Starting phenix.real_space_refine on Sun Mar 17 23:44:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzf_27796/03_2024/8dzf_27796_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzf_27796/03_2024/8dzf_27796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzf_27796/03_2024/8dzf_27796.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzf_27796/03_2024/8dzf_27796.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzf_27796/03_2024/8dzf_27796_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzf_27796/03_2024/8dzf_27796_neut_updated.pdb" } resolution = 3.69 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= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 18 5.49 5 S 84 5.16 5 C 12102 2.51 5 N 3390 2.21 5 O 3708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19308 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "F" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2171 SG CYS A 403 90.750 129.513 31.549 1.00158.25 S ATOM 2191 SG CYS A 406 94.003 131.502 31.911 1.00169.76 S ATOM 2475 SG CYS A 445 90.833 132.641 33.583 1.00185.26 S ATOM 2481 SG CYS A 446 92.703 129.447 34.824 1.00172.25 S ATOM 5357 SG CYS B 403 31.648 115.396 31.571 1.00155.58 S ATOM 5377 SG CYS B 406 31.553 119.207 31.933 1.00166.64 S ATOM 5661 SG CYS B 445 28.980 117.033 33.604 1.00183.69 S ATOM 5667 SG CYS B 446 32.682 117.054 34.845 1.00170.63 S ATOM 8543 SG CYS C 403 14.335 57.164 31.565 1.00161.18 S ATOM 8563 SG CYS C 406 10.988 58.989 31.928 1.00168.83 S ATOM 8847 SG CYS C 445 11.584 55.675 33.600 1.00184.61 S ATOM 8853 SG CYS C 446 13.418 58.890 34.840 1.00171.43 S ATOM 11729 SG CYS D 403 56.096 13.048 31.543 1.00158.48 S ATOM 11749 SG CYS D 406 52.841 11.063 31.907 1.00169.82 S ATOM 12033 SG CYS D 445 56.010 9.920 33.577 1.00186.92 S ATOM 12039 SG CYS D 446 54.144 13.117 34.819 1.00174.41 S ATOM 14915 SG CYS E 403 115.189 27.155 31.577 1.00155.20 S ATOM 14935 SG CYS E 406 115.280 23.343 31.940 1.00166.22 S ATOM 15219 SG CYS E 445 117.852 25.516 33.615 1.00184.65 S ATOM 15225 SG CYS E 446 114.148 25.498 34.851 1.00171.57 S ATOM 18101 SG CYS F 403 132.523 85.406 31.564 1.00161.64 S ATOM 18121 SG CYS F 406 135.871 83.583 31.932 1.00168.54 S ATOM 18405 SG CYS F 445 135.273 86.900 33.598 1.00184.18 S ATOM 18411 SG CYS F 446 133.439 83.685 34.843 1.00170.33 S Time building chain proxies: 10.37, per 1000 atoms: 0.54 Number of scatterers: 19308 At special positions: 0 Unit cell: (147.96, 143.64, 82.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 84 16.00 P 18 15.00 O 3708 8.00 N 3390 7.00 C 12102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.49 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 403 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 406 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 445 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 446 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 406 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 403 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 445 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 446 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 406 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 403 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 445 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 446 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 403 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 406 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 445 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 446 " pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 406 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 403 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 445 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 446 " pdb=" ZN F 601 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 406 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 403 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 445 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 446 " Number of angles added : 36 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4668 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 18 sheets defined 36.0% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 153 through 165 Processing helix chain 'A' and resid 239 through 249 Processing helix chain 'A' and resid 266 through 280 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 370 through 377 Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 422 through 427 removed outlier: 4.035A pdb=" N LYS A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 422 through 427' Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 478 through 484 Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'A' and resid 506 through 512 Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 521 through 533 Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 153 through 165 Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'B' and resid 266 through 280 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 370 through 377 Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'B' and resid 422 through 427 removed outlier: 4.035A pdb=" N LYS B 426 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE B 427 " --> pdb=" O THR B 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 422 through 427' Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 478 through 484 Processing helix chain 'B' and resid 491 through 501 Processing helix chain 'B' and resid 506 through 512 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 521 through 533 Processing helix chain 'C' and resid 108 through 119 Processing helix chain 'C' and resid 153 through 165 Processing helix chain 'C' and resid 239 through 249 Processing helix chain 'C' and resid 266 through 280 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 370 through 377 Processing helix chain 'C' and resid 410 through 415 Processing helix chain 'C' and resid 422 through 427 removed outlier: 4.034A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 422 through 427' Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 478 through 484 Processing helix chain 'C' and resid 491 through 501 Processing helix chain 'C' and resid 506 through 512 Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 521 through 533 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 153 through 165 Processing helix chain 'D' and resid 