Starting phenix.real_space_refine on Mon Oct 26 05:27:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wqk_66174/10_2026/9wqk_66174.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wqk_66174/10_2026/9wqk_66174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wqk_66174/10_2026/9wqk_66174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wqk_66174/10_2026/9wqk_66174.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wqk_66174/10_2026/9wqk_66174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wqk_66174/10_2026/9wqk_66174.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 163 5.16 5 Cl 2 4.86 5 C 12349 2.51 5 N 3194 2.21 5 O 3569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19277 Number of models: 1 Model: "" Number of chains: 8 Chain: "X" Number of atoms: 6211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6211 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 31, 'TRANS': 756} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "Y" Number of atoms: 6081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6081 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 737} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1778 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 440 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1780 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "X" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 207 Unusual residues: {' CL': 1, 'CLR': 4, 'NAG': 4, 'YKU': 1} Inner-chain residues flagged as termini: ['pdbres="GGL X 902 "'] Classifications: {'peptide': 1, 'undetermined': 10} Modifications used: {'COO': 1} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 179 Unusual residues: {' CL': 1, 'CLR': 4, 'NAG': 4} Inner-chain residues flagged as termini: ['pdbres="GGL Y4402 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" C1 NAG X 903 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG X 903 " occ=0.70 residue: pdb=" C1 NAG X 904 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG X 904 " occ=0.70 residue: pdb=" C1 NAG X 905 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG X 905 " occ=0.70 residue: pdb=" C1 NAG X 906 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG X 906 " occ=0.70 residue: pdb=" C1 NAG Y4403 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG Y4403 " occ=0.70 residue: pdb=" C1 NAG Y4404 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG Y4404 " occ=0.70 residue: pdb=" C1 NAG Y4405 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG Y4405 " occ=0.70 residue: pdb=" C1 NAG Y4406 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG Y4406 " occ=0.70 Time building chain proxies: 3.60, per 1000 atoms: 0.19 Number of scatterers: 19277 At special positions: 0 Unit cell: (127.41, 135.78, 242.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 163 16.00 O 3569 8.00 N 3194 7.00 C 12349 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS X 57 " - pdb=" SG CYS X 99 " distance=2.03 Simple disulfide: pdb=" SG CYS X 241 " - pdb=" SG CYS X 530 " distance=2.03 Simple disulfide: pdb=" SG CYS X 365 " - pdb=" SG CYS X 381 " distance=2.03 Simple disulfide: pdb=" SG CYS X 419 " - pdb=" SG CYS X 426 " distance=2.03 Simple disulfide: pdb=" SG CYS X 511 " - pdb=" SG CYS X 531 " distance=2.03 Simple disulfide: pdb=" SG CYS X 515 " - pdb=" SG CYS X 534 " distance=2.03 Simple disulfide: pdb=" SG CYS X 537 " - pdb=" SG CYS X 549 " distance=2.03 Simple disulfide: pdb=" SG CYS X 552 " - pdb=" SG CYS X 565 " distance=2.03 Simple disulfide: pdb=" SG CYS X 644 " - pdb=" SG CYS X 733 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 57 " - pdb=" SG CYS Y 99 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 241 " - pdb=" SG CYS Y 530 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 365 " - pdb=" SG CYS Y 381 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 419 " - pdb=" SG CYS Y 426 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 511 " - pdb=" SG CYS Y 531 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 515 " - pdb=" SG CYS Y 534 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 537 " - pdb=" SG CYS Y 549 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 552 " - pdb=" SG CYS Y 565 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 644 " - pdb=" SG CYS Y 733 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG X 903 " - " ASN X 88 " " NAG X 904 " - " ASN X 210 " " NAG X 905 " - " ASN X 382 " " NAG X 906 " - " ASN X 445 " " NAG Y4403 " - " ASN Y 88 " " NAG Y4404 " - " ASN Y 210 " " NAG Y4405 " - " ASN Y 382 " " NAG Y4406 " - " ASN Y 445 " Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 680.7 milliseconds 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 27 sheets defined 42.8% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'X' and resid 48 through 52 removed outlier: 3.656A pdb=" N VAL X 52 " --> pdb=" O VAL X 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 65 through 82 Processing helix chain 'X' and resid 101 through 114 Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 151 through 164 Processing helix chain 'X' and resid 176 through 181 removed outlier: 3.587A pdb=" N ASP X 181 " --> pdb=" O ASP X 178 " (cutoff:3.500A) Processing helix chain 'X' and resid 194 through 209 removed outlier: 4.082A pdb=" N GLN X 198 " --> pdb=" O SER X 194 " (cutoff:3.500A) Processing helix chain 'X' and resid 221 through 238 Processing helix chain 'X' and resid 253 through 266 Processing helix chain 'X' and resid 279 through 294 Processing helix chain 'X' and resid 310 through 315 removed outlier: 4.346A pdb=" N THR X 314 " --> pdb=" O ARG X 310 " (cutoff:3.500A) Processing helix chain 'X' and resid 317 through 322 removed outlier: 3.574A pdb=" N ALA X 321 " --> pdb=" O TYR X 317 " (cutoff:3.500A) Processing helix chain 'X' and resid 334 through 342 removed outlier: 3.834A pdb=" N ASP X 338 " --> pdb=" O VAL X 334 " (cutoff:3.500A) Processing helix chain 'X' and resid 354 through 364 Processing helix chain 'X' and resid 396 through 419 Processing helix chain 'X' and resid 426 through 430 removed outlier: 3.524A pdb=" N LYS X 430 " --> pdb=" O ASP X 427 " (cutoff:3.500A) Processing helix chain 'X' and resid 433 through 444 Processing helix chain 'X' and resid 495 through 500 Processing helix chain 'X' and resid 502 through 506 Processing helix chain 'X' and resid 577 through 604 Processing helix chain 'X' and resid 607 through 613 Processing helix chain 'X' and resid 614 through 637 removed outlier: 4.039A pdb=" N THR X 632 " --> pdb=" O GLY X 628 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE X 633 " --> pdb=" O TYR X 629 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA X 637 " --> pdb=" O PHE X 633 " (cutoff:3.500A) Processing helix chain 'X' and resid 640 through 674 Proline residue: X 655 - end of helix Processing helix chain 'X' and resid 689 through 715 Processing helix chain 'X' and resid 736 through 761 Proline residue: X 743 - end of helix Processing helix chain 'X' and resid 770 through 793 Proline residue: X 790 - end of helix Processing helix chain 'X' and resid 797 through 818 removed outlier: 3.684A pdb=" N THR X 801 " --> pdb=" O TYR X 797 " (cutoff:3.500A) Processing helix chain 'X' and resid 818 through 828 Processing helix chain 'X' and resid 829 through 832 Processing helix chain 'Y' and resid 48 through 52 Processing helix chain 'Y' and resid 65 through 81 Processing helix chain 'Y' and resid 101 through 114 Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 151 through 163 Processing helix chain 'Y' and resid 164 through 166 No H-bonds generated for 'chain 'Y' and resid 164 through 166' Processing helix chain 'Y' and resid 176 through 181 removed outlier: 3.550A pdb=" N ASP Y 181 " --> pdb=" O ASP Y 178 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 209 removed outlier: 4.132A pdb=" N GLN Y 198 " --> pdb=" O SER Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 221 through 238 removed outlier: 3.617A pdb=" N LYS Y 237 " --> pdb=" O ASP Y 233 " (cutoff:3.500A) Processing helix chain 'Y' and resid 253 through 266 Processing helix chain 'Y' and resid 279 through 294 Processing helix chain 'Y' and resid 310 through 315 removed outlier: 4.267A pdb=" N THR Y 314 " --> pdb=" O ARG Y 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 317 through 322 removed outlier: 3.574A pdb=" N ALA Y 321 " --> pdb=" O TYR Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 334 through 342 removed outlier: 3.810A pdb=" N TYR Y 340 " --> pdb=" O TRP Y 336 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 364 Processing helix chain 'Y' and resid 396 through 419 Processing helix chain 'Y' and resid 426 through 430 Processing helix chain 'Y' and resid 433 through 444 Processing helix chain 'Y' and resid 495 through 500 Processing helix chain 'Y' and resid 502 through 506 Processing helix chain 