Starting phenix.real_space_refine on Tue Sep 15 04:51:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jga_22316/09_2026/7jga_22316.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jga_22316/09_2026/7jga_22316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7jga_22316/09_2026/7jga_22316.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jga_22316/09_2026/7jga_22316.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jga_22316/09_2026/7jga_22316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jga_22316/09_2026/7jga_22316.map" model { file = "/net/cci-nas-00/data/ceres_data/7jga_22316/09_2026/7jga_22316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jga_22316/09_2026/7jga_22316.cif" } resolution = 3.2 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= 0.009 sd= 0.248 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: 7 Type Number sf(0) Gaussians Br 7 7.06 5 P 12 5.49 5 Mg 4 5.21 5 S 103 5.16 5 C 22840 2.51 5 N 6208 2.21 5 O 6623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 211 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35797 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3841 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 492} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3756 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 486} Chain breaks: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "C" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3835 Classifications: {'peptide': 515} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3486 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ASP:plan': 11, 'GLU:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "E" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3516 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "F" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3489 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 55 Chain: "G" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2117 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 37 Chain: "H" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 820 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 74 Chain: "a" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1594 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 949 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 137} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 6, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 66 Chain: "d" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 2968 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 10, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 23, 'ARG:plan': 7, 'ASP:plan': 14, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 180 Chain: "1" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "3" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "4" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "6" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 554 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "8" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "9" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.10, per 1000 atoms: 0.23 Number of scatterers: 35797 At special positions: 0 Unit cell: (126.69, 133.9, 243.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 7 34.99 S 103 16.00 P 12 15.00 Mg 4 11.99 O 6623 8.00 N 6208 7.00 C 22840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8700 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 25 sheets defined 62.3% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 7 through 22 removed outlier: 3.695A pdb=" N ILE A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.876A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 226 through 230 removed outlier: 5.937A pdb=" N MET A 229 " --> pdb=" O GLY A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 Proline residue: A 250 - end of helix removed outlier: 3.707A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 298 through 299 No H-bonds generated for 'chain 'A' and resid 298 through 299' Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.612A pdb=" N HIS A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.976A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 404 removed outlier: 5.204A pdb=" N SER A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.505A pdb=" N ALA A 408 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 432 removed outlier: 3.831A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 removed outlier: 3.963A pdb=" N VAL A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 4.157A pdb=" N SER A 458 " --> pdb=" O HIS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.538A pdb=" N GLU A 473 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 4.361A pdb=" N PHE A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 509 Processing helix chain 'B' and resid 9 through 22 removed outlier: 3.870A pdb=" N PHE B 22 " --> pdb=" O TYR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 212 through 226 Processing helix chain 'B' and resid 227 through 230 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.528A pdb=" N LYS B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Proline residue: B 250 - end of helix removed outlier: 3.622A pdb=" N HIS B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.810A pdb=" N ARG B 307 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 392 through 408 Processing helix chain 'B' and resid 414 through 432 removed outlier: 3.564A pdb=" N ALA B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 removed outlier: 4.200A pdb=" N VAL B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 478 removed outlier: 3.518A pdb=" N GLU B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 493 through 511 removed outlier: 3.882A pdb=" N VAL B 503 " --> pdb=" O LYS B 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.503A pdb=" N ARG C 142 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 242 through 263 Proline residue: C 