239 through 249 Processing helix chain 'D' and resid 266 through 280 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 410 through 415 Processing helix chain 'D' and resid 422 through 427 removed outlier: 4.034A pdb=" N LYS D 426 " --> pdb=" O ASP D 422 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE D 427 " --> pdb=" O THR D 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 422 through 427' Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 478 through 484 Processing helix chain 'D' and resid 491 through 501 Processing helix chain 'D' and resid 506 through 512 Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 521 through 533 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 153 through 165 Processing helix chain 'E' and resid 239 through 249 Processing helix chain 'E' and resid 266 through 280 Processing helix chain 'E' and resid 312 through 326 Processing helix chain 'E' and resid 342 through 354 Processing helix chain 'E' and resid 370 through 377 Processing helix chain 'E' and resid 410 through 415 Processing helix chain 'E' and resid 422 through 427 removed outlier: 4.034A pdb=" N LYS E 426 " --> pdb=" O ASP E 422 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE E 427 " --> pdb=" O THR E 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 422 through 427' Processing helix chain 'E' and resid 464 through 471 Processing helix chain 'E' and resid 478 through 484 Processing helix chain 'E' and resid 491 through 501 Processing helix chain 'E' and resid 506 through 512 Processing helix chain 'E' and resid 516 through 518 No H-bonds generated for 'chain 'E' and resid 516 through 518' Processing helix chain 'E' and resid 521 through 533 Processing helix chain 'F' and resid 108 through 119 Processing helix chain 'F' and resid 153 through 165 Processing helix chain 'F' and resid 239 through 249 Processing helix chain 'F' and resid 266 through 280 Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'F' and resid 342 through 354 Processing helix chain 'F' and resid 370 through 377 Processing helix chain 'F' and resid 410 through 415 Processing helix chain 'F' and resid 422 through 427 removed outlier: 4.034A pdb=" N LYS F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE F 427 " --> pdb=" O THR F 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 422 through 427' Processing helix chain 'F' and resid 464 through 471 Processing helix chain 'F' and resid 478 through 484 Processing helix chain 'F' and resid 491 through 501 Processing helix chain 'F' and resid 506 through 512 Processing helix chain 'F' and resid 516 through 518 No H-bonds generated for 'chain 'F' and resid 516 through 518' Processing helix chain 'F' and resid 521 through 533 Processing sheet with id= A, first strand: chain 'A' and resid 180 through 184 removed outlier: 3.933A pdb=" N ARG A 212 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 149 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 139 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU A 147 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LYS A 141 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N MET A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 357 through 362 removed outlier: 6.401A pdb=" N GLY A 254 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR A 360 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN A 256 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU A 362 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE A 258 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE A 257 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU A 393 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER A 259 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A 395 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 288 through 290 removed outlier: 6.112A pdb=" N ALA A 302 " --> pdb=" O SER A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 180 through 184 removed outlier: 3.933A pdb=" N ARG B 212 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 149 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 139 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU B 147 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS B 141 " --> pdb=" O MET B 145 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N MET B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.401A pdb=" N GLY B 254 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR B 360 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN B 256 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU B 362 " --> pdb=" O ASN B 256 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE B 258 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE B 257 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU B 393 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N SER B 259 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA B 395 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 288 through 290 removed outlier: 6.111A pdb=" N ALA B 302 " --> pdb=" O SER B 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 180 through 184 removed outlier: 3.933A pdb=" N ARG C 212 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG C 149 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 139 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU C 147 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LYS C 141 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N MET C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.401A pdb=" N GLY C 254 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR C 360 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASN C 256 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU C 362 " --> pdb=" O ASN C 256 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE C 258 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE C 257 " --> pdb=" O THR C 391 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU C 393 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER C 259 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA C 395 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 288 through 290 removed outlier: 6.111A pdb=" N ALA C 302 " --> pdb=" O SER C 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 180 through 184 removed outlier: 3.933A pdb=" N ARG D 212 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 149 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE D 139 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU D 147 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS D 141 " --> pdb=" O MET D 145 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N MET D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.401A pdb=" N GLY D 254 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR D 360 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN D 256 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU D 362 " --> pdb=" O ASN D 256 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE D 258 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE D 257 " --> pdb=" O THR D 391 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU D 393 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N SER D 259 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA D 395 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 288 through 290 removed outlier: 6.112A pdb=" N ALA D 302 " --> pdb=" O SER D 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 180 through 184 removed outlier: 3.933A pdb=" N ARG E 212 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG E 149 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE E 139 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU E 147 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LYS E 141 " --> pdb=" O MET E 145 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N MET E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 357 through 362 removed outlier: 6.401A pdb=" N GLY E 254 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR E 360 " --> pdb=" O GLY E 254 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASN E 256 " --> pdb=" O THR E 360 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU E 362 " --> pdb=" O ASN E 256 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE E 258 " --> pdb=" O LEU E 362 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE E 257 " --> pdb=" O THR E 391 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU E 393 " --> pdb=" O ILE E 257 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N SER E 259 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA E 395 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 288 through 290 removed outlier: 6.111A pdb=" N ALA E 302 " --> pdb=" O SER E 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'F' and resid 180 through 184 removed outlier: 3.934A pdb=" N ARG F 212 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG F 149 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE F 139 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU F 147 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS F 141 " --> pdb=" O MET F 145 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N MET F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 357 through 362 removed outlier: 6.402A pdb=" N GLY F 254 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR F 360 " --> pdb=" O GLY F 254 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASN F 256 " --> pdb=" O THR F 360 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU F 362 " --> pdb=" O ASN F 256 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE F 258 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE F 257 " --> pdb=" O THR F 391 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU F 393 " --> pdb=" O ILE F 257 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER F 259 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA F 395 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 288 through 290 removed outlier: 6.112A pdb=" N ALA F 302 " --> pdb=" O SER F 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= R 720 hydrogen bonds defined for protein. 2088 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: 6.01 Time building geometry restraints manager: 8.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6492 1.34 - 1.46: 3765 1.46 - 1.58: 9201 1.58 - 1.69: 24 1.69 - 1.81: 144 Bond restraints: 19626 Sorted by residual: bond pdb=" C1' ANP C 602 " pdb=" C2' ANP C 602 " ideal model delta sigma weight residual 1.542 1.305 0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C1' ANP D 602 " pdb=" C2' ANP D 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP F 602 " pdb=" C2' ANP F 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP B 602 " pdb=" C2' ANP B 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP E 602 " pdb=" C2' ANP E 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 ... (remaining 19621 not shown) Histogram of bond angle deviations from ideal: 100.67 - 107.33: 636 107.33 - 113.99: 11385 113.99 - 120.66: 7733 120.66 - 127.32: 6628 127.32 - 133.98: 222 Bond angle restraints: 26604 Sorted by residual: angle pdb=" C TYR C 131 " pdb=" N ASP C 132 " pdb=" CA ASP C 132 " ideal model delta sigma weight residual 121.54 129.90 -8.36 1.91e+00 2.74e-01 1.92e+01 angle pdb=" C TYR A 131 " pdb=" N ASP A 132 " pdb=" CA ASP A 132 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C TYR F 131 " pdb=" N ASP F 132 " pdb=" CA ASP F 132 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C TYR D 131 " pdb=" N ASP D 132 " pdb=" CA ASP D 132 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C TYR B 131 " pdb=" N ASP B 132 " pdb=" CA ASP B 132 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 ... (remaining 26599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.37: 11712 32.37 - 64.73: 294 64.73 - 97.10: 36 97.10 - 129.46: 0 129.46 - 161.83: 6 Dihedral angle restraints: 12048 sinusoidal: 4848 harmonic: 7200 Sorted by residual: dihedral pdb=" O1A ANP E 602 " pdb=" O3A ANP E 602 " pdb=" PA ANP E 602 " pdb=" PB ANP E 602 " ideal model delta sinusoidal sigma weight residual 83.11 -78.72 161.83 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" O1A ANP B 602 " pdb=" O3A ANP B 602 " pdb=" PA ANP B 602 " pdb=" PB ANP B 602 " ideal model delta sinusoidal sigma weight residual 83.11 -78.70 161.81 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" O1A ANP C 602 " pdb=" O3A ANP C 602 " pdb=" PA ANP C 602 " pdb=" PB ANP C 602 " ideal model delta sinusoidal sigma weight residual 83.11 -78.67 161.78 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 12045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2681 0.067 - 0.134: 372 0.134 - 0.201: 1 0.201 - 0.268: 6 0.268 - 0.336: 6 Chirality restraints: 3066 Sorted by residual: chirality pdb=" C2' ANP C 602 " pdb=" C1' ANP C 602 " pdb=" C3' ANP C 602 " pdb=" O2' ANP C 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.39 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C2' ANP D 602 " pdb=" C1' ANP D 602 " pdb=" C3' ANP D 602 " pdb=" O2' ANP D 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.39 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C2' ANP B 602 " pdb=" C1' ANP B 602 " pdb=" C3' ANP B 602 " pdb=" O2' ANP B 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.39 -0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 3063 not shown) Planarity restraints: 3402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 132 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.41e+00 pdb=" C ASP D 132 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP D 132 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA D 133 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 132 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C ASP B 132 " 0.020 2.00e-02 2.50e+03 pdb=" O ASP B 132 " -0.008 2.00e-02 2.50e+03 pdb=" N ALA B 133 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 132 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.39e+00 pdb=" C ASP E 132 " -0.020 2.00e-02 2.50e+03 pdb=" O ASP E 132 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA E 133 " 0.007 2.00e-02 2.50e+03 ... (remaining 3399 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4915 2.81 - 3.33: 18496 3.33 - 3.85: 31076 3.85 - 4.38: 33736 4.38 - 4.90: 60265 Nonbonded interactions: 148488 Sorted by model distance: nonbonded pdb=" O THR B 350 " pdb=" OG1 THR B 354 " model vdw 2.285 2.440 nonbonded pdb=" O THR D 350 " pdb=" OG1 THR D 354 " model vdw 2.286 2.440 nonbonded pdb=" O THR E 350 " pdb=" OG1 THR E 354 " model vdw 2.286 2.440 nonbonded pdb=" O THR C 350 " pdb=" OG1 THR C 354 " model vdw 2.286 2.440 nonbonded pdb=" O THR A 350 " pdb=" OG1 THR A 354 " model vdw 2.286 2.440 ... (remaining 148483 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.790 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 55.300 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.237 19626 Z= 0.506 Angle : 0.809 11.916 26604 Z= 0.380 Chirality : 0.046 0.336 3066 Planarity : 0.003 0.024 3402 Dihedral : 13.483 161.831 7380 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.17 % Favored : 93.58 % Rotamer: Outliers : 2.98 % Allowed : 8.04 % Favored : 88.99 % 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: -0.18 (0.17), residues: 2430 helix: 0.67 (0.16), residues: 1002 sheet: 2.18 (0.27), residues: 408 loop : -1.99 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 359 HIS 0.002 0.000 HIS B 356 PHE 0.005 0.001 PHE D 204 TYR 0.006 0.001 TYR F 278 ARG 0.002 0.000 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 386 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.9309 (tpp) cc_final: 0.8895 (tpp) REVERT: A 121 MET cc_start: 0.8906 (ttt) cc_final: 0.8684 (ttm) REVERT: A 132 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8830 (p0) REVERT: A 180 GLN cc_start: 0.7385 (mp10) cc_final: 0.6645 (mp10) REVERT: A 314 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8282 (tm-30) REVERT: A 479 GLN cc_start: 0.7889 (tt0) cc_final: 0.7537 (tt0) REVERT: A 483 LEU cc_start: 0.9266 (tp) cc_final: 0.9023 (mt) REVERT: B 113 MET cc_start: 0.9237 (tpp) cc_final: 0.8742 (tpp) REVERT: B 132 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8748 (p0) REVERT: B 203 GLN cc_start: 0.6351 (tm-30) cc_final: 0.5880 (tm-30) REVERT: B 314 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8330 (tm-30) REVERT: B 503 GLU cc_start: 0.8428 (tp30) cc_final: 0.8223 (tp30) REVERT: C 113 MET cc_start: 0.9318 (tpp) cc_final: 0.8818 (tpp) REVERT: C 132 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8723 (p0) REVERT: C 203 GLN cc_start: 0.6377 (tm-30) cc_final: 0.5479 (tm-30) REVERT: C 398 LEU cc_start: 0.9151 (mt) cc_final: 0.8915 (mt) REVERT: C 503 GLU cc_start: 0.8461 (tp30) cc_final: 0.8139 (tp30) REVERT: C 531 ASP cc_start: 0.7909 (t0) cc_final: 0.7595 (t0) REVERT: D 113 MET cc_start: 0.9316 (tpp) cc_final: 0.8896 (tpp) REVERT: D 121 MET cc_start: 0.8883 (ttt) cc_final: 0.8668 (ttm) REVERT: D 132 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8805 (p0) REVERT: D 180 GLN cc_start: 0.7455 (mp10) cc_final: 0.6741 (mp10) REVERT: D 314 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8287 (tm-30) REVERT: D 479 GLN cc_start: 0.7874 (tt0) cc_final: 0.7492 (tt0) REVERT: D 483 LEU cc_start: 0.9253 (tp) cc_final: 0.9012 (mt) REVERT: E 113 MET cc_start: 0.9282 (tpp) cc_final: 0.8772 (tpp) REVERT: E 116 PHE cc_start: 0.8956 (t80) cc_final: 0.8753 (t80) REVERT: E 132 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8792 (p0) REVERT: E 139 ILE cc_start: 0.8953 (pt) cc_final: 0.8710 (pt) REVERT: E 314 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8289 (tm-30) REVERT: E 479 GLN cc_start: 0.7896 (tt0) cc_final: 0.7596 (tt0) REVERT: E 503 GLU cc_start: 0.8423 (tp30) cc_final: 0.8214 (tp30) REVERT: F 113 MET cc_start: 0.9273 (tpp) cc_final: 0.8910 (tpp) REVERT: F 132 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8617 (p0) REVERT: F 203 GLN cc_start: 0.6361 (tm-30) cc_final: 0.5667 (tm-30) REVERT: F 248 MET cc_start: 0.9037 (ttm) cc_final: 0.8746 (ttm) REVERT: F 314 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8174 (tm-30) REVERT: F 388 GLU cc_start: 0.8560 (tp30) cc_final: 0.8162 (tp30) REVERT: F 398 LEU cc_start: 0.9136 (mt) cc_final: 0.8922 (mt) REVERT: F 503 GLU cc_start: 0.8446 (tp30) cc_final: 0.8128 (tp30) REVERT: F 531 ASP cc_start: 0.7883 (t0) cc_final: 0.7569 (t0) outliers start: 60 outliers final: 8 residues processed: 426 average time/residue: 0.2902 time to fit residues: 190.8071 Evaluate side-chains 263 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 249 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 385 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 143 optimal weight: 0.1980 chunk 223 optimal weight: 0.0570 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 272 ASN A 357 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN B 357 GLN C 256 ASN C 272 ASN C 357 GLN D 256 ASN D 272 ASN D 357 GLN ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 ASN E 357 GLN F 256 ASN F 272 ASN F 357 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19626 Z= 0.159 Angle : 0.541 6.029 26604 Z= 0.264 Chirality : 0.043 0.136 3066 Planarity : 0.003 0.021 3402 Dihedral : 13.153 150.783 