'Y' and resid 577 through 604 Processing helix chain 'Y' and resid 607 through 612 removed outlier: 3.842A pdb=" N SER Y 612 " --> pdb=" O PRO Y 608 " (cutoff:3.500A) Processing helix chain 'Y' and resid 614 through 636 removed outlier: 3.977A pdb=" N ILE Y 636 " --> pdb=" O THR Y 632 " (cutoff:3.500A) Processing helix chain 'Y' and resid 640 through 673 Proline residue: Y 655 - end of helix Processing helix chain 'Y' and resid 689 through 715 removed outlier: 3.689A pdb=" N GLN Y 693 " --> pdb=" O SER Y 689 " (cutoff:3.500A) Processing helix chain 'Y' and resid 737 through 760 Proline residue: Y 743 - end of helix removed outlier: 3.641A pdb=" N LYS Y 760 " --> pdb=" O PHE Y 756 " (cutoff:3.500A) Processing helix chain 'Y' and resid 765 through 793 removed outlier: 4.253A pdb=" N ASN Y 769 " --> pdb=" O PRO Y 765 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU Y 770 " --> pdb=" O ALA Y 766 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA Y 771 " --> pdb=" O ASN Y 767 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS Y 772 " --> pdb=" O PHE Y 768 " (cutoff:3.500A) Proline residue: Y 790 - end of helix Processing helix chain 'Y' and resid 797 through 818 Processing helix chain 'Y' and resid 818 through 827 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.750A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 215 removed outlier: 4.674A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.813A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.836A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.533A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.710A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 53 through 56 removed outlier: 4.135A pdb=" N GLY F 56 " --> pdb=" O SER F 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 53 through 56' Processing helix chain 'F' and resid 220 through 224 removed outlier: 3.734A pdb=" N VAL F 224 " --> pdb=" O ALA F 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 28 through 31 removed outlier: 6.157A pdb=" N ILE X 35 " --> pdb=" O GLY X 92 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLU X 94 " --> pdb=" O ILE X 35 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE X 37 " --> pdb=" O GLU X 94 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ARG X 96 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA X 39 " --> pdb=" O ARG X 96 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE X 36 " --> pdb=" O ILE X 143 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY X 145 " --> pdb=" O ILE X 36 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE X 170 " --> pdb=" O VAL X 144 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL X 146 " --> pdb=" O ILE X 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 241 through 248 removed outlier: 7.783A pdb=" N VAL X 214 " --> pdb=" O ALA X 243 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER X 245 " --> pdb=" O VAL X 214 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA X 216 " --> pdb=" O SER X 245 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LYS X 247 " --> pdb=" O ALA X 216 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS X 218 " --> pdb=" O LYS X 247 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR X 213 " --> pdb=" O VAL X 273 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ALA X 275 " --> pdb=" O TYR X 213 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER X 215 " --> pdb=" O ALA X 275 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N PHE X 277 " --> pdb=" O SER X 215 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL X 217 " --> pdb=" O PHE X 277 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL X 274 " --> pdb=" O LEU X 302 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU X 301 " --> pdb=" O ILE X 325 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE X 327 " --> pdb=" O LEU X 301 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY X 303 " --> pdb=" O ILE X 327 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N LEU X 329 " --> pdb=" O GLY X 303 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY X 324 " --> pdb=" O PHE X 471 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TYR X 466 " --> pdb=" O SER X 486 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER X 486 " --> pdb=" O TYR X 466 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE X 468 " --> pdb=" O VAL X 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 445 through 447 Processing sheet with id=AA4, first strand: chain 'X' and resid 519 through 523 Processing sheet with id=AA5, first strand: chain 'X' and resid 541 through 545 removed outlier: 6.672A pdb=" N THR X 548 " --> pdb=" O PHE X 544 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 556 through 558 Processing sheet with id=AA7, first strand: chain 'X' and resid 719 through 722 Processing sheet with id=AA8, first strand: chain 'Y' and resid 29 through 31 removed outlier: 6.351A pdb=" N ILE Y 35 " --> pdb=" O GLY Y 92 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU Y 94 " --> pdb=" O ILE Y 35 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE Y 37 " --> pdb=" O GLU Y 94 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ARG Y 96 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA Y 39 " --> pdb=" O ARG Y 96 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE Y 36 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY Y 145 " --> pdb=" O ILE Y 36 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N ILE Y 170 " --> pdb=" O VAL Y 144 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL Y 146 " --> pdb=" O ILE Y 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 241 through 248 removed outlier: 7.745A pdb=" N VAL Y 214 " --> pdb=" O ALA Y 243 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER Y 245 " --> pdb=" O VAL Y 214 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA Y 216 " --> pdb=" O SER Y 245 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LYS Y 247 " --> pdb=" O ALA Y 216 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N HIS Y 218 " --> pdb=" O LYS Y 247 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL Y 273 " --> pdb=" O TYR Y 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY Y 324 " --> pdb=" O PHE Y 471 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR Y 466 " --> pdb=" O SER Y 486 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER Y 486 " --> pdb=" O TYR Y 466 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE Y 468 " --> pdb=" O VAL Y 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 445 through 447 Processing sheet with id=AB2, first strand: chain 'Y' and resid 519 through 523 Processing sheet with id=AB3, first strand: chain 'Y' and resid 541 through 545 removed outlier: 6.759A pdb=" N THR Y 548 " --> pdb=" O PHE Y 544 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 556 through 558 Processing sheet with id=AB5, first strand: chain 'Y' and resid 719 through 722 Processing sheet with id=AB6, first strand: chain 'A' and resid 185 through 191 Processing sheet with id=AB7, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.747A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.561A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.863A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.654A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.077A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.412A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.796A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.752A pdb=" N MET F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 11 removed outlier: 4.359A pdb=" N PHE F 110 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 146 through 149 removed outlier: 6.541A pdb=" N LEU F 174 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR F 190 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP F 176 " --> pdb=" O LEU F 188 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 155 through 160 955 hydrogen bonds defined for protein. 