250 - end of helix removed outlier: 3.706A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 Processing helix chain 'C' and resid 293 through 297 removed outlier: 3.606A pdb=" N ALA C 296 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 299 No H-bonds generated for 'chain 'C' and resid 298 through 299' Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.830A pdb=" N HIS C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 307 " --> pdb=" O TYR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.626A pdb=" N GLY C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 removed outlier: 3.907A pdb=" N ASP C 336 " --> pdb=" O LYS C 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 339 through 349 removed outlier: 3.531A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 removed outlier: 3.540A pdb=" N GLN C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 408 Processing helix chain 'C' and resid 414 through 432 removed outlier: 3.630A pdb=" N ALA C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 removed outlier: 3.960A pdb=" N VAL C 446 " --> pdb=" O GLU C 442 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 458 removed outlier: 4.146A pdb=" N SER C 458 " --> pdb=" O HIS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 479 removed outlier: 3.602A pdb=" N GLU C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 490 removed outlier: 4.316A pdb=" N PHE C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 removed outlier: 3.538A pdb=" N LYS C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 91 through 95 removed outlier: 3.666A pdb=" N VAL D 94 " --> pdb=" O GLY D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 130 Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 165 through 180 Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 223 through 244 removed outlier: 3.675A pdb=" N ARG D 227 " --> pdb=" O PRO D 223 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 271 Processing helix chain 'D' and resid 282 through 292 Processing helix chain 'D' and resid 310 through 314 Processing helix chain 'D' and resid 317 through 325 Processing helix chain 'D' and resid 334 through 339 Processing helix chain 'D' and resid 362 through 389 removed outlier: 5.030A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 Processing helix chain 'D' and resid 395 through 412 removed outlier: 3.958A pdb=" N ARG D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG D 407 " --> pdb=" O ASN D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 422 Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.910A pdb=" N LYS D 441 " --> pdb=" O GLU D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 Processing helix chain 'D' and resid 460 through 471 removed outlier: 3.707A pdb=" N SER D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.516A pdb=" N LYS E 95 " --> pdb=" O ASP E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 165 through 177 removed outlier: 3.846A pdb=" N ASN E 175 " --> pdb=" O GLN E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 207 Processing helix chain 'E' and resid 208 through 211 removed outlier: 3.802A pdb=" N LYS E 211 " --> pdb=" O ASN E 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 223 through 244 removed outlier: 5.539A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 271 removed outlier: 4.062A pdb=" N THR E 260 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 292 Processing helix chain 'E' and resid 311 through 314 Processing helix chain 'E' and resid 317 through 324 Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 357 through 362 Processing helix chain 'E' and resid 362 through 390 removed outlier: 5.383A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE E 388 " --> pdb=" O ASP E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 412 removed outlier: 3.717A pdb=" N ARG E 404 " --> pdb=" O GLN E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 419 through 424 Processing helix chain 'E' and resid 431 through 445 Processing helix chain 'E' and resid 451 through 455 Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'F' and resid 25 through 29 removed outlier: 4.044A pdb=" N VAL F 29 " --> pdb=" O ARG F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'F' and resid 111 through 115 removed outlier: 4.355A pdb=" N ASP F 114 " --> pdb=" O TYR F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 130 removed outlier: 3.528A pdb=" N LEU F 130 " --> pdb=" O PHE F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'F' and resid 165 through 181 removed outlier: 4.090A pdb=" N ARG F 179 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 207 Processing helix chain 'F' and resid 208 through 211 removed outlier: 3.503A pdb=" N LYS F 211 " --> pdb=" O ASN F 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing helix chain 'F' and resid 223 through 244 removed outlier: 4.765A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 268 removed outlier: 4.006A pdb=" N THR F 260 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY F 263 " --> pdb=" O PHE F 259 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 292 Processing helix chain 'F' and resid 293 through 295 No H-bonds generated for 'chain 'F' and resid 293 through 295' Processing helix chain 'F' and resid 311 through 314 Processing helix chain 'F' and resid 317 through 324 Processing helix chain 'F' and resid 325 through 327 No H-bonds generated for 'chain 'F' and resid 325 through 327' Processing helix chain 'F' and resid 334 through 340 Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 362 through 389 removed outlier: 3.825A pdb=" N VAL F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 413 removed outlier: 3.768A pdb=" N ARG F 407 " --> pdb=" O ASN F 403 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG F 410 " --> pdb=" O ARG F 406 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 418 No H-bonds generated for 'chain 'F' and resid 416 through 418' Processing helix chain 'F' and resid 