2896 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.95 % Favored : 92.80 % Rotamer: Outliers : 2.58 % Allowed : 12.25 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2430 helix: 1.37 (0.17), residues: 990 sheet: 2.20 (0.27), residues: 408 loop : -2.03 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 359 HIS 0.004 0.001 HIS B 127 PHE 0.014 0.001 PHE C 204 TYR 0.009 0.001 TYR C 319 ARG 0.004 0.000 ARG A 475 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 267 time to evaluate : 2.230 Fit side-chains REVERT: A 113 MET cc_start: 0.9341 (tpp) cc_final: 0.8937 (tpp) REVERT: A 116 PHE cc_start: 0.8833 (t80) cc_final: 0.8555 (t80) REVERT: A 180 GLN cc_start: 0.7419 (mp10) cc_final: 0.6674 (mp10) REVERT: A 314 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8262 (tm-30) REVERT: A 335 MET cc_start: 0.8006 (tpp) cc_final: 0.7740 (tpp) REVERT: A 503 GLU cc_start: 0.8364 (tp30) cc_final: 0.8090 (tp30) REVERT: B 113 MET cc_start: 0.9249 (tpp) cc_final: 0.8776 (tpp) REVERT: B 125 ASP cc_start: 0.7629 (m-30) cc_final: 0.7305 (m-30) REVERT: B 203 GLN cc_start: 0.6576 (tm-30) cc_final: 0.6008 (tm-30) REVERT: B 314 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8372 (tm-30) REVERT: C 113 MET cc_start: 0.9326 (tpp) cc_final: 0.8857 (tpp) REVERT: C 248 MET cc_start: 0.8794 (ttm) cc_final: 0.8584 (ttm) REVERT: C 353 MET cc_start: 0.8817 (ptm) cc_final: 0.8606 (ptm) REVERT: C 398 LEU cc_start: 0.9214 (mt) cc_final: 0.8993 (mt) REVERT: C 503 GLU cc_start: 0.8488 (tp30) cc_final: 0.8176 (tp30) REVERT: D 113 MET cc_start: 0.9339 (tpp) cc_final: 0.8941 (tpp) REVERT: D 116 PHE cc_start: 0.8882 (t80) cc_final: 0.8610 (t80) REVERT: D 180 GLN cc_start: 0.7440 (mp10) cc_final: 0.6679 (mp10) REVERT: D 203 GLN cc_start: 0.6536 (tm-30) cc_final: 0.6328 (tm-30) REVERT: D 314 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8322 (tm-30) REVERT: D 479 GLN cc_start: 0.7876 (tt0) cc_final: 0.7649 (tt0) REVERT: D 503 GLU cc_start: 0.8368 (tp30) cc_final: 0.8099 (tp30) REVERT: E 113 MET cc_start: 0.9298 (tpp) cc_final: 0.8820 (tpp) REVERT: E 125 ASP cc_start: 0.7761 (m-30) cc_final: 0.7282 (m-30) REVERT: E 204 PHE cc_start: 0.7893 (m-80) cc_final: 0.7326 (m-80) REVERT: E 314 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8297 (tm-30) REVERT: E 503 GLU cc_start: 0.8472 (tp30) cc_final: 0.8266 (tp30) REVERT: F 113 MET cc_start: 0.9293 (tpp) cc_final: 0.8878 (tpp) REVERT: F 204 PHE cc_start: 0.7675 (m-80) cc_final: 0.7462 (m-80) REVERT: F 314 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8118 (tm-30) REVERT: F 353 MET cc_start: 0.8849 (ptm) cc_final: 0.8629 (ptm) REVERT: F 388 GLU cc_start: 0.8592 (tp30) cc_final: 0.8149 (tp30) REVERT: F 398 LEU cc_start: 0.9206 (mt) cc_final: 0.8987 (mt) REVERT: F 503 GLU cc_start: 0.8477 (tp30) cc_final: 0.8176 (tp30) outliers start: 52 outliers final: 32 residues processed: 308 average time/residue: 0.2389 time to fit residues: 123.2220 Evaluate side-chains 246 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 214 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 451 ASN Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 385 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 152 optimal weight: 0.0470 chunk 61 optimal weight: 0.5980 chunk 223 optimal weight: 0.0470 chunk 241 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 221 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 179 optimal weight: 6.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19626 Z= 0.132 Angle : 0.524 8.127 26604 Z= 0.253 Chirality : 0.042 0.133 3066 Planarity : 0.002 0.021 3402 Dihedral : 12.260 145.176 2896 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.46 % Favored : 93.29 % Rotamer: Outliers : 3.03 % Allowed : 14.04 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 2430 helix: 1.53 (0.17), residues: 1002 sheet: 2.15 (0.26), residues: 408 loop : -2.05 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 482 HIS 0.001 0.000 HIS F 127 PHE 0.014 0.001 PHE C 204 TYR 0.010 0.001 TYR C 164 ARG 0.003 0.000 ARG A 475 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 242 time to evaluate : 2.379 Fit side-chains REVERT: A 113 MET cc_start: 0.9319 (tpp) cc_final: 0.8915 (tpp) REVERT: A 116 PHE cc_start: 0.8845 (t80) cc_final: 0.8572 (t80) REVERT: A 179 TYR cc_start: 0.8614 (m-80) cc_final: 0.8356 (m-80) REVERT: A 180 GLN cc_start: 0.7342 (mp10) cc_final: 0.6648 (mp10) REVERT: A 314 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8311 (tm-30) REVERT: A 503 GLU cc_start: 0.8400 (tp30) cc_final: 0.8062 (tp30) REVERT: B 113 MET cc_start: 0.9242 (tpp) cc_final: 0.8768 (tpp) REVERT: B 125 ASP cc_start: 0.7685 (m-30) cc_final: 0.7261 (m-30) REVERT: B 203 GLN cc_start: 0.6498 (tm-30) cc_final: 0.6114 (tm-30) REVERT: B 314 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8327 (tm-30) REVERT: C 113 MET cc_start: 0.9337 (tpp) cc_final: 0.8855 (tpp) REVERT: C 203 GLN cc_start: 0.6675 (tm-30) cc_final: 0.6424 (tm-30) REVERT: C 353 MET cc_start: 0.8652 (ptm) cc_final: 0.8401 (ptm) REVERT: C 503 GLU cc_start: 0.8484 (tp30) cc_final: 0.8151 (tp30) REVERT: D 113 MET cc_start: 0.9333 (tpp) cc_final: 0.8928 (tpp) REVERT: D 116 PHE cc_start: 0.8844 (t80) cc_final: 0.8564 (t80) REVERT: D 179 TYR cc_start: 0.8667 (m-80) cc_final: 0.8407 (m-80) REVERT: D 180 GLN cc_start: 0.7463 (mp10) cc_final: 0.6692 (mp10) REVERT: D 314 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8314 (tm-30) REVERT: D 503 GLU cc_start: 0.8426 (tp30) cc_final: 0.8083 (tp30) REVERT: E 113 MET cc_start: 0.9284 (tpp) cc_final: 0.8805 (tpp) REVERT: E 125 ASP cc_start: 0.7729 (m-30) cc_final: 0.7315 (m-30) REVERT: E 314 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8283 (tm-30) REVERT: E 507 MET cc_start: 0.7977 (mmm) cc_final: 0.7667 (mtp) REVERT: F 113 MET cc_start: 0.9276 (tpp) cc_final: 0.8821 (tpp) REVERT: F 203 GLN cc_start: 0.6792 (tm-30) cc_final: 0.6532 (tm-30) REVERT: F 314 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8250 (tm-30) REVERT: F 353 MET cc_start: 0.8689 (ptm) cc_final: 0.8427 (ptm) REVERT: F 388 GLU cc_start: 0.8578 (tp30) cc_final: 0.8171 (tp30) REVERT: F 503 GLU cc_start: 0.8488 (tp30) cc_final: 0.8154 (tp30) outliers start: 61 outliers final: 33 residues processed: 290 average time/residue: 0.2337 time to fit residues: 114.5036 Evaluate side-chains 249 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 451 ASN Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 