2709 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: 3.96 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 3104 1.27 - 1.41: 4903 1.41 - 1.55: 11436 1.55 - 1.69: 33 1.69 - 1.82: 235 Bond restraints: 19711 Sorted by residual: bond pdb=" C19 YKU X 901 " pdb=" C21 YKU X 901 " ideal model delta sigma weight residual 1.429 1.527 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C13 YKU X 901 " pdb=" N12 YKU X 901 " ideal model delta sigma weight residual 1.359 1.448 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C15 CLR Y4410 " pdb=" C16 CLR Y4410 " ideal model delta sigma weight residual 1.541 1.620 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C15 CLR X 911 " pdb=" C16 CLR X 911 " ideal model delta sigma weight residual 1.541 1.620 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C15 CLR X 908 " pdb=" C16 CLR X 908 " ideal model delta sigma weight residual 1.541 1.619 -0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 19706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 26078 1.64 - 3.28: 503 3.28 - 4.92: 109 4.92 - 6.56: 46 6.56 - 8.20: 9 Bond angle restraints: 26745 Sorted by residual: angle pdb=" C ILE A 212 " pdb=" N HIS A 213 " pdb=" CA HIS A 213 " ideal model delta sigma weight residual 120.72 114.84 5.88 1.67e+00 3.59e-01 1.24e+01 angle pdb=" C13 CLR Y4408 " pdb=" C17 CLR Y4408 " pdb=" C20 CLR Y4408 " ideal model delta sigma weight residual 119.60 111.40 8.20 3.00e+00 1.11e-01 7.47e+00 angle pdb=" C13 CLR Y4401 " pdb=" C17 CLR Y4401 " pdb=" C20 CLR Y4401 " ideal model delta sigma weight residual 119.60 111.66 7.94 3.00e+00 1.11e-01 7.00e+00 angle pdb=" C13 CLR X 911 " pdb=" C17 CLR X 911 " pdb=" C20 CLR X 911 " ideal model delta sigma weight residual 119.60 111.84 7.76 3.00e+00 1.11e-01 6.69e+00 angle pdb=" C13 CLR Y4410 " pdb=" C17 CLR Y4410 " pdb=" C20 CLR Y4410 " ideal model delta sigma weight residual 119.60 111.92 7.68 3.00e+00 1.11e-01 6.55e+00 ... (remaining 26740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 11488 21.58 - 43.17: 677 43.17 - 64.75: 75 64.75 - 86.34: 26 86.34 - 107.92: 21 Dihedral angle restraints: 12287 sinusoidal: 5265 harmonic: 7022 Sorted by residual: dihedral pdb=" CB CYS X 241 " pdb=" SG CYS X 241 " pdb=" SG CYS X 530 " pdb=" CB CYS X 530 " ideal model delta sinusoidal sigma weight residual -86.00 -160.04 74.04 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS X 365 " pdb=" SG CYS X 365 " pdb=" SG CYS X 381 " pdb=" CB CYS X 381 " ideal model delta sinusoidal sigma weight residual -86.00 -153.47 67.47 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 12284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2749 0.081 - 0.162: 246 0.162 - 0.243: 27 0.243 - 0.324: 6 0.324 - 0.405: 9 Chirality restraints: 3037 Sorted by residual: chirality pdb=" C14 CLR Y4408 " pdb=" C13 CLR Y4408 " pdb=" C15 CLR Y4408 " pdb=" C8 CLR Y4408 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" C14 CLR Y4410 " pdb=" C13 CLR Y4410 " pdb=" C15 CLR Y4410 " pdb=" C8 CLR Y4410 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C14 CLR X 908 " pdb=" C13 CLR X 908 " pdb=" C15 CLR X 908 " pdb=" C8 CLR X 908 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 3034 not shown) Planarity restraints: 3347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 213 " -0.012 2.00e-02 2.50e+03 1.51e-02 3.44e+00 pdb=" CG HIS A 213 " 0.032 2.00e-02 2.50e+03 pdb=" ND1 HIS A 213 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS A 213 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS A 213 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 213 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Y 277 " 0.013 2.00e-02 2.50e+03 1.27e-02 2.81e+00 pdb=" CG PHE Y 277 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE Y 277 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE Y 277 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE Y 277 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE Y 277 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE Y 277 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE X 277 " -0.011 2.00e-02 2.50e+03 1.06e-02 1.98e+00 pdb=" CG PHE X 277 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE X 277 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE X 277 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE X 277 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE X 277 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE X 277 " -0.001 2.00e-02 2.50e+03 ... (remaining 3344 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 445 2.69 - 3.24: 18798 3.24 - 3.80: 31481 3.80 - 4.35: 41128 4.35 - 4.90: 69184 Nonbonded interactions: 161036 Sorted by model distance: nonbonded pdb=" OG1 THR X 559 " pdb=" OD1 ASP X 561 " model vdw 2.141 3.040 nonbonded pdb=" O TYR Y 213 " pdb=" OG SER Y 509 " model vdw 2.160 3.040 nonbonded pdb=" O VAL Y 609 " pdb=" OG SER Y 613 " model vdw 2.162 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR F 175 " model vdw 2.167 3.040 nonbonded pdb=" O GLN X 553 " pdb=" OG SER X 556 " model vdw 2.178 3.040 ... (remaining 161031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'X' and (resid 25 through 673 or resid 687 through 831 or resid 904 throu \ gh 906 or resid 909 through 911)) selection = (chain 'Y' and (resid 25 through 367 or (resid 368 and (name N or name CA or nam \ e C or name O or name CB )) or resid 369 or (resid 370 and (name N or name CA or \ name C or name O or name CB )) or resid 371 through 501 or (resid 502 through 5 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 504 through \ 524 or (resid 525 and (name N or name CA or name C or name O or name CB )) or r \ esid 526 through 831 or resid 4403 through 4405 or resid 4408 through 4410)) } 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=0.70 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: 4.130 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: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.260 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.006 0.098 19739 Z= 0.265 Angle : 0.631 8.198 26809 Z= 0.299 Chirality : 0.053 0.405 3037 Planarity : 0.003 0.034 3339 Dihedral : 14.396 107.922 7715 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2396 helix: 2.22 (0.17), residues: 913 sheet: -0.72 (0.24), residues: 438 loop : -0.04 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 831 TYR 0.018 0.001 TYR F 94 PHE 0.029 0.001 PHE Y 277 TRP 0.019 0.002 TRP B 82 HIS 0.019 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.27 (19711) covalent geometry : angle 0.62557 / 0.30 (26745) SS BOND : bond 0.00281 / 0.18 ( 20) SS BOND : angle 1.22833 / 0.76 ( 40) hydrogen bonds : bond 0.11864 / 7.81 ( 949) hydrogen bonds : angle 5.31313 / 3.78 ( 2709) link_NAG-ASN : bond 0.00331 / 0.20 ( 8) link_NAG-ASN : angle 2.57590 / 1.60 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 207 LYS cc_start: 0.8113 (tttt) cc_final: 0.7688 (mtpt) REVERT: X 234 MET cc_start: 0.8319 (mtt) cc_final: 0.7787 (mtt) REVERT: X 238 GLU cc_start: 0.7593 (mm-30) cc_final: 0.6981 (mm-30) REVERT: X 567 LEU cc_start: 0.8844 (mt) cc_final: 0.8624 (mt) REVERT: X 605 ARG cc_start: 0.8444 (ptt180) cc_final: 0.7657 (ptp90) REVERT: X 619 TYR cc_start: 0.8895 (m-10) cc_final: 0.8258 (m-80) REVERT: X 622 LEU cc_start: 0.9171 (mt) cc_final: 0.8556 (mm) REVERT: X 626 CYS cc_start: 0.8511 (t) cc_final: 0.8187 (m) REVERT: X 786 LEU cc_start: 0.9185 (mt) cc_final: 0.8979 (mp) REVERT: X 799 ILE cc_start: 0.8358 (mt) cc_final: 0.7659 (mm) REVERT: X 803 CYS cc_start: 0.8395 (m) cc_final: 0.7960 (m) REVERT: Y 505 ASN cc_start: 0.7707 (m110) cc_final: 0.7326 (t0) REVERT: Y 562 LEU cc_start: 0.8712 (mt) cc_final: 0.8485 (mm) REVERT: Y 586 PHE cc_start: 0.8139 (t80) cc_final: 0.7760 (t80) REVERT: Y 618 CYS cc_start: 0.8677 (m) cc_final: 0.8436 (m) REVERT: Y 659 TYR cc_start: 0.8025 (m-80) cc_final: 0.7790 (m-10) REVERT: Y 729 VAL cc_start: 0.8682 (t) cc_final: 0.7036 (p) REVERT: Y 746 TYR cc_start: 0.8250 (t80) cc_final: 0.7913 (t80) REVERT: Y 802 MET cc_start: 0.7930 (tpp) cc_final: 0.7622 (tpp) REVERT: A 35 LYS cc_start: 0.8633 (mttt) cc_final: 0.8414 (mmtm) REVERT: A 241 ASN cc_start: 0.7774 (t0) cc_final: 0.7393 (t0) REVERT: A 274 PHE cc_start: 0.7171 (t80) cc_final: 0.6947 (t80) REVERT: A 302 TYR cc_start: 0.8475 (t80) cc_final: 0.8271 (t80) REVERT: A 339 VAL cc_start: 0.9395 (t) cc_final: 0.9123 (m) REVERT: A 341 ASP cc_start: 0.8750 (t0) cc_final: 0.8511 (t0) REVERT: B 59 TYR cc_start: 0.8608 (m-10) cc_final: 0.8088 (m-80) REVERT: B 127 LYS cc_start: 0.9250 (mttt) cc_final: 0.9040 (mttm) REVERT: B 138 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6893 (mt-10) REVERT: B 215 GLU cc_start: 0.7947 (tt0) cc_final: 0.7692 (tt0) REVERT: B 220 GLN cc_start: 0.8224 (mt0) cc_final: 0.8015 (mt0) REVERT: B 280 LYS cc_start: 0.9004 (tttt) cc_final: 0.8690 (ttmm) REVERT: B 322 ASP cc_start: 0.8593 (m-30) cc_final: 0.8380 (m-30) REVERT: F 60 TYR cc_start: 0.8925 (m-80) cc_final: 0.8477 (m-80) REVERT: F 191 ARG cc_start: 0.8214 (mtm-85) cc_final: 0.7981 (mtt90) REVERT: F 216 ILE cc_start: 0.8794 (mt) cc_final: 0.8487 (mt) REVERT: F 226 VAL cc_start: 0.8574 (t) cc_final: 0.8199 (m) REVERT: F 230 MET cc_start: 0.8640 (ttp) cc_final: 0.8297 (ttp) REVERT: F 231 GLN cc_start: 0.9193 (pp30) cc_final: 0.8608 (pp30) outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.1500 time to fit residues: 116.3332 Evaluate side-chains 425 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 255 GLN X 553 GLN X 693 GLN X 769 ASN A 195 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.069927 restraints weight = 42607.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.071707 restraints weight = 21824.