419 through 424 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 451 through 456 removed outlier: 3.798A pdb=" N PHE F 455 " --> pdb=" O GLU F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 469 Processing helix chain 'G' and resid 5 through 61 removed outlier: 3.793A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 90 through 111 removed outlier: 4.524A pdb=" N ALA G 94 " --> pdb=" O GLY G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 146 through 163 removed outlier: 3.529A pdb=" N ALA G 150 " --> pdb=" O THR G 146 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 303 removed outlier: 3.521A pdb=" N ALA G 234 " --> pdb=" O THR G 230 " (cutoff:3.500A) Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 91 through 100 removed outlier: 3.535A pdb=" N ALA H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 117 Processing helix chain 'a' and resid 32 through 53 removed outlier: 4.008A pdb=" N THR a 38 " --> pdb=" O ALA a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 109 removed outlier: 4.404A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL a 108 " --> pdb=" O ASN a 104 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU a 109 " --> pdb=" O TRP a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.893A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 157 through 165 Processing helix chain 'a' and resid 167 through 169 No H-bonds generated for 'chain 'a' and resid 167 through 169' Processing helix chain 'a' and resid 170 through 205 removed outlier: 3.703A pdb=" N ILE a 175 " --> pdb=" O ALA a 171 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL a 176 " --> pdb=" O PRO a 172 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 3.585A pdb=" N ARG a 188 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 246 removed outlier: 4.605A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.949A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 49 Processing helix chain 'b' and resid 49 through 161 removed outlier: 3.596A pdb=" N GLY b 143 " --> pdb=" O GLN b 139 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 137 Processing helix chain 'd' and resid 139 through 157 Processing helix chain 'd' and resid 173 through 193 removed outlier: 3.596A pdb=" N SER d 189 " --> pdb=" O GLU d 185 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY d 193 " --> pdb=" O SER d 189 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 216 removed outlier: 3.617A pdb=" N ASN d 201 " --> pdb=" O ASP d 197 " (cutoff:3.500A) Processing helix chain 'd' and resid 216 through 224 Processing helix chain 'd' and resid 230 through 242 Processing helix chain 'd' and resid 246 through 259 removed outlier: 3.839A pdb=" N THR d 255 " --> pdb=" O ASP d 251 " (cutoff:3.500A) Processing helix chain 'd' and resid 263 through 286 removed outlier: 3.952A pdb=" N LEU d 267 " --> pdb=" O THR d 263 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 288 through 306 removed outlier: 3.564A pdb=" N GLU d 293 " --> pdb=" O VAL d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 314 Processing helix chain 'd' and resid 319 through 331 removed outlier: 3.848A pdb=" N ARG d 323 " --> pdb=" O PRO d 319 " (cutoff:3.500A) Processing helix chain 'd' and resid 338 through 351 Processing helix chain 'd' and resid 356 through 373 Processing helix chain 'd' and resid 386 through 402 Processing helix chain 'd' and resid 431 through 442 Processing helix chain '1' and resid 6 through 46 removed outlier: 3.935A pdb=" N THR 1 10 " --> pdb=" O ASN 1 6 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA 1 13 " --> pdb=" O ILE 1 9 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY 1 18 " --> pdb=" O LEU 1 14 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY 1 23 " --> pdb=" O LEU 1 19 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY 1 33 " --> pdb=" O GLY 1 29 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA 1 38 " --> pdb=" O ILE 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 47 through 52 removed outlier: 4.382A pdb=" N GLY 1 51 " --> pdb=" O GLU 1 48 " (cutoff:3.500A) Processing helix chain '1' and resid 53 through 80 Processing helix chain '2' and resid 6 through 46 Processing helix chain '2' and resid 49 through 82 removed outlier: 3.738A pdb=" N PHE 2 54 " --> pdb=" O GLN 2 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR 2 55 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Proline residue: 2 56 - end of helix removed outlier: 3.600A pdb=" N LEU 2 63 " --> pdb=" O ILE 2 59 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA 2 67 " --> pdb=" O LEU 2 63 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE 2 70 " --> pdb=" O ALA 2 66 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 46 Processing helix chain '3' and resid 49 through 80 removed outlier: 3.675A pdb=" N PHE 3 54 " --> pdb=" O GLN 3 50 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR 3 55 " --> pdb=" O GLY 3 51 " (cutoff:3.500A) Proline residue: 3 56 - end of helix removed outlier: 4.243A pdb=" N ALA 3 67 " --> pdb=" O LEU 3 63 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR 3 68 " --> pdb=" O VAL 3 64 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE 3 70 " --> pdb=" O ALA 3 66 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU 3 77 " --> pdb=" O ALA 3 73 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 46 Processing helix chain '4' and resid 49 through 81 removed outlier: 4.215A pdb=" N THR 4 55 " --> pdb=" O GLY 4 51 " (cutoff:3.500A) Proline residue: 4 56 - end of helix Processing helix chain '5' and resid 6 through 46 removed outlier: 3.633A pdb=" N ALA 5 38 " --> pdb=" O ILE 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 81 removed outlier: 5.141A pdb=" N THR 5 55 " --> pdb=" O GLY 5 51 " (cutoff:3.500A) Proline residue: 5 56 - end of helix Processing helix chain '6' and resid 6 through 46 Processing helix chain '6' and resid 49 through 81 removed outlier: 3.565A pdb=" N PHE 6 54 " --> pdb=" O GLN 