 time to fit residues: 179.6431 Evaluate side-chains 246 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 209 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 713 ASP Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 732 ASN Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 713 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 237 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 285 optimal weight: 6.9990 chunk 308 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 725 GLN ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN B 554 ASN B 736 ASN C 175 GLN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN C 725 GLN ** C 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 451 HIS D 554 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25896 Z= 0.331 Angle : 0.653 9.579 35216 Z= 0.332 Chirality : 0.049 0.556 4022 Planarity : 0.005 0.050 4488 Dihedral : 9.988 66.921 4016 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.14 % Allowed : 10.39 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.13), residues: 3136 helix: -1.93 (0.12), residues: 1368 sheet: -2.54 (0.23), residues: 406 loop : -2.05 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 617 HIS 0.007 0.001 HIS C 297 PHE 0.026 0.002 PHE A 623 TYR 0.018 0.002 TYR B 341 ARG 0.006 0.001 ARG D 436 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 214 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LEU cc_start: 0.8031 (mp) cc_final: 0.7746 (mp) REVERT: A 630 MET cc_start: 0.7890 (mmt) cc_final: 0.7261 (tmm) REVERT: A 804 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7733 (m-10) REVERT: B 247 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8506 (m110) REVERT: B 307 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6647 (tm130) REVERT: B 468 ARG cc_start: 0.8067 (ttp-110) cc_final: 0.7794 (ptp-110) REVERT: B 562 ASP cc_start: 0.7512 (t0) cc_final: 0.7288 (t0) REVERT: B 616 MET cc_start: 0.5680 (mmt) cc_final: 0.5161 (tpp) REVERT: B 814 MET cc_start: 0.8311 (ttm) cc_final: 0.7989 (ttm) REVERT: C 422 ASN cc_start: 0.7979 (m-40) cc_final: 0.7284 (p0) REVERT: C 553 ASP cc_start: 0.7865 (t0) cc_final: 0.7546 (t70) REVERT: C 754 TYR cc_start: 0.8425 (m-10) cc_final: 0.7776 (m-80) REVERT: C 804 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7544 (m-10) REVERT: C 820 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7603 (tm-30) REVERT: D 247 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8551 (m110) REVERT: D 307 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6601 (tm130) REVERT: D 468 ARG cc_start: 0.7990 (ttp-110) cc_final: 0.7665 (ptp-110) REVERT: D 562 ASP cc_start: 0.7694 (t0) cc_final: 0.7473 (t0) REVERT: D 582 ASP cc_start: 0.8029 (m-30) cc_final: 0.7744 (p0) REVERT: D 616 MET cc_start: 0.5093 (mmt) cc_final: 0.4287 (mpp) REVERT: D 683 PHE cc_start: 0.8365 (t80) cc_final: 0.8085 (t80) REVERT: D 722 ILE cc_start: 0.8120 (mt) cc_final: 0.7825 (mp) outliers start: 85 outliers final: 58 residues processed: 281 average time/residue: 0.3601 time to fit residues: 162.2695 Evaluate side-chains 263 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 199 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 713 ASP Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 725 GLN Chi-restraints excluded: chain C residue 804 PHE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 713 ASP Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 1.9990 chunk 214 optimal weight: 50.0000 chunk 148 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 136 optimal weight: 30.0000 chunk 191 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 303 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 GLN ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 725 GLN ** C 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 736 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25896 Z= 0.299 Angle : 0.615 9.341 35216 Z= 0.313 Chirality : 0.047 0.401 4022 Planarity : 0.004 0.047 4488 Dihedral : 8.803 60.184 4016 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.37 % Allowed : 11.72 % Favored : 84.91 % 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: -2.72 (0.14), residues: 3136 helix: -1.36 (0.13), residues: 1368 sheet: -2.27 (0.24), residues: 406 loop : -1.99 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 193 HIS 0.003 0.001 HIS D 451 PHE 0.033 0.002 PHE C 623 TYR 0.014 0.001 TYR B 440 ARG 0.005 0.000 ARG A 501 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 205 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 630 MET cc_start: 0.7827 (mmt) cc_final: 0.7296 (tmm) REVERT: A 804 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7557 (m-10) REVERT: B 169 TYR cc_start: 0.8272 (m-10) cc_final: 0.8046 (m-10) REVERT: B 247 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8532 (m110) REVERT: B 307 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6834 (tm130) REVERT: B 468 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7795 (ptp-110) REVERT: B 616 MET cc_start: 0.5688 (mmt) cc_final: 0.4867 (tpp) REVERT: C 422 ASN cc_start: 0.8017 (m-40) cc_final: 0.7294 (p0) REVERT: C 553 ASP cc_start: 0.7928 (t0) cc_final: 0.7620 (t70) REVERT: C 754 TYR cc_start: 0.8436 (m-10) cc_final: 0.7885 (m-80) REVERT: C 804 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7621 (m-10) REVERT: C 820 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7585 (tm-30) REVERT: D 247 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8532 (m110) REVERT: D 307 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6755 (tm130) REVERT: D 468 ARG cc_start: 0.8027 (ttp-110) cc_final: 0.7678 (ptp-110) REVERT: D 582 ASP cc_start: 0.8026 (m-30) cc_final: 0.7661 (p0) REVERT: D 616 MET cc_start: 0.5120 (mmt) cc_final: 0.4313 (mpp) REVERT: D 722 ILE cc_start: 0.8175 (mt) cc_final: 0.7870 (mp) REVERT: D 772 ASP cc_start: 0.8074 (m-30) cc_final: 0.7869 (m-30) outliers start: 91 outliers final: 61 residues processed: 275 average time/residue: 0.3683 time to fit residues: 166.3052 Evaluate side-chains 263 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 196 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 713 ASP Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 725 GLN Chi-restraints excluded: chain C residue 804 PHE Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 570 ASP Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 154 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 GLN ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN ** C 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 704 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25896 Z= 0.195 Angle : 0.565 11.210 35216 Z= 0.285 Chirality : 0.045 0.374 4022 Planarity : 0.004 0.044 4488 Dihedral : 8.057 58.235 4016 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.11 % Allowed : 12.61 % Favored : 84.28 % 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: -2.29 (0.14), residues: 3136 helix: -0.96 (0.13), residues: 1358 sheet: -1.84 (0.25), residues: 392 loop : -1.89 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 193 HIS 0.002 0.001 HIS C 139 PHE 0.027 0.001 PHE C 683 TYR 0.017 0.001 TYR B 440 ARG 0.005 0.000 ARG A 501 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 210 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 630 MET cc_start: 0.7823 (mmt) cc_final: 0.7319 (tmm) REVERT: A 725 GLN cc_start: 0.6873 (OUTLIER) cc_final: 0.6072 (mt0) REVERT: A 804 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7479 (m-10) REVERT: B 153 LEU cc_start: 0.8920 (mp) cc_final: 0.8701 (mp) REVERT: B 169 TYR cc_start: 0.8216 (m-10) cc_final: 0.7990 (m-10) REVERT: B 468 ARG cc_start: 0.8028 (ttp-110) cc_final: 0.7722 (ptp-110) REVERT: B 616 MET cc_start: 0.5730 (mmt) cc_final: 0.4922 (tpp) REVERT: B 814 MET cc_start: 0.8032 (ttm) cc_final: 0.7761 (ttm) REVERT: C 422 ASN cc_start: 0.8027 (m-40) cc_final: 0.7305 (p0) REVERT: C 553 ASP cc_start: 0.7872 (t0) cc_final: 0.7628 (t70) REVERT: C 754 TYR cc_start: 0.8384 (m-10) cc_final: 0.7978 (m-80) REVERT: C 804 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7594 (m-10) REVERT: C 820 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7547 (tm-30) REVERT: D 247 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8569 (m110) REVERT: D 249 MET cc_start: 0.8633 (mmm) cc_final: 0.8414 (mtp) REVERT: D 468 ARG cc_start: 0.8039 (ttp-110) cc_final: 0.7822 (ptp-110) REVERT: D 582 ASP cc_start: 0.7957 (m-30) cc_final: 0.7619 (p0) REVERT: D 616 MET cc_start: 0.5097 (mmt) cc_final: 0.4750 (mpp) REVERT: D 722 ILE cc_start: 0.8136 (mt) cc_final: 0.7831 (mp) outliers start: 84 outliers final: 58 residues processed: 276 average time/residue: 0.3474 time to fit residues: 155.0775 Evaluate side-chains 255 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 193 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 713 ASP Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 804 PHE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 570 ASP Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 74 optimal weight: 0.0470 chunk 303 optimal weight: 0.8980 chunk 252 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN B 383 GLN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25896 Z= 0.182 Angle : 0.550 10.733 35216 Z= 0.277 Chirality : 0.044 0.368 4022 Planarity : 0.004 0.045 4488 Dihedral : 7.461 58.451 4016 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.11 % Allowed : 13.09 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.15), residues: 3136 helix: -0.68 (0.14), residues: 1354 sheet: -1.68 (0.26), residues: 392 loop : -1.87 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 681 HIS 0.002 0.000 HIS C 139 PHE 0.022 0.001 PHE A 683 TYR 0.010 0.001 TYR A 425 ARG 0.006 0.000 ARG C 501 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 210 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 630 MET cc_start: 0.7813 (mmt) cc_final: 0.7318 (tmm) REVERT: A 804 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7437 (m-10) REVERT: B 153 LEU cc_start: 0.8932 (mp) cc_final: 0.8725 (mp) REVERT: B 169 TYR cc_start: 0.8251 (m-10) cc_final: 0.7982 (m-10) REVERT: B 307 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6898 (tm130) REVERT: B 433 THR cc_start: 0.7615 (m) cc_final: 0.7243 (t) REVERT: B 616 MET cc_start: 0.5656 (mmt) cc_final: 0.4939 (tpp) REVERT: B 814 MET cc_start: 0.7978 (ttm) cc_final: 0.7647 (ttm) REVERT: C 422 ASN cc_start: 0.8026 (m-40) cc_final: 0.7312 (p0) REVERT: C 553 ASP cc_start: 0.7847 (t70) cc_final: 0.7641 (t70) REVERT: C 754 TYR cc_start: 0.8395 (m-10) cc_final: 0.7918 (m-80) REVERT: C 804 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7618 (m-10) REVERT: C 820 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7517 (tm-30) REVERT: D 307 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6903 (tm130) REVERT: D 433 THR cc_start: 0.7657 (m) cc_final: 0.7321 (t) REVERT: D 582 ASP cc_start: 0.7924 (m-30) cc_final: 0.7577 (p0) REVERT: D 616 MET cc_start: 0.5128 (mmt) cc_final: 0.4562 (mpp) REVERT: D 722 ILE cc_start: 0.8124 (mt) cc_final: 0.7792 (mp) outliers start: 84 outliers final: 62 residues processed: 274 average time/residue: 0.3525 time to fit residues: 157.1698 Evaluate side-chains 258 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 192 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 713 ASP Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 725 GLN Chi-restraints excluded: chain C residue 804 PHE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 570 ASP Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 221 optimal weight: 7.9990 chunk 171 optimal weight: 0.6980 chunk 255 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 302 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 chunk 184 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 307 GLN D 405 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25896 Z= 0.206 Angle : 0.549 10.678 35216 Z= 0.277 Chirality : 0.044 0.363 4022 Planarity : 0.004 0.045 4488 Dihedral : 7.128 58.829 4016 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.18 % Allowed : 13.42 % Favored : 83.39 % 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: -1.90 (0.15), residues: 3136 helix: -0.48 (0.14), residues: 1364 sheet: -1.59 (0.27), residues: 392 loop : -1.89 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 681 HIS 0.004 0.001 HIS D 314 PHE 0.030 0.001 PHE C 683 TYR 0.009 0.001 TYR D 226 ARG 0.007 0.000 ARG B 501 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 193 time to evaluate : 2.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 630 MET cc_start: 0.7814 (mmt) cc_final: 0.7384 (tmm) REVERT: A 804 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7541 (m-10) REVERT: B 153 LEU cc_start: 0.8913 (mp) cc_final: 0.8703 (mp) REVERT: B 169 TYR cc_start: 0.8268 (m-10) cc_final: 0.7979 (m-10) REVERT: B 307 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6686 (tm130) REVERT: B 433 THR cc_start: 0.7767 (m) cc_final: 0.7537 (t) REVERT: B 616 MET cc_start: 0.5686 (mmt) cc_final: 0.4948 (tpp) REVERT: C 422 ASN cc_start: 0.7998 (m-40) cc_final: 0.7290 (p0) REVERT: C 553 ASP cc_start: 0.7868 (t70) cc_final: 0.7661 (t70) REVERT: C 754 TYR cc_start: 0.8428 (m-10) cc_final: 0.8072 (m-10) REVERT: C 804 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7583 (m-10) REVERT: C 820 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7511 (tm-30) REVERT: D 307 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6650 (tm130) REVERT: D 433 THR cc_start: 0.7682 (m) cc_final: 0.7196 (t) REVERT: D 582 ASP cc_start: 0.7938 (m-30) cc_final: 0.7533 (p0) REVERT: D 616 MET cc_start: 0.5191 (mmt) cc_final: 0.4594 (mpp) outliers start: 86 outliers final: 68 