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.072863 restraints weight = 13429.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.073583 restraints weight = 9622.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.074067 restraints weight = 7689.279| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19739 Z= 0.147 Angle : 0.587 11.493 26809 Z= 0.302 Chirality : 0.044 0.244 3037 Planarity : 0.004 0.040 3339 Dihedral : 9.664 82.871 3334 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.17 % Allowed : 9.66 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.17), residues: 2396 helix: 2.11 (0.17), residues: 924 sheet: -0.53 (0.25), residues: 422 loop : -0.17 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 242 TYR 0.034 0.001 TYR Y 645 PHE 0.018 0.001 PHE F 29 TRP 0.015 0.001 TRP A 211 HIS 0.015 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (19711) covalent geometry : angle 0.58083 / 0.30 (26745) SS BOND : bond 0.00678 / 0.51 ( 20) SS BOND : angle 1.48609 / 1.10 ( 40) hydrogen bonds : bond 0.04401 / 3.03 ( 949) hydrogen bonds : angle 4.58075 / 3.25 ( 2709) link_NAG-ASN : bond 0.00369 / 0.22 ( 8) link_NAG-ASN : angle 2.38452 / 1.52 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 429 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 207 LYS cc_start: 0.8055 (tttt) cc_final: 0.7703 (mtpt) REVERT: X 234 MET cc_start: 0.8196 (mtt) cc_final: 0.7730 (mtt) REVERT: X 238 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7051 (mm-30) REVERT: X 247 LYS cc_start: 0.8724 (pttt) cc_final: 0.8471 (pttm) REVERT: X 605 ARG cc_start: 0.8311 (ptt180) cc_final: 0.7718 (ptp90) REVERT: X 615 ARG cc_start: 0.7225 (ptm160) cc_final: 0.6813 (ptm160) REVERT: X 619 TYR cc_start: 0.8806 (m-10) cc_final: 0.8247 (m-80) REVERT: X 622 LEU cc_start: 0.9074 (mt) cc_final: 0.8432 (mm) REVERT: X 629 TYR cc_start: 0.8846 (m-80) cc_final: 0.8541 (m-80) REVERT: X 671 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7869 (mtp85) REVERT: X 688 MET cc_start: 0.7565 (mmm) cc_final: 0.7004 (mmm) REVERT: X 786 LEU cc_start: 0.9270 (mt) cc_final: 0.9059 (mp) REVERT: X 799 ILE cc_start: 0.8456 (mt) cc_final: 0.7802 (mm) REVERT: X 803 CYS cc_start: 0.8239 (m) cc_final: 0.7824 (m) REVERT: X 808 LEU cc_start: 0.8344 (mt) cc_final: 0.8115 (mp) REVERT: Y 366 ARG cc_start: 0.7778 (ptp-170) cc_final: 0.7460 (ptp90) REVERT: Y 571 GLN cc_start: 0.7240 (mp10) cc_final: 0.7001 (mp10) REVERT: Y 688 MET cc_start: 0.3525 (OUTLIER) cc_final: 0.2857 (mmp) REVERT: Y 797 TYR cc_start: 0.7498 (m-80) cc_final: 0.7239 (m-80) REVERT: Y 802 MET cc_start: 0.7755 (tpp) cc_final: 0.7554 (tpp) REVERT: A 17 LYS cc_start: 0.8861 (mttt) cc_final: 0.8546 (mmtp) REVERT: A 188 HIS cc_start: 0.7944 (t-90) cc_final: 0.7494 (t-170) REVERT: A 255 ASN cc_start: 0.8317 (m-40) cc_final: 0.7440 (m110) REVERT: A 341 ASP cc_start: 0.8466 (t0) cc_final: 0.8162 (t0) REVERT: B 17 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8576 (tm-30) REVERT: B 277 SER cc_start: 0.8903 (t) cc_final: 0.8595 (p) REVERT: B 322 ASP cc_start: 0.8299 (m-30) cc_final: 0.8096 (m-30) REVERT: G 20 LYS cc_start: 0.8937 (mtmt) cc_final: 0.8736 (mtmm) REVERT: F 208 SER cc_start: 0.7132 (p) cc_final: 0.6806 (m) REVERT: F 226 VAL cc_start: 0.8609 (t) cc_final: 0.8202 (m) REVERT: F 230 MET cc_start: 0.8525 (ttp) cc_final: 0.8224 (ttp) REVERT: F 231 GLN cc_start: 0.9191 (pp30) cc_final: 0.8776 (pp30) REVERT: F 243 THR cc_start: 0.8039 (m) cc_final: 0.7617 (p) outliers start: 24 outliers final: 14 residues processed: 436 average time/residue: 0.1524 time to fit residues: 98.6773 Evaluate side-chains 418 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 403 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 733 CYS Chi-restraints excluded: chain X residue 738 LEU Chi-restraints excluded: chain X residue 814 LEU Chi-restraints excluded: chain Y residue 688 MET Chi-restraints excluded: chain Y residue 698 PHE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [179, 117, 121, 134, 164, 195, 27, 147, 167, 21, 144] chunk 179 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 134 optimal weight: 0.3980 chunk 164 optimal weight: 0.9990 chunk 195 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 505 ASN Y 693 GLN A 195 HIS B 88 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.087843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.069072 restraints weight = 43187.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.071071 restraints weight = 20140.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.072353 restraints weight = 11862.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.073158 restraints weight = 8193.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.073656 restraints weight = 6357.583| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19739 Z= 0.141 Angle : 0.580 15.106 26809 Z= 0.297 Chirality : 0.044 0.241 3037 Planarity : 0.003 0.043 3339 Dihedral : 8.050 69.889 3334 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.99 % Allowed : 10.68 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.17), residues: 2396 helix: 2.03 (0.16), residues: 925 sheet: -0.37 (0.25), residues: 420 loop : -0.25 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 304 TYR 0.040 0.001 TYR Y 645 PHE 0.025 0.001 PHE F 29 TRP 0.014 0.001 TRP A 211 HIS 0.012 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (19711) covalent geometry : angle 0.57302 / 0.30 (26745) SS BOND : bond 0.00288 / 0.20 ( 20) SS BOND : angle 1.56064 / 1.05 ( 40) hydrogen bonds : bond 0.04199 / 2.92 ( 949) hydrogen bonds : angle 4.50701 / 3.21 ( 2709) link_NAG-ASN : bond 0.00381 / 0.22 ( 8) link_NAG-ASN : angle 2.29967 / 1.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 423 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 207 LYS cc_start: 0.8064 (tttt) cc_final: 0.7727 (mtpt) REVERT: X 234 MET cc_start: 0.8124 (mtt) cc_final: 0.7692 (mtt) REVERT: X 238 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7057 (mm-30) REVERT: X 247 LYS cc_start: 0.8809 (pttt) cc_final: 0.8552 (pttm) REVERT: X 605 ARG cc_start: 0.8340 (ptt180) cc_final: 0.7758 (ptp90) REVERT: X 615 ARG cc_start: 0.7268 (ptm160) cc_final: 0.6928 (ptm160) REVERT: X 619 TYR cc_start: 0.8823 (m-10) cc_final: 0.8243 (m-80) REVERT: X 627 LEU cc_start: 0.8577 (tp) cc_final: 0.8334 (tp) REVERT: X 629 TYR cc_start: 0.8851 (m-80) cc_final: 0.8500 (m-80) REVERT: X 641 GLN cc_start: 0.8018 (mp10) cc_final: 0.7759 (pm20) REVERT: X 786 LEU cc_start: 0.9256 (mt) cc_final: 0.9037 (mp) REVERT: X 799 ILE cc_start: 0.8478 (mt) cc_final: 0.7775 (mm) REVERT: X 803 CYS cc_start: 0.8304 (m) cc_final: 0.7962 (m) REVERT: X 808 LEU cc_start: 0.8304 (mt) cc_final: 0.8094 (mp) REVERT: Y 72 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8129 (ttt) REVERT: Y 94 GLU cc_start: 0.8093 (tt0) cc_final: 0.7853 (tt0) REVERT: Y 366 ARG cc_start: 0.7828 (ptp-170) cc_final: 0.7457 (ptp90) REVERT: Y 571 GLN cc_start: 0.7324 (mp10) cc_final: 0.7042 (mp10) REVERT: Y 802 MET cc_start: 0.7747 (tpp) cc_final: 0.7460 (tpp) REVERT: A 17 LYS cc_start: 0.8915 (mttt) cc_final: 0.8549 (mmtp) REVERT: A 241 ASN cc_start: 0.7659 (t0) cc_final: 0.6866 (t0) REVERT: A 254 CYS cc_start: 0.8994 (t) cc_final: 0.8666 (p) REVERT: A 255 ASN cc_start: 0.8298 (m-40) cc_final: 0.8079 (m-40) REVERT: A 341 ASP cc_start: 0.8516 (t0) cc_final: 0.8156 (t0) REVERT: B 17 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8569 (tm-30) REVERT: B 42 ARG cc_start: 0.7691 (ttt-90) cc_final: 0.6954 (ttt-90) REVERT: B 44 GLN cc_start: 0.8077 (pm20) cc_final: 0.7268 (pm20) REVERT: B 262 MET cc_start: 0.7495 (ttm) cc_final: 0.7157 (ttm) REVERT: G 20 LYS cc_start: 0.8974 (mtmt) cc_final: 0.8721 (mtmm) REVERT: F 5 VAL cc_start: 0.8413 (t) cc_final: 0.8073 (p) REVERT: F 60 TYR cc_start: 0.8939 (m-80) cc_final: 0.8457 (m-80) REVERT: F 208 SER cc_start: 0.7063 (p) cc_final: 0.6816 (m) REVERT: F 216 ILE cc_start: 0.8494 (mt) cc_final: 0.8291 (mt) REVERT: F 226 VAL cc_start: 0.8628 (t) cc_final: 0.8253 (m) REVERT: F 230 MET cc_start: 0.8541 (ttp) cc_final: 0.8287 (ttt) REVERT: F 231 GLN cc_start: 0.9236 (pp30) cc_final: 0.8704 (pp30) REVERT: F 243 THR cc_start: 0.8042 (m) cc_final: 0.7620 (p) outliers start: 41 outliers final: 28 residues processed: 438 average time/residue: 0.1527 time to fit residues: 100.3218 Evaluate side-chains 422 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 393 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 366 ARG Chi-restraints excluded: chain X residue 635 LEU Chi-restraints excluded: chain X residue 733 CYS Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 589 LEU Chi-restraints excluded: chain Y residue 643 TYR Chi-restraints excluded: chain Y residue 698 PHE Chi-restraints excluded: chain Y residue 707 ILE Chi-restraints excluded: chain Y residue 720 MET Chi-restraints excluded: chain Y residue 735 THR Chi-restraints excluded: chain Y residue 812 VAL Chi-restraints excluded: chain Y residue 816 CYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [139, 64, 12, 196, 208, 194, 95, 15, 40, 197, 212] chunk 139 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 194 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.0000 chunk 197 optimal weight: 0.9990 chunk 212 optimal weight: 6.