6 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR 6 55 " --> pdb=" O GLY 6 51 " (cutoff:3.500A) Proline residue: 6 56 - end of helix Processing helix chain '7' and resid 6 through 46 Processing helix chain '7' and resid 49 through 80 removed outlier: 4.291A pdb=" N THR 7 55 " --> pdb=" O GLY 7 51 " (cutoff:3.500A) Proline residue: 7 56 - end of helix Processing helix chain '8' and resid 6 through 45 Processing helix chain '8' and resid 46 through 48 No H-bonds generated for 'chain '8' and resid 46 through 48' Processing helix chain '8' and resid 49 through 81 removed outlier: 3.635A pdb=" N LEU 8 53 " --> pdb=" O ALA 8 49 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR 8 55 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) Proline residue: 8 56 - end of helix removed outlier: 3.852A pdb=" N ILE 8 70 " --> pdb=" O ALA 8 66 " (cutoff:3.500A) Processing helix chain '9' and resid 6 through 46 removed outlier: 3.813A pdb=" N ARG 9 45 " --> pdb=" O SER 9 41 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN 9 46 " --> pdb=" O GLY 9 42 " (cutoff:3.500A) Processing helix chain '9' and resid 49 through 80 removed outlier: 4.319A pdb=" N THR 9 55 " --> pdb=" O GLY 9 51 " (cutoff:3.500A) Proline residue: 9 56 - end of helix removed outlier: 3.586A pdb=" N TYR 9 68 " --> pdb=" O VAL 9 64 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE 9 70 " --> pdb=" O ALA 9 66 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 5.025A pdb=" N LEU A 55 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG A 93 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU A 30 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 36 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 64 removed outlier: 5.025A pdb=" N LEU A 55 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG A 93 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU A 30 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.715A pdb=" N VAL A 267 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU A 327 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE A 269 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE A 329 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE A 271 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLU A 331 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 69 removed outlier: 4.099A pdb=" N GLU B 54 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 55 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL B 34 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU B 69 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N THR E 80 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N GLU E 39 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR E 82 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N HIS E 37 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA E 84 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN E 34 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG E 63 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N HIS E 56 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU E 61 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLU E 23 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL E 12 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 102 Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.530A pdb=" N ILE B 330 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 149 removed outlier: 4.497A pdb=" N ILE B 162 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 351 through 352 Processing sheet with id=AB1, first strand: chain 'C' and resid 62 through 69 removed outlier: 4.091A pdb=" N GLU C 54 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU C 55 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N HIS C 43 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU F 78 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU F 39 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA F 35 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN F 34 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG F 63 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N HIS F 56 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU F 61 " --> pdb=" O HIS F 56 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLU F 23 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL F 12 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AB3, first strand: chain 'C' and resid 110 through 111 removed outlier: 3.729A pdb=" N ILE C 330 " --> pdb=" O ILE C 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 351 through 352 Processing sheet with id=AB5, first strand: chain 'C' and resid 534 through 540 removed outlier: 11.200A pdb=" N GLU C 534 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU C 536 " --> pdb=" O PRO G 205 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLN G 196 " --> pdb=" O ARG G 191 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ARG G 191 " --> pdb=" O GLN G 196 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA G 198 " --> pdb=" O GLU G 189 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU G 189 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA G 200 " --> pdb=" O PHE G 187 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N PHE G 187 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ARG G 202 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE G 185 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG G 76 " --> pdb=" O GLU G 182 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N PHE G 190 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA G 77 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N TYR G 117 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL G 79 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL G 81 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N VAL G 135 " --> pdb=" O PRO G 114 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU G 116 " --> pdb=" O VAL G 135 