residues processed: 261 average time/residue: 0.3281 time to fit residues: 141.9652 Evaluate side-chains 263 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 191 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 713 ASP Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 725 GLN Chi-restraints excluded: chain C residue 804 PHE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 570 ASP Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 180 optimal weight: 0.3980 chunk 91 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 58 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN B 725 GLN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25896 Z= 0.165 Angle : 0.528 10.582 35216 Z= 0.266 Chirality : 0.044 0.370 4022 Planarity : 0.004 0.046 4488 Dihedral : 6.802 58.836 4016 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.70 % Allowed : 13.98 % Favored : 83.32 % 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: -1.70 (0.15), residues: 3136 helix: -0.25 (0.14), residues: 1348 sheet: -1.53 (0.27), residues: 392 loop : -1.84 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 681 HIS 0.003 0.001 HIS D 314 PHE 0.023 0.001 PHE B 683 TYR 0.009 0.001 TYR A 425 ARG 0.006 0.000 ARG B 501 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 204 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8421 (mmmm) REVERT: A 630 MET cc_start: 0.7852 (mmt) cc_final: 0.7430 (tmm) REVERT: A 804 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7435 (m-10) REVERT: B 169 TYR cc_start: 0.8245 (m-80) cc_final: 0.7966 (m-10) REVERT: B 616 MET cc_start: 0.5724 (mmt) cc_final: 0.5014 (tpp) REVERT: B 814 MET cc_start: 0.7973 (ttm) cc_final: 0.7596 (ttm) REVERT: C 422 ASN cc_start: 0.7993 (m-40) cc_final: 0.7283 (p0) REVERT: C 754 TYR cc_start: 0.8429 (m-10) cc_final: 0.7913 (m-80) REVERT: C 804 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7622 (m-10) REVERT: C 820 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7482 (tm-30) REVERT: D 307 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6596 (tm130) REVERT: D 433 THR cc_start: 0.7680 (m) cc_final: 0.7466 (t) REVERT: D 582 ASP cc_start: 0.7895 (m-30) cc_final: 0.7537 (p0) REVERT: D 616 MET cc_start: 0.5259 (mmt) cc_final: 0.4649 (mpp) REVERT: D 873 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6440 (mp) outliers start: 73 outliers final: 58 residues processed: 259 average time/residue: 0.3549 time to fit residues: 151.7481 Evaluate side-chains 249 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 186 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 713 ASP Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 804 PHE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 570 ASP Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 873 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 5.9990 chunk 289 optimal weight: 4.9990 chunk 264 optimal weight: 6.9990 chunk 282 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 254 optimal weight: 3.9990 chunk 266 optimal weight: 9.9990 chunk 281 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25896 Z= 0.227 Angle : 0.552 10.411 35216 Z= 0.277 Chirality : 0.045 0.363 4022 Planarity : 0.004 0.046 4488 Dihedral : 6.673 58.518 4016 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.70 % Allowed : 14.31 % Favored : 82.99 % 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: -1.60 (0.15), residues: 3136 helix: -0.10 (0.14), residues: 1340 sheet: -1.49 (0.27), residues: 388 loop : -1.84 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 681 HIS 0.003 0.001 HIS D 314 PHE 0.031 0.001 PHE C 683 TYR 0.020 0.001 TYR B 504 ARG 0.006 0.000 ARG A 501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 198 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 630 MET cc_start: 0.7844 (mmt) cc_final: 0.7419 (tmm) REVERT: A 804 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7521 (m-10) REVERT: B 169 TYR cc_start: 0.8295 (m-80) cc_final: 0.7988 (m-10) REVERT: B 616 MET cc_start: 0.5724 (mmt) cc_final: 0.5006 (tpp) REVERT: C 422 ASN cc_start: 0.7992 (m-40) cc_final: 0.7275 (p0) REVERT: C 754 TYR cc_start: 0.8404 (m-10) cc_final: 0.7934 (m-80) REVERT: C 760 ARG cc_start: 0.7759 (mtm180) cc_final: 0.7343 (mtm110) REVERT: C 804 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7566 (m-10) REVERT: C 820 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7496 (tm-30) REVERT: D 433 THR cc_start: 0.7701 (m) cc_final: 0.7457 (t) REVERT: D 582 ASP cc_start: 0.7905 (m-30) cc_final: 0.7507 (p0) REVERT: D 616 MET cc_start: 0.5290 (mmt) cc_final: 0.4702 (mpp) REVERT: D 873 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6378 (mp) outliers start: 73 outliers final: 62 residues processed: 258 average time/residue: 0.3631 time to fit residues: 156.8222 Evaluate side-chains 256 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 191 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 608 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 713 ASP Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 725 GLN Chi-restraints excluded: chain C residue 804 PHE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 570 ASP Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 0.0970 chunk 298 optimal weight: 10.0000 chunk 182 optimal weight: 0.5980 chunk 141 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 312 optimal weight: 0.0010 chunk 287 optimal weight: 0.5980 chunk 249 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 192 optimal weight: 0.0010 chunk 152 optimal weight: 2.9990 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 383 GLN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25896 Z= 0.130 Angle : 0.520 10.601 35216 Z= 0.261 Chirality : 0.043 0.398 4022 Planarity : 0.004 0.046 4488 Dihedral : 6.270 59.043 4016 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.07 % Allowed : 15.20 % Favored : 82.73 % 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: -1.34 (0.15), residues: 3136 helix: 0.14 (0.14), residues: 1340 sheet: -1.47 (0.28), residues: 344 loop : -1.71 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 681 HIS 0.003 0.001 HIS C 139 PHE 0.026 0.001 PHE B 683 TYR 0.018 0.001 TYR B 504 ARG 0.006 0.000 ARG B 501 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 204 time to evaluate : 2.801 Fit side-chains REVERT: A 610 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8384 (mmmm) REVERT: A 630 MET cc_start: 0.7901 (mmt) cc_final: 0.7471 (tmm) REVERT: A 804 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7390 (m-10) REVERT: B 169 TYR cc_start: 0.8169 (m-80) cc_final: 0.7917 (m-10) REVERT: B 242 LEU cc_start: 0.8145 (tt) cc_final: 0.6930 (tp) REVERT: B 616 MET cc_start: 0.5760 (mmt) cc_final: 0.5083 (tpp) REVERT: C 422 ASN cc_start: 0.7927 (m-40) cc_final: 0.7207 (p0) REVERT: C 608 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6989 (t80) REVERT: C 760 ARG cc_start: 0.7699 (mtm180) cc_final: 0.7292 (mtm110) REVERT: C 820 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7468 (tm-30) REVERT: D 433 THR cc_start: 0.7856 (m) cc_final: 0.7539 (t) REVERT: D 509 SER cc_start: 0.8515 (p) cc_final: 0.7854 (m) REVERT: D 523 ASP cc_start: 0.8165 (m-30) cc_final: 0.7507 (m-30) REVERT: D 582 ASP cc_start: 0.7789 (m-30) cc_final: 0.7499 (p0) REVERT: D 616 MET cc_start: 0.5197 (mmt) cc_final: 0.4754 (mpp) REVERT: D 873 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6366 (mp) outliers start: 56 outliers final: 44 residues processed: 248 average time/residue: 0.3396 time to fit residues: 139.2904 Evaluate side-chains 241 residues out of total 2756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 193 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 719 ASN Chi-restraints excluded: chain C residue 814 MET Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 570 ASP Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.0020 chunk 265 optimal weight: 4.9990 chunk 76 optimal weight: 30.0000 chunk 229 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 249 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 429 ASN ** 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 = 0.4101 r_free = 0.4101 target = 0.130777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.098666 restraints weight = 49411.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.099023 restraints weight = 34301.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.099624 restraints weight = 34894.741| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25896 Z= 0.254 Angle : 0.561 10.074 35216 Z= 0.282 Chirality : 0.045 0.377 4022 Planarity : 0.004 0.045 4488 Dihedral : 6.347 59.495 4014 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.03 % Allowed : 15.46 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.15), residues: 3136 helix: 0.14 (0.14), residues: 1348 sheet: -1.39 (0.27), residues: 388 loop : -1.79 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 681 HIS 0.004 0.001 HIS D 314 PHE 0.034 0.001 PHE C 683 TYR 0.021 0.001 TYR B 504 ARG 0.007 0.000 ARG A 501 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4519.16 seconds wall clock time: 84 minutes 3.53 seconds (5043.53 seconds total)