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.088275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.069932 restraints weight = 42647.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.071752 restraints weight = 21349.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.072911 restraints weight = 13132.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.073569 restraints weight = 9389.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.074084 restraints weight = 7571.435| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19739 Z= 0.139 Angle : 0.588 16.149 26809 Z= 0.300 Chirality : 0.044 0.240 3037 Planarity : 0.003 0.042 3339 Dihedral : 7.170 69.067 3334 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.94 % Allowed : 11.84 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.17), residues: 2396 helix: 2.00 (0.17), residues: 932 sheet: -0.36 (0.25), residues: 420 loop : -0.29 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 313 TYR 0.042 0.001 TYR Y 645 PHE 0.019 0.001 PHE A 274 TRP 0.014 0.001 TRP A 211 HIS 0.011 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (19711) covalent geometry : angle 0.57996 / 0.30 (26745) SS BOND : bond 0.00259 / 0.18 ( 20) SS BOND : angle 1.82737 / 1.46 ( 40) hydrogen bonds : bond 0.04065 / 2.83 ( 949) hydrogen bonds : angle 4.45360 / 3.17 ( 2709) link_NAG-ASN : bond 0.00404 / 0.24 ( 8) link_NAG-ASN : angle 2.30780 / 1.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 406 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 207 LYS cc_start: 0.7995 (tttt) cc_final: 0.7708 (mtpt) REVERT: X 238 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7036 (mm-30) REVERT: X 605 ARG cc_start: 0.8287 (ptt180) cc_final: 0.7974 (ptp-170) REVERT: X 615 ARG cc_start: 0.7225 (ptm160) cc_final: 0.6813 (ptm160) REVERT: X 619 TYR cc_start: 0.8823 (m-10) cc_final: 0.8267 (m-80) REVERT: X 627 LEU cc_start: 0.8565 (tp) cc_final: 0.8313 (tp) REVERT: X 629 TYR cc_start: 0.8825 (m-80) cc_final: 0.8456 (m-80) REVERT: X 786 LEU cc_start: 0.9284 (mt) cc_final: 0.9058 (mp) REVERT: X 799 ILE cc_start: 0.8513 (mt) cc_final: 0.7840 (mm) REVERT: X 803 CYS cc_start: 0.8216 (m) cc_final: 0.7877 (m) REVERT: X 808 LEU cc_start: 0.8366 (mt) cc_final: 0.8136 (mp) REVERT: Y 72 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8080 (ttt) REVERT: Y 94 GLU cc_start: 0.8025 (tt0) cc_final: 0.7817 (tt0) REVERT: Y 366 ARG cc_start: 0.7775 (ptp-170) cc_final: 0.7405 (ptp90) REVERT: Y 571 GLN cc_start: 0.7367 (mp10) cc_final: 0.7119 (mp10) REVERT: Y 802 MET cc_start: 0.7785 (tpp) cc_final: 0.7557 (tpp) REVERT: A 17 LYS cc_start: 0.8905 (mttt) cc_final: 0.8566 (mmtp) REVERT: A 252 SER cc_start: 0.9084 (OUTLIER) cc_final: 0.8770 (p) REVERT: A 255 ASN cc_start: 0.8325 (m-40) cc_final: 0.8116 (m-40) REVERT: A 341 ASP cc_start: 0.8407 (t0) cc_final: 0.8063 (t0) REVERT: B 262 MET cc_start: 0.7386 (ttm) cc_final: 0.7140 (ttm) REVERT: B 277 SER cc_start: 0.8954 (t) cc_final: 0.8590 (p) REVERT: G 20 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8574 (mtmt) REVERT: F 5 VAL cc_start: 0.8267 (t) cc_final: 0.7848 (m) REVERT: F 60 TYR cc_start: 0.8937 (m-80) cc_final: 0.8524 (m-80) REVERT: F 220 GLU cc_start: 0.7518 (pm20) cc_final: 0.6973 (pm20) REVERT: F 226 VAL cc_start: 0.8662 (t) cc_final: 0.8305 (m) REVERT: F 230 MET cc_start: 0.8545 (ttp) cc_final: 0.8292 (ttt) REVERT: F 231 GLN cc_start: 0.9244 (pp30) cc_final: 0.8723 (pp30) REVERT: F 243 THR cc_start: 0.7991 (m) cc_final: 0.7594 (p) outliers start: 40 outliers final: 25 residues processed: 425 average time/residue: 0.1468 time to fit residues: 93.6203 Evaluate side-chains 415 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 388 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 366 ARG Chi-restraints excluded: chain X residue 384 SER Chi-restraints excluded: chain X residue 567 LEU Chi-restraints excluded: chain X residue 635 LEU Chi-restraints excluded: chain X residue 797 TYR Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 589 LEU Chi-restraints excluded: chain Y residue 643 TYR Chi-restraints excluded: chain Y residue 698 PHE Chi-restraints excluded: chain Y residue 812 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [64, 159, 219, 112, 26, 181, 1, 44, 48, 221, 229] chunk 64 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 221 optimal weight: 0.0060 chunk 229 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 721 HIS Y 693 GLN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.088019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.069745 restraints weight = 42599.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.071499 restraints weight = 21582.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.072622 restraints weight = 13530.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.073320 restraints weight = 9761.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.073796 restraints weight = 7821.724| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19739 Z= 0.147 Angle : 0.581 16.227 26809 Z= 0.298 Chirality : 0.044 0.248 3037 Planarity : 0.003 0.041 3339 Dihedral : 6.808 69.360 3334 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.33 % Allowed : 13.06 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.17), residues: 2396 helix: 2.03 (0.17), residues: 932 sheet: -0.22 (0.26), residues: 401 loop : -0.27 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 202 TYR 0.033 0.001 TYR Y 645 PHE 0.025 0.001 PHE F 29 TRP 0.013 0.001 TRP A 211 HIS 0.010 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (19711) covalent geometry : angle 0.57475 / 0.30 (26745) SS BOND : bond 0.00386 / 0.26 ( 20) SS BOND : angle 1.45652 / 1.19 ( 40) hydrogen bonds : bond 0.04049 / 2.81 ( 949) hydrogen bonds : angle 4.41000 / 3.14 ( 2709) link_NAG-ASN : bond 0.00388 / 0.23 ( 8) link_NAG-ASN : angle 2.32751 / 1.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 404 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 207 LYS cc_start: 0.8036 (tttt) cc_final: 0.7792 (mtpt) REVERT: X 238 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6976 (mm-30) REVERT: X 605 ARG cc_start: 0.8285 (ptt180) cc_final: 0.7949 (ptp-170) REVERT: X 615 ARG cc_start: 0.7196 (ptm160) cc_final: 0.6819 (ptm160) REVERT: X 619 TYR cc_start: 0.8829 (m-10) cc_final: 0.8288 (m-80) REVERT: X 627 LEU cc_start: 0.8625 (tp) cc_final: 0.8387 (tp) REVERT: X 629 TYR cc_start: 0.8831 (m-80) cc_final: 0.8466 (m-80) REVERT: X 698 PHE cc_start: 0.8211 (m-80) cc_final: 0.8005 (m-80) REVERT: X 786 LEU cc_start: 0.9275 (mt) cc_final: 0.9048 (mp) REVERT: X 803 CYS cc_start: 0.8234 (m) cc_final: 0.7928 (m) REVERT: X 808 LEU cc_start: 0.8334 (mt) cc_final: 0.8110 (mp) REVERT: Y 72 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8145 (ttt) REVERT: Y 94 GLU cc_start: 0.8057 (tt0) cc_final: 0.7848 (tt0) REVERT: Y 366 ARG cc_start: 0.7766 (ptp-170) cc_final: 0.7394 (ptp90) REVERT: Y 571 GLN cc_start: 0.7390 (mp10) cc_final: 0.7107 (mp10) REVERT: Y 688 MET cc_start: 0.3342 (OUTLIER) cc_final: 0.2606 (tpp) REVERT: Y 802 MET cc_start: 0.7781 (tpp) cc_final: 0.7563 (tpp) REVERT: A 17 LYS cc_start: 0.8914 (mttt) cc_final: 0.8544 (mmtp) REVERT: A 252 SER cc_start: 0.9083 (OUTLIER) cc_final: 0.8731 (p) REVERT: A 255 ASN cc_start: 0.8552 (m-40) cc_final: 0.8226 (m-40) REVERT: A 336 PHE cc_start: 0.8893 (t80) cc_final: 0.8573 (t80) REVERT: A 341 ASP cc_start: 0.8435 (t0) cc_final: 0.8085 (t0) REVERT: B 145 TYR cc_start: 0.9010 (p90) cc_final: 0.8706 (p90) REVERT: B 262 MET cc_start: 0.7415 (ttm) cc_final: 0.7141 (ttm) REVERT: B 277 SER cc_start: 0.8978 (t) cc_final: 0.8598 (p) REVERT: G 20 LYS cc_start: 0.8951 (mtmt) cc_final: 0.8581 (mtmt) REVERT: F 5 VAL cc_start: 0.8334 (t) cc_final: 0.7932 (m) REVERT: F 60 TYR cc_start: 0.8905 (m-80) cc_final: 0.8524 (m-80) REVERT: F 226 VAL cc_start: 0.8681 (t) cc_final: 0.8324 (m) REVERT: F 230 MET cc_start: 0.8573 (ttp) cc_final: 0.8286 (ttt) REVERT: F 231 GLN cc_start: 0.9246 (pp30) cc_final: 0.8679 (pp30) REVERT: F 243 THR cc_start: 0.8014 (m) cc_final: 0.7632 (p) outliers start: 48 outliers final: 36 residues processed: 425 average time/residue: 0.1487 time to fit residues: 94.7037 Evaluate side-chains 431 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 392 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 635 LEU Chi-restraints excluded: chain X residue 649 ILE Chi-restraints excluded: chain X residue 738 LEU Chi-restraints excluded: chain X residue 814 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 589 LEU Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 643 TYR Chi-restraints excluded: chain Y residue 688 MET Chi-restraints excluded: chain Y residue 698 PHE Chi-restraints excluded: chain Y residue 707 ILE Chi-restraints excluded: chain Y residue 714 MET Chi-restraints excluded: chain Y residue 720 MET Chi-restraints excluded: chain Y residue 764 VAL Chi-restraints excluded: chain Y residue 812 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [49, 182, 18, 208, 23, 97, 9, 55, 67, 195, 94] chunk 49 optimal weight: 4.9990 chunk 182 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 195 optimal weight: 0.0970 chunk 94 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 553 GLN Y 693 GLN A 195 HIS B 75 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.088213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.069904 restraints weight = 42615.