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N SER G 137 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL G 118 " --> pdb=" O SER G 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 16 removed outlier: 6.683A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU D 61 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N HIS D 56 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG D 63 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN D 34 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA D 35 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU D 39 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU D 78 " --> pdb=" O GLU D 39 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 87 through 90 removed outlier: 4.100A pdb=" N GLU D 116 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 98 through 99 removed outlier: 6.406A pdb=" N PHE D 99 " --> pdb=" O PHE D 217 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLN D 219 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER D 185 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL D 216 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE D 187 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLY D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY D 189 " --> pdb=" O GLY D 218 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE D 156 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS D 155 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR D 331 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA D 157 " --> pdb=" O THR D 331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 87 through 90 removed outlier: 4.094A pdb=" N GLU E 116 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 100 removed outlier: 6.633A pdb=" N SER E 185 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL E 216 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE E 187 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLY E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY E 189 " --> pdb=" O GLY E 218 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N TYR E 309 " --> pdb=" O ILE E 253 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE E 156 " --> pdb=" O GLN E 306 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL E 308 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU E 158 " --> pdb=" O VAL E 308 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS E 155 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N THR E 331 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA E 157 " --> pdb=" O THR E 331 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 136 through 137 removed outlier: 4.272A pdb=" N TYR E 150 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 87 through 90 removed outlier: 4.076A pdb=" N GLU F 116 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.377A pdb=" N PHE F 99 " --> pdb=" O PHE F 217 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS F 155 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR F 331 " --> pdb=" O LYS F 155 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA F 157 " --> pdb=" O THR F 331 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 136 through 137 removed outlier: 4.249A pdb=" N TYR F 150 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 223 through 225 removed outlier: 3.860A pdb=" N GLN H 44 " --> pdb=" O GLU G 225 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 30 through 34 removed outlier: 3.769A pdb=" N PHE H 22 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA H 49 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN H 83 " --> pdb=" O ASP H 66 " (cutoff:3.500A) 2417 hydrogen bonds defined for protein. 6933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.25 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 12116 1.36 - 1.51: 10684 1.51 - 1.65: 13428 1.65 - 1.80: 121 1.80 - 1.94: 73 Bond restraints: 36422 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.93e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.47e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.44e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.466 -0.057 1.00e-02 1.00e+04 3.21e+01 ... (remaining 36417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 49388 4.72 - 9.44: 96 9.44 - 14.16: 0 14.16 - 18.88: 3 18.88 - 23.60: 3 Bond angle restraints: 49490 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.27 23.60 1.00e+00 1.00e+00 5.57e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 117.34 22.53 1.00e+00 1.00e+00 5.07e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 119.02 20.85 1.00e+00 1.00e+00 4.35e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 118.21 18.62 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 118.28 18.55 1.00e+00 1.00e+00 3.44e+02 ... (remaining 49485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.18: 19940 19.18 - 38.36: 1178 38.36 - 57.55: 219 57.55 - 76.73: 88 76.73 - 95.91: 53 Dihedral angle restraints: 21478 sinusoidal: 7901 harmonic: 13577 Sorted by residual: dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 -149.62 89.63 1 2.00e+01 2.50e-03 2.38e+01 dihedral pdb=" CA ALA F 276 " pdb=" C ALA F 276 " pdb=" N VAL F 277 " pdb=" CA VAL F 277 " ideal model delta harmonic sigma weight residual -180.00 -155.63 -24.37 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLN E 247 " pdb=" C GLN E 247 " pdb=" N ASP E 248 " pdb=" CA ASP E 248 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 21475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 5445 0.086 - 0.171: 346 0.171 - 0.257: 9 0.257 - 0.343: 5 0.343 - 0.429: 5 Chirality restraints: 5810 Sorted by residual: chirality pdb=" C07 BQ1 6 601 " pdb=" C06 BQ1 6 601 " pdb=" C10 BQ1 6 601 " pdb=" C12 BQ1 6 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.83 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" C07 BQ1 4 601 " pdb=" C06 BQ1 4 601 " pdb=" C10 BQ1 4 601 " pdb=" C12 BQ1 4 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.82 