237 optimal weight: 0.2980 chunk 117 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19626 Z= 0.193 Angle : 0.537 7.440 26604 Z= 0.263 Chirality : 0.043 0.136 3066 Planarity : 0.003 0.022 3402 Dihedral : 11.363 136.386 2895 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.70 % Favored : 92.06 % Rotamer: Outliers : 3.62 % Allowed : 13.59 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2430 helix: 1.77 (0.18), residues: 996 sheet: 2.11 (0.26), residues: 408 loop : -2.11 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 482 HIS 0.002 0.000 HIS F 238 PHE 0.012 0.001 PHE A 204 TYR 0.010 0.001 TYR A 319 ARG 0.002 0.000 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 219 time to evaluate : 2.403 Fit side-chains REVERT: A 113 MET cc_start: 0.9333 (tpp) cc_final: 0.8946 (tpp) REVERT: A 180 GLN cc_start: 0.7474 (mp10) cc_final: 0.6761 (mp10) REVERT: A 314 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8287 (tm-30) REVERT: A 503 GLU cc_start: 0.8437 (tp30) cc_final: 0.8087 (tp30) REVERT: B 113 MET cc_start: 0.9262 (tpp) cc_final: 0.8784 (tpp) REVERT: B 125 ASP cc_start: 0.7707 (m-30) cc_final: 0.7305 (m-30) REVERT: B 203 GLN cc_start: 0.6596 (tm-30) cc_final: 0.6285 (tm-30) REVERT: B 314 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8315 (tm-30) REVERT: C 113 MET cc_start: 0.9337 (tpp) cc_final: 0.8862 (tpp) REVERT: C 503 GLU cc_start: 0.8487 (tp30) cc_final: 0.8228 (tp30) REVERT: D 113 MET cc_start: 0.9336 (tpp) cc_final: 0.8958 (tpp) REVERT: D 180 GLN cc_start: 0.7506 (mp10) cc_final: 0.6767 (mp10) REVERT: D 314 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8328 (tm-30) REVERT: D 503 GLU cc_start: 0.8468 (tp30) cc_final: 0.8087 (tp30) REVERT: E 113 MET cc_start: 0.9277 (tpp) cc_final: 0.8798 (tpp) REVERT: E 125 ASP cc_start: 0.7845 (m-30) cc_final: 0.7531 (m-30) REVERT: E 314 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8304 (tm-30) REVERT: E 507 MET cc_start: 0.7996 (mmm) cc_final: 0.7709 (mtp) REVERT: F 113 MET cc_start: 0.9286 (tpp) cc_final: 0.8896 (tpp) REVERT: F 314 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8293 (tm-30) REVERT: F 388 GLU cc_start: 0.8660 (tp30) cc_final: 0.8162 (tp30) REVERT: F 503 GLU cc_start: 0.8548 (tp30) cc_final: 0.8226 (tp30) outliers start: 73 outliers final: 50 residues processed: 271 average time/residue: 0.2390 time to fit residues: 109.6244 Evaluate side-chains 248 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 198 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 451 ASN Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 218 PHE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 347 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 451 ASN Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 218 PHE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 470 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 0.7980 chunk 134 optimal weight: 0.0370 chunk 3 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 chunk 98 optimal weight: 0.2980 chunk 202 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 213 optimal weight: 0.0060 chunk 60 optimal weight: 3.9990 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19626 Z= 0.134 Angle : 0.529 8.257 26604 Z= 0.252 Chirality : 0.042 0.136 3066 Planarity : 0.002 0.023 3402 Dihedral : 10.956 132.154 2894 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.91 % Favored : 92.84 % Rotamer: Outliers : 2.73 % Allowed : 14.34 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2430 helix: 1.86 (0.17), residues: 996 sheet: 2.06 (0.27), residues: 408 loop : -2.00 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.000 HIS D 127 PHE 0.015 0.001 PHE A 204 TYR 0.008 0.001 TYR A 319 ARG 0.003 0.000 ARG D 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 219 time to evaluate : 2.455 Fit side-chains REVERT: A 113 MET cc_start: 0.9330 (tpp) cc_final: 0.8941 (tpp) REVERT: A 180 GLN cc_start: 0.7366 (mp10) cc_final: 0.6657 (mp10) REVERT: A 314 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8290 (tm-30) REVERT: A 503 GLU cc_start: 0.8436 (tp30) cc_final: 0.8013 (tp30) REVERT: B 113 MET cc_start: 0.9254 (tpp) cc_final: 0.8775 (tpp) REVERT: B 125 ASP cc_start: 0.7691 (m-30) cc_final: 0.7292 (m-30) REVERT: B 203 GLN cc_start: 0.6588 (tm-30) cc_final: 0.6253 (tm-30) REVERT: B 314 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8322 (tm-30) REVERT: B 350 THR cc_start: 0.9081 (p) cc_final: 0.8865 (p) REVERT: C 113 MET cc_start: 0.9333 (tpp) cc_final: 0.8862 (tpp) REVERT: C 203 GLN cc_start: 0.6729 (tm-30) cc_final: 0.6472 (tm-30) REVERT: C 503 GLU cc_start: 0.8535 (tp30) cc_final: 0.8216 (tp30) REVERT: D 113 MET cc_start: 0.9326 (tpp) cc_final: 0.8947 (tpp) REVERT: D 180 GLN cc_start: 0.7396 (mp10) cc_final: 0.6685 (mp10) REVERT: D 314 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8297 (tm-30) REVERT: D 503 GLU cc_start: 0.8447 (tp30) cc_final: 0.8023 (tp30) REVERT: E 113 MET cc_start: 0.9275 (tpp) cc_final: 0.8791 (tpp) REVERT: E 125 ASP cc_start: 0.7810 (m-30) cc_final: 0.7512 (m-30) REVERT: E 314 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8279 (tm-30) REVERT: E 335 MET cc_start: 0.8093 (tpp) cc_final: 0.7866 (tpp) REVERT: E 350 THR cc_start: 0.9075 (p) cc_final: 0.8855 (p) REVERT: E 507 MET cc_start: 0.7908 (mmm) cc_final: 0.7659 (mtp) REVERT: F 113 MET cc_start: 0.9284 (tpp) cc_final: 0.8873 (tpp) REVERT: F 203 GLN cc_start: 0.6829 (tm-30) cc_final: 0.6589 (tm-30) REVERT: F 314 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8289 (tm-30) outliers start: 55 outliers final: 38 residues processed: 257 average time/residue: 0.2338 time to fit residues: 101.4651 Evaluate side-chains 247 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 209 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 479 GLN Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 218 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 393 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 197 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19626 Z= 0.261 Angle : 0.570 7.473 26604 Z= 0.279 Chirality : 0.043 0.139 3066 Planarity : 0.003 0.024 3402 Dihedral : 10.923 125.504 2890 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.74 % Favored : 92.02 % Rotamer: Outliers : 3.37 % Allowed : 14.48 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2430 helix: 1.86 (0.18), residues: 996 sheet: 2.02 (0.27), residues: 408 loop : -2.13 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 482 HIS 0.002 0.000 HIS F 238 PHE 0.010 0.001 PHE A 237 TYR 0.009 0.001 TYR A 319 ARG 0.003 0.000 ARG D 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 197 time to evaluate : 2.379 Fit side-chains REVERT: A 113 MET cc_start: 0.9332 (tpp) cc_final: 0.8947 (tpp) REVERT: A 180 GLN cc_start: 0.7389 (mp10) cc_final: 0.6665 (mp10) REVERT: A 314 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8292 (tm-30) REVERT: A 503 GLU cc_start: 0.8436 (tp30) cc_final: 0.8028 (tp30) REVERT: B 113 MET cc_start: 0.9283 (tpp) cc_final: 0.8799 (tpp) REVERT: B 125 ASP cc_start: 0.7812 (m-30) cc_final: 0.7533 (m-30) REVERT: C 113 MET cc_start: 0.9355 (tpp) cc_final: 0.8896 (tpp) REVERT: C 503 GLU cc_start: 0.8526 (tp30) cc_final: 0.8148 (tp30) REVERT: D 113 MET cc_start: 0.9330 (tpp) cc_final: 0.8939 (tpp) REVERT: D 180 GLN cc_start: 0.7452 (mp10) cc_final: 0.6769 (mp10) REVERT: D 314 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8293 (tm-30) REVERT: D 503 GLU cc_start: 0.8446 (tp30) cc_final: 0.8029 (tp30) REVERT: E 113 MET cc_start: 0.9292 (tpp) cc_final: 0.8815 (tpp) REVERT: E 335 MET cc_start: 0.8163 (tpp) cc_final: 0.7933 (tpp) REVERT: E 507 MET cc_start: 0.8000 (mmm) cc_final: 0.7773 (mtp) REVERT: F 204 PHE cc_start: 0.7510 (m-80) cc_final: 0.7197 (m-80) REVERT: F 314 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8318 (tm-30) outliers start: 68 outliers final: 50 residues processed: 241 average time/residue: 0.2334 time to fit residues: 94.7079 Evaluate side-chains 235 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 185 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 218 PHE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 470 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 135 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 237 optimal weight: 0.0040 chunk 148 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19626 Z= 0.147 Angle : 0.534 8.855 26604 Z= 0.257 Chirality : 0.042 0.142 3066 Planarity : 0.002 0.025 3402 Dihedral : 10.547 123.439 2890 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.75 % Favored : 93.00 % Rotamer: Outliers : 2.38 % Allowed : 15.62 % Favored : 81.99 % 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: 0.49 (0.18), residues: 2430 helix: 1.89 (0.17), residues: 996 sheet: 1.95 (0.27), residues: 408 loop : -2.12 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 482 HIS 0.004 0.000 HIS E 127 PHE 0.017 0.001 PHE A 204 TYR 0.009 0.001 TYR C 164 ARG 0.002 0.000 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 205 time to evaluate : 2.222 Fit side-chains REVERT: A 113 MET cc_start: 0.9324 (tpp) cc_final: 0.8940 (tpp) REVERT: A 180 GLN cc_start: 0.7422 (mp10) cc_final: 0.6702 (mp10) REVERT: A 314 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8281 (tm-30) REVERT: A 503 GLU cc_start: 0.8453 (tp30) cc_final: 0.8010 (tp30) REVERT: B 113 MET cc_start: 0.9280 (tpp) cc_final: 0.8798 (tpp) REVERT: B 125 ASP cc_start: 0.7763 (m-30) cc_final: 0.7495 (m-30) REVERT: B 350 THR cc_start: 0.9104 (p) cc_final: 0.8881 (p) REVERT: C 113 MET cc_start: 0.9339 (tpp) cc_final: 0.8873 (tpp) REVERT: C 335 MET cc_start: 0.8065 (tpp) cc_final: 0.7830 (tpp) REVERT: C 503 GLU cc_start: 0.8500 (tp30) cc_final: 0.8251 (tp30) REVERT: D 113 MET cc_start: 0.9333 (tpp) cc_final: 0.8952 (tpp) REVERT: D 180 GLN cc_start: 0.7464 (mp10) cc_final: 0.6761 (mp10) REVERT: D 314 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8279 (tm-30) REVERT: D 503 GLU cc_start: 0.8464 (tp30) cc_final: 0.7989 (tp30) REVERT: E 113 MET cc_start: 0.9283 (tpp) cc_final: 0.8800 (tpp) REVERT: E 507 MET cc_start: 0.7899 (mmm) cc_final: 0.7694 (mtp) REVERT: F 113 MET cc_start: 0.8922 (mtt) cc_final: 0.8647 (mpp) REVERT: F 203 GLN cc_start: 0.6877 (tm-30) cc_final: 0.6665 (tm-30) REVERT: F 314 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8279 (tm-30) REVERT: F 335 MET cc_start: 0.8044 (tpp) cc_final: 0.7820 (tpp) outliers start: 48 outliers final: 39 residues processed: 236 average time/residue: 0.2423 time to fit residues: 97.5137 Evaluate side-chains 233 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 194 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 393 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 71 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 161 optimal weight: 0.3980 chunk 117 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19626 Z= 0.148 Angle : 0.529 8.390 26604 Z= 0.254 Chirality : 0.042 0.141 3066 Planarity : 0.002 0.025 3402 Dihedral : 10.267 120.230 2890 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.49 % Favored : 92.26 % Rotamer: Outliers : 2.73 % Allowed : 15.53 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2430 helix: 1.99 (0.17), residues: 990 sheet: 1.91 (0.27), residues: 408 loop : -2.03 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 482 HIS 0.004 0.000 HIS B 127 PHE 0.015 0.001 PHE A 204 TYR 0.011 0.001 TYR C 164 ARG 0.002 0.000 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 202 time to evaluate : 2.092 Fit side-chains REVERT: A 113 MET cc_start: 0.9320 (tpp) cc_final: 0.8944 (tpp) REVERT: A 180 GLN cc_start: 0.7397 (mp10) cc_final: 0.6715 (mp10) REVERT: A 314 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8278 (tm-30) REVERT: A 503 GLU cc_start: 0.8460 (tp30) cc_final: 0.7984 (tp30) REVERT: B 113 MET cc_start: 0.9285 (tpp) cc_final: 0.8807 (tpp) REVERT: B 125 ASP cc_start: 0.7736 (m-30) cc_final: 0.7424 (m-30) REVERT: B 203 GLN cc_start: 0.6620 (tm-30) cc_final: 0.6262 (tm-30) REVERT: B 314 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8300 (tm-30) REVERT: B 350 THR cc_start: 0.9092 (p) cc_final: 0.8859 (p) REVERT: C 113 MET cc_start: 0.9332 (tpp) cc_final: 0.8853 (tpp) REVERT: D 113 MET cc_start: 0.9328 (tpp) cc_final: 0.8975 (tpp) REVERT: D 180 GLN cc_start: 0.7459 (mp10) cc_final: 0.6762 (mp10) REVERT: D 314 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8279 (tm-30) REVERT: D 503 GLU cc_start: 0.8480 (tp30) cc_final: 0.8027 (tp30) REVERT: E 113 MET cc_start: 0.9281 (tpp) cc_final: 0.8799 (tpp) REVERT: E 350 THR cc_start: 0.9093 (p) cc_final: 0.8858 (p) REVERT: E 507 MET cc_start: 0.7906 (mmm) cc_final: 0.7676 (mtp) REVERT: F 203 GLN cc_start: 0.6827 (tm-30) cc_final: 0.6610 (tm-30) REVERT: F 314 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8270 (tm-30) outliers