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.071660 restraints weight = 21680.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.072800 restraints weight = 13514.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.073475 restraints weight = 9726.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.073967 restraints weight = 7847.912| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19739 Z= 0.149 Angle : 0.580 16.360 26809 Z= 0.299 Chirality : 0.044 0.268 3037 Planarity : 0.003 0.041 3339 Dihedral : 6.653 69.601 3334 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.38 % Allowed : 14.37 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.17), residues: 2396 helix: 2.03 (0.17), residues: 931 sheet: -0.25 (0.26), residues: 401 loop : -0.29 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 304 TYR 0.044 0.001 TYR Y 645 PHE 0.023 0.001 PHE F 29 TRP 0.013 0.001 TRP A 211 HIS 0.009 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (19711) covalent geometry : angle 0.57388 / 0.30 (26745) SS BOND : bond 0.00273 / 0.19 ( 20) SS BOND : angle 1.27665 / 0.95 ( 40) hydrogen bonds : bond 0.04020 / 2.81 ( 949) hydrogen bonds : angle 4.41389 / 3.15 ( 2709) link_NAG-ASN : bond 0.00382 / 0.23 ( 8) link_NAG-ASN : angle 2.35251 / 1.47 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 396 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 207 LYS cc_start: 0.8024 (tttt) cc_final: 0.7775 (mtpt) REVERT: X 238 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7018 (mm-30) REVERT: X 477 ASP cc_start: 0.6606 (m-30) cc_final: 0.6245 (m-30) REVERT: X 605 ARG cc_start: 0.8258 (ptt180) cc_final: 0.7973 (ptp-170) REVERT: X 615 ARG cc_start: 0.7211 (ptm160) cc_final: 0.6829 (ptm160) REVERT: X 619 TYR cc_start: 0.8829 (m-10) cc_final: 0.8294 (m-80) REVERT: X 627 LEU cc_start: 0.8654 (tp) cc_final: 0.8398 (tp) REVERT: X 629 TYR cc_start: 0.8820 (m-80) cc_final: 0.8433 (m-80) REVERT: X 698 PHE cc_start: 0.8195 (m-80) cc_final: 0.7993 (m-80) REVERT: X 720 MET cc_start: 0.8063 (ppp) cc_final: 0.7672 (ppp) REVERT: X 781 THR cc_start: 0.8779 (t) cc_final: 0.8566 (p) REVERT: X 786 LEU cc_start: 0.9260 (mt) cc_final: 0.9043 (mp) REVERT: X 803 CYS cc_start: 0.8265 (m) cc_final: 0.7947 (m) REVERT: X 808 LEU cc_start: 0.8334 (mt) cc_final: 0.8114 (mp) REVERT: Y 72 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8167 (ttt) REVERT: Y 366 ARG cc_start: 0.7756 (ptp-170) cc_final: 0.7366 (ptp90) REVERT: Y 414 MET cc_start: 0.8774 (ttt) cc_final: 0.8573 (ttt) REVERT: Y 571 GLN cc_start: 0.7403 (mp10) cc_final: 0.7121 (mp10) REVERT: Y 649 ILE cc_start: 0.8642 (mt) cc_final: 0.8369 (mm) REVERT: Y 802 MET cc_start: 0.7802 (tpp) cc_final: 0.7584 (tpp) REVERT: A 17 LYS cc_start: 0.8897 (mttt) cc_final: 0.8538 (mmtp) REVERT: A 188 HIS cc_start: 0.7921 (t-90) cc_final: 0.7652 (t-170) REVERT: A 252 SER cc_start: 0.9067 (t) cc_final: 0.8729 (p) REVERT: A 255 ASN cc_start: 0.8516 (m-40) cc_final: 0.8111 (m-40) REVERT: A 336 PHE cc_start: 0.8885 (t80) cc_final: 0.8587 (t80) REVERT: A 341 ASP cc_start: 0.8443 (t0) cc_final: 0.8101 (t0) REVERT: B 59 TYR cc_start: 0.8520 (m-80) cc_final: 0.8066 (m-80) REVERT: B 75 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8297 (mm110) REVERT: B 145 TYR cc_start: 0.9025 (p90) cc_final: 0.8625 (p90) REVERT: B 277 SER cc_start: 0.8969 (t) cc_final: 0.8596 (p) REVERT: B 280 LYS cc_start: 0.8520 (ttmm) cc_final: 0.7937 (ttmm) REVERT: G 20 LYS cc_start: 0.8902 (mtmt) cc_final: 0.8574 (mtmt) REVERT: F 5 VAL cc_start: 0.8307 (t) cc_final: 0.7887 (m) REVERT: F 60 TYR cc_start: 0.8902 (m-80) cc_final: 0.8544 (m-80) REVERT: F 226 VAL cc_start: 0.8698 (t) cc_final: 0.8297 (m) REVERT: F 230 MET cc_start: 0.8561 (ttp) cc_final: 0.8232 (ttp) REVERT: F 231 GLN cc_start: 0.9235 (pp30) cc_final: 0.8705 (pp30) REVERT: F 243 THR cc_start: 0.8029 (m) cc_final: 0.7627 (p) outliers start: 49 outliers final: 36 residues processed: 419 average time/residue: 0.1462 time to fit residues: 92.7333 Evaluate side-chains 422 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 384 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 366 ARG Chi-restraints excluded: chain X residue 567 LEU Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 635 LEU Chi-restraints excluded: chain X residue 649 ILE Chi-restraints excluded: chain X residue 738 LEU Chi-restraints excluded: chain X residue 782 CYS Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 416 MET Chi-restraints excluded: chain Y residue 589 LEU Chi-restraints excluded: chain Y residue 698 PHE Chi-restraints excluded: chain Y residue 707 ILE Chi-restraints excluded: chain Y residue 714 MET Chi-restraints excluded: chain Y residue 764 VAL Chi-restraints excluded: chain Y residue 812 VAL Chi-restraints excluded: chain Y residue 816 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [223, 26, 227, 168, 122, 130, 2, 178, 118, 57, 187] chunk 223 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 30 HIS ** Y 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS B 75 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.086398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.067938 restraints weight = 43044.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.069677 restraints weight = 22015.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.070776 restraints weight = 13770.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.071461 restraints weight = 9992.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.071914 restraints weight = 8050.784| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19739 Z= 0.244 Angle : 0.630 14.419 26809 Z= 0.326 Chirality : 0.046 0.268 3037 Planarity : 0.004 0.041 3339 Dihedral : 6.700 76.031 3334 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.33 % Allowed : 15.10 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.17), residues: 2396 helix: 1.92 (0.17), residues: 931 sheet: -0.39 (0.25), residues: 416 loop : -0.38 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 272 TYR 0.024 0.002 TYR F 94 PHE 0.026 0.002 PHE F 29 TRP 0.012 0.001 TRP B 82 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.24 (19711) covalent geometry : angle 0.62382 / 0.32 (26745) SS BOND : bond 0.00320 / 0.22 ( 20) SS BOND : angle 1.47471 / 1.08 ( 40) hydrogen bonds : bond 0.04467 / 3.12 ( 949) hydrogen bonds : angle 4.56271 / 3.26 ( 2709) link_NAG-ASN : bond 0.00426 / 0.26 ( 8) link_NAG-ASN : angle 2.47157 / 1.54 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 397 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 207 LYS cc_start: 0.8096 (tttt) cc_final: 0.7815 (mtpt) REVERT: X 238 GLU cc_start: 0.7527 (mm-30) cc_final: 0.6974 (mm-30) REVERT: X 477 ASP cc_start: 0.6643 (m-30) cc_final: 0.6371 (m-30) REVERT: X 615 ARG cc_start: 0.7301 (ptm160) cc_final: 0.6860 (ptm160) REVERT: X 619 TYR cc_start: 0.8842 (m-10) cc_final: 0.8336 (m-80) REVERT: X 627 LEU cc_start: 0.8746 (tp) cc_final: 0.8457 (tp) REVERT: X 629 TYR cc_start: 0.8850 (m-80) cc_final: 0.8470 (m-80) REVERT: X 786 LEU cc_start: 0.9265 (mt) cc_final: 0.9035 (mp) REVERT: X 799 ILE cc_start: 0.8541 (mt) cc_final: 0.7840 (mm) REVERT: X 803 CYS cc_start: 0.8388 (m) cc_final: 0.8025 (m) REVERT: X 808 LEU cc_start: 0.8354 (mt) cc_final: 0.8130 (mp) REVERT: Y 72 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8243 (ttt) REVERT: Y 366 ARG cc_start: 0.7794 (ptp-170) cc_final: 0.7403 (ptp90) REVERT: Y 414 MET cc_start: 0.8750 (ttt) cc_final: 0.8497 (ttt) REVERT: Y 571 GLN cc_start: 0.7380 (mp10) cc_final: 0.6986 (mp10) REVERT: Y 730 TYR cc_start: 0.7658 (m-10) cc_final: 0.7440 (m-10) REVERT: Y 802 MET cc_start: 0.7867 (tpp) cc_final: 0.7624 (tpp) REVERT: A 17 LYS cc_start: 0.8944 (mttt) cc_final: 0.8591 (mmtp) REVERT: A 188 HIS cc_start: 0.7968 (t-90) cc_final: 0.7658 (t-170) REVERT: A 252 SER cc_start: 0.9083 (t) cc_final: 0.8787 (p) REVERT: A 255 ASN cc_start: 0.8469 (m-40) cc_final: 0.8249 (m-40) REVERT: A 341 ASP