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA PRO b 51 " pdb=" N PRO b 51 " pdb=" C PRO b 51 " pdb=" CB PRO b 51 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 5807 not shown) Planarity restraints: 6389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 284 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C ALA E 284 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA E 284 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP E 285 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 85 " 0.008 2.00e-02 2.50e+03 1.47e-02 4.33e+00 pdb=" CG TYR b 85 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR b 85 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR b 85 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR b 85 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR b 85 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR b 85 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR b 85 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG d 27 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C ARG d 27 " 0.034 2.00e-02 2.50e+03 pdb=" O ARG d 27 " -0.013 2.00e-02 2.50e+03 pdb=" N THR d 28 " -0.012 2.00e-02 2.50e+03 ... (remaining 6386 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 68 2.39 - 3.02: 22654 3.02 - 3.65: 54412 3.65 - 4.27: 84939 4.27 - 4.90: 142668 Nonbonded interactions: 304741 Sorted by model distance: nonbonded pdb=" O1B ATP A 600 " pdb="MG MG A 601 " model vdw 1.768 2.170 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.836 2.170 nonbonded pdb=" OH TYR 7 68 " pdb=" OD1 ASN 8 71 " model vdw 1.879 3.040 nonbonded pdb=" O ALA H 29 " pdb=" NH2 ARG 3 45 " model vdw 1.907 3.120 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.956 2.170 ... (remaining 304736 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 '1' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '2' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '3' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and (n \ ame N or name CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '4' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '5' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and (n \ ame N or name CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '6' and (resid 5 through 47 or (resid 48 through 49 and (name N or name C \ A or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and (nam \ e N or name CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '7' and (resid 5 through 47 or (resid 48 through 49 and (name N or name C \ A or name C or name O or name CB )) or resid 50 through 85)) selection = (chain '8' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '9' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) } ncs_group { reference = (chain 'A' and ((resid 9 through 17 and (name N or name CA or name C or name O o \ r name CB )) or resid 18 or (resid 19 through 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 or (resid 29 and (name N or name CA or nam \ e C or name O or name CB )) or resid 30 through 38 or (resid 39 and (name N or n \ ame CA or name C or name O or name CB )) or resid 40 through 44 or (resid 45 and \ (name N or name CA or name C or name O or name CB )) or resid 46 through 80 or \ (resid 81 and (name N or name CA or name C or name O or name CB )) or resid 82 t \ hrough 132 or (resid 133 and (name N or name CA or name C or name O or name CB ) \ ) or resid 134 through 190 or (resid 191 through 192 and (name N or name CA or n \ ame C or name O or name CB )) or resid 193 through 294 or (resid 295 through 296 \ and (name N or name CA or name C or name O or name CB )) or resid 297 through 3 \ 16 or (resid 317 through 318 and (name N or name CA or name C or name O or name \ CB )) or resid 319 through 355 or (resid 356 and (name N or name CA or name C or \ name O or name CB )) or resid 357 or (resid 358 and (name N or name CA or name \ C or name O or name CB )) or resid 359 through 401 or (resid 402 and (name N or \ name CA or name C or name O or name CB )) or resid 403 through 411 or (resid 412 \ and (name N or name CA or name C or name O or name CB )) or resid 413 through 4 \ 16 or (resid 417 through 419 and (name N or name CA or name C or name O or name \ CB )) or resid 420 through 456 or (resid 457 and (name N or name CA or name C or \ name O or name CB )) or resid 458 through 467 or (resid 468 and (name N or name \ CA or name C or name O or name CB )) or resid 469 through 475 or (resid 476 thr \ ough 477 and (name N or name CA or name C or name O or name CB )) or resid 478 t \ hrough 493 or (resid 494 through 499 and (name N or name CA or name C or name O \ or name CB )) or resid 500 through 505 or (resid 506 and (name N or name CA or n \ ame C or name O or name CB )) or resid 507 through 514 or (resid 515 and (name N \ or name CA or name C or name O or name CB )) or resid 518 through 601)) selection = (chain 'B' and (resid 9 through 18 or (resid 19 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 or resid 29 through 38 or (resid \ 39 and (name N or name CA or name C or name O or name CB )) or resid 40 through \ 80 or (resid 81 and (name N or name CA or name C or name O or name CB )) or res \ id 82 through 190 or (resid 191 through 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 316 or (resid 317 through 318 and (nam \ e N or name CA or name C or name O or name CB )) or resid 319 through 400 or (re \ sid 401 through 402 and (name N or name CA or name C or name O or name CB )) or \ resid 403 through 413 or (resid 414 through 419 and (name N or name CA or name C \ or name O or name CB )) or resid 420 through 456 or (resid 457 and (name N or n \ ame CA or name C or name O or name CB )) or resid 458 through 469 or (resid 470 \ and (name N or name CA or name C or name O or name CB )) or resid 471 through 49 \ 3 or (resid 494 through 499 and (name N or name CA or name C or name O or name C \ B )) or resid 500 through 514 or (resid 515 and (name N or name CA or name C or \ name O or