start: 55 outliers final: 50 residues processed: 238 average time/residue: 0.2345 time to fit residues: 94.8541 Evaluate side-chains 244 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 194 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 218 PHE Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 393 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 220 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 208 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19626 Z= 0.176 Angle : 0.547 9.280 26604 Z= 0.262 Chirality : 0.042 0.138 3066 Planarity : 0.002 0.025 3402 Dihedral : 10.049 115.636 2890 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.65 % Favored : 92.10 % Rotamer: Outliers : 2.78 % Allowed : 15.67 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2430 helix: 1.93 (0.17), residues: 1002 sheet: 1.88 (0.27), residues: 408 loop : -2.12 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 482 HIS 0.002 0.000 HIS A 480 PHE 0.015 0.001 PHE A 204 TYR 0.012 0.001 TYR C 164 ARG 0.002 0.000 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 195 time to evaluate : 2.219 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.9319 (tpp) cc_final: 0.8936 (tpp) REVERT: A 180 GLN cc_start: 0.7414 (mp10) cc_final: 0.6680 (mp10) REVERT: A 314 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8287 (tm-30) REVERT: A 503 GLU cc_start: 0.8463 (tp30) cc_final: 0.7973 (tp30) REVERT: B 113 MET cc_start: 0.9294 (tpp) cc_final: 0.8816 (tpp) REVERT: B 125 ASP cc_start: 0.7805 (m-30) cc_final: 0.7510 (m-30) REVERT: B 203 GLN cc_start: 0.6648 (tm-30) cc_final: 0.6326 (tm-30) REVERT: B 314 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8297 (tm-30) REVERT: C 335 MET cc_start: 0.8046 (tpp) cc_final: 0.7793 (tpp) REVERT: D 113 MET cc_start: 0.9331 (tpp) cc_final: 0.8979 (tpp) REVERT: D 180 GLN cc_start: 0.7506 (mp10) cc_final: 0.6791 (mp10) REVERT: D 314 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8285 (tm-30) REVERT: D 503 GLU cc_start: 0.8482 (tp30) cc_final: 0.8017 (tp30) REVERT: E 113 MET cc_start: 0.9294 (tpp) cc_final: 0.8809 (tpp) REVERT: E 350 THR cc_start: 0.9089 (p) cc_final: 0.8863 (p) REVERT: E 507 MET cc_start: 0.7939 (mmm) cc_final: 0.7696 (mtp) REVERT: F 113 MET cc_start: 0.8920 (ptp) cc_final: 0.8569 (mpp) REVERT: F 203 GLN cc_start: 0.6908 (tm-30) cc_final: 0.6616 (tm-30) REVERT: F 204 PHE cc_start: 0.7612 (m-80) cc_final: 0.7246 (m-80) REVERT: F 314 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8109 (tm-30) outliers start: 56 outliers final: 52 residues processed: 229 average time/residue: 0.2378 time to fit residues: 92.6168 Evaluate side-chains 245 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 193 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 218 PHE Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 195 optimal weight: 0.0050 chunk 20 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19626 Z= 0.150 Angle : 0.543 8.843 26604 Z= 0.259 Chirality : 0.042 0.138 3066 Planarity : 0.002 0.026 3402 Dihedral : 9.834 113.496 2890 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.33 % Favored : 92.43 % Rotamer: Outliers : 2.48 % Allowed : 16.17 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 2430 helix: 2.00 (0.17), residues: 990 sheet: 1.86 (0.27), residues: 408 loop : -2.06 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 482 HIS 0.001 0.000 HIS B 127 PHE 0.017 0.001 PHE A 204 TYR 0.012 0.001 TYR C 164 ARG 0.002 0.000 ARG C 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 202 time to evaluate : 2.130 Fit side-chains REVERT: A 113 MET cc_start: 0.9320 (tpp) cc_final: 0.8970 (tpp) REVERT: A 180 GLN cc_start: 0.7423 (mp10) cc_final: 0.6716 (mp10) REVERT: A 314 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8227 (tm-30) REVERT: A 503 GLU cc_start: 0.8479 (tp30) cc_final: 0.7990 (tp30) REVERT: B 113 MET cc_start: 0.9291 (tpp) cc_final: 0.8811 (tpp) REVERT: B 125 ASP cc_start: 0.7780 (m-30) cc_final: 0.7529 (m-30) REVERT: B 203 GLN cc_start: 0.6650 (tm-30) cc_final: 0.6287 (tm-30) REVERT: B 314 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8281 (tm-30) REVERT: C 335 MET cc_start: 0.8039 (tpp) cc_final: 0.7790 (tpp) REVERT: D 113 MET cc_start: 0.9328 (tpp) cc_final: 0.8973 (tpp) REVERT: D 180 GLN cc_start: 0.7435 (mp10) cc_final: 0.6784 (mp10) REVERT: D 314 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8236 (tm-30) REVERT: D 503 GLU cc_start: 0.8486 (tp30) cc_final: 0.8018 (tp30) REVERT: E 113 MET cc_start: 0.9291 (tpp) cc_final: 0.8802 (tpp) REVERT: E 314 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8258 (tm-30) REVERT: E 350 THR cc_start: 0.9092 (p) cc_final: 0.8862 (p) REVERT: E 507 MET cc_start: 0.7876 (mmm) cc_final: 0.7654 (mtp) REVERT: F 113 MET cc_start: 0.8914 (ptp) cc_final: 0.8554 (mpp) REVERT: F 203 GLN cc_start: 0.6897 (tm-30) cc_final: 0.6603 (tm-30) REVERT: F 204 PHE cc_start: 0.7623 (m-80) cc_final: 0.7253 (m-80) REVERT: F 314 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8116 (tm-30) REVERT: F 335 MET cc_start: 0.8005 (tpp) cc_final: 0.7716 (tpp) outliers start: 50 outliers final: 49 residues processed: 233 average time/residue: 0.2361 time to fit residues: 92.9586 Evaluate side-chains 246 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 197 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 218 PHE Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.099491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.075815 restraints weight = 40908.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.079287 restraints weight = 21746.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.081838 restraints weight = 14183.601| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19626 Z= 0.175 Angle : 0.550 8.628 26604 Z= 0.264 Chirality : 0.042 0.136 3066 Planarity : 0.002 0.026 3402 Dihedral : 9.706 110.578 2890 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.74 % Favored : 92.02 % Rotamer: Outliers : 2.78 % Allowed : 15.82 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2430 helix: 1.94 (0.17), residues: 1002 sheet: 1.85 (0.27), residues: 408 loop : -2.16 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 482 HIS 0.001 0.000 HIS F 238 PHE 0.015 0.001 PHE A 204 TYR 0.013 0.001 TYR C 164 ARG 0.002 0.000 ARG A 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3255.11 seconds wall clock time: 60 minutes 3.39 seconds (3603.39 seconds total)