cc_start: 0.8461 (t0) cc_final: 0.8133 (t0) REVERT: B 262 MET cc_start: 0.7374 (ttm) cc_final: 0.7093 (ttm) REVERT: B 280 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8271 (ttmm) REVERT: F 60 TYR cc_start: 0.8925 (m-80) cc_final: 0.8580 (m-80) REVERT: F 189 ILE cc_start: 0.8705 (mm) cc_final: 0.8501 (mm) REVERT: F 226 VAL cc_start: 0.8708 (t) cc_final: 0.8320 (m) REVERT: F 230 MET cc_start: 0.8583 (ttp) cc_final: 0.8250 (ttp) REVERT: F 231 GLN cc_start: 0.9233 (pp30) cc_final: 0.8680 (pp30) REVERT: F 243 THR cc_start: 0.8124 (m) cc_final: 0.7725 (p) outliers start: 48 outliers final: 37 residues processed: 417 average time/residue: 0.1450 time to fit residues: 92.1422 Evaluate side-chains 428 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 390 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 366 ARG Chi-restraints excluded: chain X residue 567 LEU Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 620 ILE Chi-restraints excluded: chain X residue 635 LEU Chi-restraints excluded: chain X residue 732 ILE Chi-restraints excluded: chain X residue 738 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 589 LEU Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 643 TYR Chi-restraints excluded: chain Y residue 698 PHE Chi-restraints excluded: chain Y residue 707 ILE Chi-restraints excluded: chain Y residue 714 MET Chi-restraints excluded: chain Y residue 764 VAL Chi-restraints excluded: chain Y residue 812 VAL Chi-restraints excluded: chain Y residue 824 ILE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [111, 189, 159, 207, 67, 237, 57, 100, 79, 120, 147] chunk 111 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 693 GLN A 195 HIS ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.087492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.069007 restraints weight = 42683.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.070741 restraints weight = 21964.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.071862 restraints weight = 13830.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.072573 restraints weight = 10052.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.072945 restraints weight = 8094.082| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19739 Z= 0.171 Angle : 0.618 14.918 26809 Z= 0.319 Chirality : 0.044 0.272 3037 Planarity : 0.004 0.041 3339 Dihedral : 6.556 75.844 3334 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.14 % Allowed : 16.36 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.17), residues: 2396 helix: 1.94 (0.17), residues: 933 sheet: -0.41 (0.26), residues: 416 loop : -0.41 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 272 TYR 0.039 0.001 TYR Y 645 PHE 0.051 0.001 PHE Y 818 TRP 0.013 0.001 TRP B 169 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (19711) covalent geometry : angle 0.61251 / 0.32 (26745) SS BOND : bond 0.00266 / 0.18 ( 20) SS BOND : angle 1.33056 / 0.94 ( 40) hydrogen bonds : bond 0.04193 / 2.92 ( 949) hydrogen bonds : angle 4.52009 / 3.23 ( 2709) link_NAG-ASN : bond 0.00376 / 0.23 ( 8) link_NAG-ASN : angle 2.44275 / 1.54 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 392 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 207 LYS cc_start: 0.8073 (tttt) cc_final: 0.7798 (mtpt) REVERT: X 238 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6941 (mm-30) REVERT: X 477 ASP cc_start: 0.6570 (m-30) cc_final: 0.6306 (m-30) REVERT: X 615 ARG cc_start: 0.7327 (ptm160) cc_final: 0.6982 (ptm160) REVERT: X 619 TYR cc_start: 0.8832 (m-10) cc_final: 0.8324 (m-80) REVERT: X 629 TYR cc_start: 0.8831 (m-80) cc_final: 0.8466 (m-80) REVERT: X 786 LEU cc_start: 0.9231 (mt) cc_final: 0.9016 (mp) REVERT: X 803 CYS cc_start: 0.8357 (m) cc_final: 0.8031 (m) REVERT: X 808 LEU cc_start: 0.8346 (mt) cc_final: 0.8125 (mp) REVERT: Y 72 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8120 (ttt) REVERT: Y 366 ARG cc_start: 0.7776 (ptp-170) cc_final: 0.7406 (ptp90) REVERT: Y 414 MET cc_start: 0.8756 (ttt) cc_final: 0.8498 (ttt) REVERT: Y 571 GLN cc_start: 0.7483 (mp10) cc_final: 0.7200 (mp10) REVERT: Y 649 ILE cc_start: 0.8521 (mt) cc_final: 0.8317 (mm) REVERT: Y 802 MET cc_start: 0.7829 (tpp) cc_final: 0.7626 (tpp) REVERT: A 17 LYS cc_start: 0.8918 (mttt) cc_final: 0.8558 (mmtp) REVERT: A 188 HIS cc_start: 0.7950 (t-90) cc_final: 0.7622 (t-170) REVERT: A 242 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7500 (mtt-85) REVERT: A 252 SER cc_start: 0.9072 (t) cc_final: 0.8741 (p) REVERT: A 255 ASN cc_start: 0.8585 (m-40) cc_final: 0.8203 (m-40) REVERT: A 341 ASP cc_start: 0.8512 (t0) cc_final: 0.8147 (t0) REVERT: B 145 TYR cc_start: 0.9059 (p90) cc_final: 0.8743 (p90) REVERT: B 262 MET cc_start: 0.7344 (ttm) cc_final: 0.7054 (ttm) REVERT: B 277 SER cc_start: 0.8966 (t) cc_final: 0.8581 (p) REVERT: B 280 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8308 (ttmm) REVERT: G 20 LYS cc_start: 0.8885 (mtmt) cc_final: 0.8336 (mtmm) REVERT: F 5 VAL cc_start: 0.8333 (t) cc_final: 0.7901 (m) REVERT: F 60 TYR cc_start: 0.8917 (m-80) cc_final: 0.8561 (m-80) REVERT: F 189 ILE cc_start: 0.8696 (mm) cc_final: 0.8488 (mm) REVERT: F 226 VAL cc_start: 0.8684 (t) cc_final: 0.8302 (m) REVERT: F 230 MET cc_start: 0.8566 (ttp) cc_final: 0.8237 (ttp) REVERT: F 231 GLN cc_start: 0.9237 (pp30) cc_final: 0.8709 (pp30) REVERT: F 243 THR cc_start: 0.8058 (m) cc_final: 0.7657 (p) outliers start: 44 outliers final: 36 residues processed: 410 average time/residue: 0.1438 time to fit residues: 89.0200 Evaluate side-chains 425 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 388 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 419 CYS Chi-restraints excluded: chain X residue 567 LEU Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 620 ILE Chi-restraints excluded: chain X residue 635 LEU Chi-restraints excluded: chain X residue 732 ILE Chi-restraints excluded: chain X residue 738 LEU Chi-restraints excluded: chain X residue 782 CYS Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 589 LEU Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 643 TYR Chi-restraints excluded: chain Y residue 698 PHE Chi-restraints excluded: chain Y residue 707 ILE Chi-restraints excluded: chain Y residue 764 VAL Chi-restraints excluded: chain Y residue 812 VAL Chi-restraints excluded: chain Y residue 816 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [229, 3, 163, 193, 86, 48, 24, 29, 76, 136, 176] chunk 229 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.087497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.068993 restraints weight = 42509.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.070723 restraints weight = 21787.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.071787 restraints weight = 13727.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.072515 restraints weight = 10018.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.072938 restraints weight = 8075.266| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19739 Z= 0.176 Angle : 0.629 15.183 26809 Z= 0.324 Chirality : 0.044 0.289 3037 Planarity : 0.004 0.041 3339 Dihedral : 6.488 75.858 3334 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.09 % Allowed : 16.50 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2396 helix: 1.92 (0.17), residues: 933 sheet: -0.42 (0.25), residues: 420 loop : -0.41 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 727 TYR 0.032 0.001 TYR Y 645 PHE 0.045 0.001 PHE Y 818 TRP 0.012 0.001 TRP A 211 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (19711) covalent geometry : angle 0.62303 / 0.32 (26745) SS BOND : bond 0.00269 / 0.18 ( 20) SS BOND : angle 1.32466 / 0.93 ( 40) hydrogen bonds : bond 0.04201 / 2.92 ( 949) hydrogen bonds : angle 4.52203 / 3.23 ( 2709) link_NAG-ASN : bond 0.00373 / 0.22 ( 8) link_NAG-ASN : angle 2.43327 / 1.53 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 389 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 207 LYS cc_start: 0.8063 (tttt) cc_final: 0.7794 (mtpt) REVERT: X 238 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6946 (mm-30) REVERT: X 477 ASP cc_start: 0.6573 (m-30) cc_final: 0.6317 (m-30) REVERT: X 615 ARG cc_start: 0.7322 (ptm160) cc_final: 0.6978 (ptm160) REVERT: X 619 TYR cc_start: 0.8853 (m-10) cc_final: 0.8306 (m-80) REVERT: X 629 TYR cc_start: 0.8786 (m-80) cc_final: 0.8433 (m-80) REVERT: X 786 LEU cc_start: 0.9220 (mt) cc_final: 0.8992 (mp) REVERT: X 803 CYS cc_start: 0.8377 (m) cc_final: 0.8028 (m) REVERT: Y 72 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8162 (ttt) REVERT: Y 366 ARG cc_start: 0.7752 (ptp-170) cc_final: 0.7389 (ptp90) REVERT: Y 414 MET cc_start: 0.8761 (ttt) cc_final: 0.8520 (ttt) REVERT: Y 571 GLN cc_start: 0.7418 (mp10) cc_final: 0.7199 (mp10) REVERT: Y 649 ILE cc_start: 0.8494 (mt) cc_final: 0.8275 (mm) REVERT: Y 802 MET cc_start: 0.7833 (tpp) cc_final: 0.7629 (tpp) REVERT: A 17 LYS cc_start: 0.8936 (mttt) cc_final: 0.8590 (mmtp) REVERT: A 186 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7384 (tm-30) REVERT: A 188 HIS cc_start: 0.7982 (t-90) cc_final: 0.7526 (t-170) REVERT: A 252 SER cc_start: 0.9072 (t) cc_final: 0.8747 (p) REVERT: A 255 ASN cc_start: 0.8581 (m-40) cc_final: 0.8169 (m-40) REVERT: A 341 ASP cc_start: 0.8516 (t0) cc_final: 0.8164 (t0) REVERT: B 42 ARG cc_start: 0.7757 (tmt170) cc_final: 0.7143 (tmt170) REVERT: B 145 TYR cc_start: 0.9078 (p90) cc_final: 0.8723 (p90) REVERT: B 262 MET cc_start: 0.7390 (ttm) cc_final: 0.7124 (ttm) REVERT: B 277 SER cc_start: 0.8970 (t) cc_final: 0.8589 (p) REVERT: B 280 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8375 (ttmm) REVERT: G 20 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8299 (mtmt) REVERT: F 5 VAL cc_start: 0.8303 (t) cc_final: 0.7903 (m) REVERT: F 60 TYR cc_start: 0.8919 (m-80) cc_final: 0.8563 (m-80) REVERT: F 189 ILE cc_start: 0.8695 (mm) cc_final: 0.8489 (mm) REVERT: F 226 VAL cc_start: 0.8686 (t) cc_final: 0.8307 (m) REVERT: F 230 MET cc_start: 0.8565 (ttp) cc_final: 0.8232 (ttp) REVERT: F 231 GLN cc_start: 0.9245 (pp30) cc_final: 0.8710 (pp30) REVERT: F 243 THR cc_start: 0.8062 (m) cc_final: 0.7671 (p) outliers start: 43 outliers final: 37 residues processed: 408 average time/residue: 0.1486 time to fit residues: 91.6216 Evaluate side-chains 422 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 384 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 419 CYS Chi-restraints excluded: chain X residue 567 LEU Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 620 ILE Chi-restraints excluded: chain X residue 635 LEU Chi-restraints excluded: chain X residue 738 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 505 ASN Chi-restraints excluded: chain Y residue 589 LEU Chi-restraints excluded: chain Y residue 643 TYR Chi-restraints excluded: chain Y residue 698 PHE Chi-restraints excluded: chain Y residue 707 ILE Chi-restraints excluded: chain Y residue 708 ILE Chi-restraints excluded: chain Y residue 764 VAL Chi-restraints excluded: chain Y residue 812 VAL Chi-restraints excluded: chain Y residue 816 CYS Chi-restraints excluded: chain Y residue 824 ILE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [49, 118, 183, 173, 168, 37, 76, 224, 204, 70, 74] chunk 49 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 224 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 693 GLN A 195 HIS ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.087043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.068548 restraints weight = 42643.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.070285 restraints weight = 21748.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.071368 restraints weight = 13645.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.072044 restraints weight = 9934.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.072513 restraints weight = 8061.562| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19739 Z= 0.201 Angle : 0.647 15.742 26809 Z= 0.333 Chirality : 0.045 0.300 3037 Planarity : 0.004 0.041 3339 Dihedral : 6.499 77.137 3334 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.94 % Allowed : 16.70 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.17), residues: 2396 helix: 1.87 (0.17), residues: 932 sheet: -0.45 (0.25), residues: 420 loop : -0.45 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 727 TYR 0.033 0.001 TYR Y 645 PHE 0.066 0.002 PHE Y 818 TRP 0.015 0.001 TRP B 82 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (19711) covalent geometry : angle 0.64181 / 0.33 (26745) SS BOND : bond 0.00282 / 0.19 ( 20) SS BOND : angle 1.38234 / 0.97 ( 40) hydrogen bonds : bond 0.04314 / 3.00 ( 949) hydrogen bonds : angle 4.56974 / 3.25 ( 2709) link_NAG-ASN : bond 0.00387 / 0.23 ( 8) link_NAG-ASN : angle 2.46246 / 1.55 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 387 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 207 LYS cc_start: 0.8083 (tttt) cc_final: 0.7768 (mtpt) REVERT: X 238 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6999 (mm-30) REVERT: X 477 ASP cc_start: 0.6605 (m-30) cc_final: 0.6346 (m-30) REVERT: X 615 ARG cc_start: 0.7347 (ptm160) cc_final: 0.6833 (ptm160) REVERT: X 619 TYR cc_start: 0.8847 (m-10) cc_final: 0.8277 (m-80) REVERT: X 786 LEU cc_start: 0.9210 (mt) cc_final: 0.8983 (mp) REVERT: X 803 CYS cc_start: 0.8399 (m) cc_final: 0.8020 (m) REVERT: Y 72 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8152 (ttt) REVERT: Y 366 ARG cc_start: 0.7757 (ptp-170) cc_final: 0.7411 (ptp90) REVERT: Y 414 MET cc_start: 0.8749 (ttt) cc_final: 0.8497 (ttt) REVERT: Y 571 GLN cc_start: 0.7453 (mp10) cc_final: 0.7236 (mp10) REVERT: Y 649 ILE cc_start: 0.8514 (mt) cc_final: 0.8279 (mm) REVERT: Y 802 MET cc_start: 0.7846 (tpp) cc_final: 0.7641 (tpp) REVERT: A 17 LYS cc_start: 0.8929 (mttt) cc_final: 0.8596 (mmtp) REVERT: A 186 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7416 (tm-30) REVERT: A 188 HIS cc_start: 0.8002 (t-90) cc_final: 0.7698 (t-170) REVERT: A 252 SER cc_start: 0.9039 (t) cc_final: 0.8788 (p) REVERT: A 255 ASN cc_start: 0.8508 (m-40) cc_final: 0.8306 (m-40) REVERT: A 256 ASN cc_start: 0.8940 (t0) cc_final: 0.8699 (t0) REVERT: A 341 ASP cc_start: 0.8525 (t0) cc_final: 0.8178 (t0) REVERT: B 42 ARG cc_start: 0.7754 (tmt170) cc_final: 0.7552 (ptm160) REVERT: B 277 SER cc_start: 0.8965 (t) cc_final: 0.8564 (p) REVERT: G 20 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8364 (mttt) REVERT: F 5 VAL cc_start: 0.8338 (t) cc_final: 0.7913 (m) REVERT: F 60 TYR cc_start: 0.8932 (m-80) cc_final: 0.8580 (m-80) REVERT: F 189 ILE cc_start: 0.8708 (mm) cc_final: 0.8490 (mm) REVERT: F 226 VAL cc_start: 0.8705 (t) cc_final: 0.8323 (m) REVERT: F 230 MET cc_start: 0.8564 (ttp) cc_final: 0.8226 (ttp) REVERT: F 231 GLN cc_start: 0.9241 (pp30) cc_final: 0.8702 (pp30) REVERT: F 243 THR cc_start: 0.8097 (m) cc_final: 0.7699 (p) outliers start: 40 outliers final: 36 residues processed: 405 average time/residue: 0.1480 time to fit residues: 90.9002 Evaluate side-chains 421 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 384 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 419 CYS Chi-restraints excluded: chain X residue 567 LEU Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 620 ILE Chi-restraints excluded: chain X residue 635 LEU Chi-restraints excluded: chain X residue 738 LEU Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 505 ASN Chi-restraints excluded: chain Y residue 589 LEU Chi-restraints excluded: chain Y residue 643 TYR Chi-restraints excluded: chain Y residue 698 PHE Chi-restraints excluded: chain Y residue 707 ILE Chi-restraints excluded: chain Y residue 708 ILE Chi-restraints excluded: chain Y residue 764 VAL Chi-restraints excluded: chain Y residue 812 VAL Chi-restraints excluded: chain Y residue 824 ILE Chi-restraints excluded: chain Y residue 825 ILE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [92, 167, 34, 85, 15, 196, 74, 22, 156, 50, 154] chunk 92 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 74 optimal weight: 0.0070 chunk 22 optimal weight: 0.7980 chunk 156 optimal weight: 0.2980 chunk 50 optimal weight: 0.2980 chunk 154 optimal weight: 5.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 45 HIS ** Y 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.088875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.070463 restraints weight = 42353.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.072194 restraints weight = 21631.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.073308 restraints weight = 13561.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.074004 restraints weight = 9832.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.074380 restraints weight = 7911.944| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19739 Z= 0.130 Angle : 0.627 13.670 26809 Z= 0.324 Chirality : 0.044 0.281 3037 Planarity : 0.004 0.046 3339 Dihedral : 6.297 72.859 3334 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.46 % Allowed : 17.43 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.17), residues: 2396 helix: 1.98 (0.17), residues: 932 sheet: -0.38 (0.26), residues: 413 loop : -0.39 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 202 TYR 0.051 0.001 TYR Y 645 PHE 0.067 0.001 PHE Y 818 TRP 0.018 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (19711) covalent geometry : angle 0.62161 / 0.32 (26745) SS BOND : bond 0.00235 / 0.16 ( 20) SS BOND : angle 1.18867 / 0.82 ( 40) hydrogen bonds : bond 0.03945 / 2.74 ( 949) hydrogen bonds : angle 4.47088 / 3.18 ( 2709) link_NAG-ASN : bond 0.00394 / 0.24 ( 8) link_NAG-ASN : angle 2.37897 / 1.51 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4055.69 seconds wall clock time: 70 minutes 35.45 seconds (4235.45 seconds total)