name CB )) or resid 518 through 601)) selection = (chain 'C' and (resid 9 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 132 or (resid 133 and (name N or na \ me CA or name C or name O or name CB )) or resid 134 through 294 or (resid 295 t \ hrough 296 and (name N or name CA or name C or name O or name CB )) or resid 297 \ through 355 or (resid 356 and (name N or name CA or name C or name O or name CB \ )) or resid 357 or (resid 358 and (name N or name CA or name C or name O or nam \ e CB )) or resid 359 through 400 or (resid 401 through 402 and (name N or name C \ A or name C or name O or name CB )) or resid 403 through 411 or (resid 412 and ( \ name N or name CA or name C or name O or name CB )) or resid 413 or (resid 414 t \ hrough 419 and (name N or name CA or name C or name O or name CB )) or resid 420 \ through 461 or (resid 462 through 463 and (name N or name CA or name C or name \ O or name CB )) or resid 464 through 467 or (resid 468 and (name N or name CA or \ name C or name O or name CB )) or resid 469 or (resid 470 and (name N or name C \ A or name C or name O or name CB )) or resid 471 through 475 or (resid 476 throu \ gh 477 and (name N or name CA or name C or name O or name CB )) or resid 478 thr \ ough 494 or (resid 495 through 499 and (name N or name CA or name C or name O or \ name CB )) or resid 500 through 505 or (resid 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 515 or resid 537 through 538 or \ resid 540 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 through 104 or (resid 105 and (name N or na \ me CA or name C or name O or name CB )) or resid 106 through 137 or (resid 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 220 \ or (resid 221 through 222 and (name N or name CA or name C or name O or name CB \ )) or resid 223 through 253 or (resid 254 and (name N or name CA or name C or n \ ame O or name CB )) or resid 255 through 285 or (resid 286 and (name N or name C \ A or name C or name O or name CB )) or resid 287 through 288 or (resid 289 and ( \ name N or name CA or name C or name O or name CB )) or resid 290 through 291 or \ (resid 292 and (name N or name CA or name C or name O or name CB )) or resid 293 \ through 370 or (resid 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 395 or (resid 396 through 398 and (name N or name CA or \ name C or name O or name CB )) or resid 399 through 461 or (resid 462 through 4 \ 63 and (name N or name CA or name C or name O or name CB )) or resid 464 through \ 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) or r \ esid 467 through 471)) selection = (chain 'E' and (resid 8 through 103 or (resid 104 through 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 through 107 or (resid 108 an \ d (name N or name CA or name C or name O or name CB )) or resid 109 through 113 \ or (resid 114 and (name N or name CA or name C or name O or name CB )) or resid \ 115 through 134 or (resid 135 and (name N or name CA or name C or name O or name \ CB )) or resid 136 through 137 or (resid 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 198 or (resid 199 and (name N or nam \ e CA or name C or name O or name CB )) or resid 200 through 202 or (resid 203 an \ d (name N or name CA or name C or name O or name CB )) or resid 204 through 205 \ or (resid 206 through 207 and (name N or name CA or name C or name O or name CB \ )) or resid 208 through 220 or (resid 221 through 222 and (name N or name CA or \ name C or name O or name CB )) or resid 223 through 291 or (resid 292 and (name \ N or name CA or name C or name O or name CB )) or resid 293 through 369 or (resi \ d 370 through 371 and (name N or name CA or name C or name O or name CB )) or re \ sid 372 through 380 or (resid 381 and (name N or name CA or name C or name O or \ name CB )) or resid 382 through 383 or (resid 384 and (name N or name CA or name \ C or name O or name CB )) or resid 385 through 391 or (resid 392 through 393 an \ d (name N or name CA or name C or name O or name CB )) or resid 394 through 395 \ or (resid 396 through 398 and (name N or name CA or name C or name O or name CB \ )) or resid 399 through 402 or (resid 403 and (name N or name CA or name C or na \ me O or name CB )) or resid 404 through 432 or (resid 433 and (name N or name CA \ or name C or name O or name CB )) or resid 434 through 461 or (resid 462 throug \ h 463 and (name N or name CA or name C or name O or name CB )) or resid 464 thro \ ugh 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) o \ r resid 467 through 471)) selection = (chain 'F' and (resid 8 through 103 or (resid 104 through 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 or (resid 107 through 108 an \ d (name N or name CA or name C or name O or name CB )) or resid 109 through 113 \ or (resid 114 and (name N or name CA or name C or name O or name CB )) or resid \ 115 through 198 or (resid 199 and (name N or name CA or name C or name O or name \ CB )) or resid 200 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 205 or (resid 206 through 207 and (n \ ame N or name CA or name C or name O or name CB )) or resid 208 through 253 or ( \ resid 254 and (name N or name CA or name C or name O or name CB )) or resid 255 \ through 285 or (resid 286 and (name N or name CA or name C or name O or name CB \ )) or resid 287 through 362 or (resid 363 through 364 and (name N or name CA or \ name C or name O or name CB )) or resid 365 through 369 or (resid 370 through 37 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 372 through \ 380 or (resid 381 and (name N or name CA or name C or name O or name CB )) or re \ sid 382 through 391 or (resid 392 through 393 and (name N or name CA or name C o \ r name O or name CB )) or resid 394 through 402 or (resid 403 and (name N or nam \ e CA or name C or name O or name CB )) or resid 404 through 424 or (resid 425 an \ d (name N or name CA or name C or name O or name CB )) or resid 426 through 471) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 34.780 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 : 0.011 0.902 36425 Z= 0.837 Angle : 0.786 23.598 49490 Z= 0.498 Chirality : 0.047 0.429 5810 Planarity : 0.004 0.078 6389 Dihedral : 14.544 95.910 12778 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.05 % Favored : 97.80 % Rotamer: Outliers : 0.14 % Allowed : 4.86 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % 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: -1.98 (0.11), residues: 4774 helix: -1.14 (0.09), residues: 2551 sheet: -1.19 (0.21), residues: 514 loop : -1.34 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 167 TYR 0.024 0.002 TYR b 85 PHE 0.032 0.002 PHE a 99 TRP 0.010 0.002 TRP a 212 HIS 0.010 0.001 HIS d 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.36 (36422) covalent geometry : angle 0.78603 / 0.50 (49490) hydrogen bonds : bond 0.14744 / 9.86 ( 2408) hydrogen bonds : angle 7.35703 / 5.18 ( 6933) Misc. bond : bond 0.83275 / 41.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 865 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8545 (mm110) cc_final: 0.8162 (mm-40) REVERT: A 71 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7597 (mt-10) REVERT: A 77 VAL cc_start: 0.8656 (p) cc_final: 0.8435 (m) REVERT: A 133 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6679 (mt-10) REVERT: A 160 THR cc_start: 0.8099 (p) cc_final: 0.7802 (t) REVERT: A 184 ASP cc_start: 0.6695 (m-30) cc_final: 0.6399 (m-30) REVERT: A 200 GLN cc_start: 0.8403 (mt0) cc_final: 0.8158 (mm110) REVERT: A 336 ASP cc_start: 0.7578 (t0) cc_final: 0.7303 (t0) REVERT: A 356 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7132 (mt-10) REVERT: A 372 VAL cc_start: 0.8204 (t) cc_final: 0.7854 (p) REVERT: A 384 LYS cc_start: 0.7848 (mmmt) cc_final: 0.7647 (tptp) REVERT: A 388 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7575 (mt-10) REVERT: A 429 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7447 (mm-30) REVERT: A 473 GLU cc_start: 0.8141 (tp30) cc_final: 0.7881 (tt0) REVERT: A 498 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7107 (mm-30) REVERT: B 19 VAL cc_start: 0.8176 (t) cc_final: 0.7907 (t) REVERT: B 194 LEU cc_start: 0.8340 (mt) cc_final: 0.8016 (mt) REVERT: B 348 ILE cc_start: 0.8132 (mt) cc_final: 0.7891 (mt) REVERT: B 349 THR cc_start: 0.8752 (p) cc_final: 0.8430 (p) REVERT: B 393 LEU cc_start: 0.6849 (tp) cc_final: 0.6585 (tp) REVERT: B 488 GLU cc_start: 0.7299 (tt0) cc_final: 0.6800 (pt0) REVERT: C 44 VAL cc_start: 0.8358 (t) cc_final: 0.8054 (m) REVERT: C 83 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7275 (mt-10) REVERT: C 300 ASP cc_start: 0.8271 (p0) cc_final: 0.7761 (p0) REVERT: C 335 ASN cc_start: 0.8837 (t0) cc_final: 0.8620 (t0) REVERT: C 365 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7608 (mtt-85) REVERT: C 399 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7474 (mm-40) REVERT: C 491 LYS cc_start: 0.8529 (mttp) cc_final: 0.8302 (mtmm) REVERT: D 67 MET cc_start: 0.8393 (mmp) cc_final: 0.8187 (mmt) REVERT: D 120 ILE cc_start: 0.8248 (pt) cc_final: 0.8045 (pt) REVERT: D 173 MET cc_start: 0.7771 (mmm) cc_final: 0.7226 (mmt) REVERT: D 179 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7476 (mtm180) REVERT: D 185 SER cc_start: 0.8700 (t) cc_final: 0.8304 (m) REVERT: D 222 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7602 (mt-10) REVERT: D 233 SER cc_start: 0.8112 (t) cc_final: 0.7482 (m) REVERT: D 237 MET cc_start: 0.7963 (mtt) cc_final: 0.7736 (mtp) REVERT: D 287 MET cc_start: 0.8326 (tpp) cc_final: 0.8067 (tpt) REVERT: D 292 GLU cc_start: 0.7495 (tp30) cc_final: 0.7263 (tp30) REVERT: D 305 MET cc_start: 0.8055 (mtp) cc_final: 0.7773 (mtp) REVERT: D 342 ILE cc_start: 0.7968 (mm) cc_final: 0.7737 (mt) REVERT: D 398 ASP cc_start: 0.6697 (m-30) cc_final: 0.6461 (m-30) REVERT: D 432 LEU cc_start: 0.7764 (tp) cc_final: 0.7531 (tp) REVERT: D 441 LYS cc_start: 0.7455 (mtpt) cc_final: 0.6620 (mttp) REVERT: D 447 PHE cc_start: 0.8235 (m-80) cc_final: 0.7810 (m-10) REVERT: D 456 PHE cc_start: 0.8226 (m-80) cc_final: 0.7944 (m-80) REVERT: E 279 TYR cc_start: 0.8378 (m-80) cc_final: 0.8120 (m-80) REVERT: E 315 TYR cc_start: 0.8439 (m-80) cc_final: 0.7753 (m-80) REVERT: E 332 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6875 (mt-10) REVERT: E 440 ASP cc_start: 0.7948 (t70) cc_final: 0.7696 (t70) REVERT: E 453 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8076 (mm-40) REVERT: E 457 LEU cc_start: 0.8722 (mt) cc_final: 0.8428 (mp) REVERT: F 66 SER cc_start: 0.8643 (m) cc_final: 0.8329 (p) REVERT: F 193 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7235 (mtt-85) REVERT: F 239 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6879 (mt-10) REVERT: F 458 ILE cc_start: 0.8404 (tp) cc_final: 0.8082 (tp) REVERT: G 26 GLU cc_start: 0.6717 (tt0) cc_final: 0.6385 (tt0) REVERT: G 41 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7074 (tm-30) REVERT: G 85 ASP cc_start: 0.7256 (t70) cc_final: 0.6314 (t0) REVERT: G 121 ARG cc_start: 0.7568 (ttm-80) cc_final: 0.7254 (mtp180) REVERT: G 136 GLU cc_start: 0.7736 (tp30) cc_final: 0.7479 (tp30) REVERT: G 162 MET cc_start: 0.7159 (mtp) cc_final: 0.6909 (mtp) REVERT: G 255 GLU cc_start: 0.7536 (tt0) cc_final: 0.7259 (tt0) REVERT: H 7 GLU cc_start: 0.6986 (tt0) cc_final: 0.6609 (mt-10) REVERT: a 100 ILE cc_start: 0.7257 (tp) cc_final: 0.6957 (mp) REVERT: a 163 VAL cc_start: 0.6323 (t) cc_final: 0.6013 (p) REVERT: d 132 ILE cc_start: 0.6366 (mt) cc_final: 0.6129 (mt) REVERT: d 298 ARG cc_start: 0.7275 (ttt90) cc_final: 0.6668 (ttm170) outliers start: 5 outliers final: 2 residues processed: 869 average time/residue: 0.2512 time to fit residues: 347.4197 Evaluate side-chains 603 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 600 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain d residue 253 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.6980 chunk 470 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 259 HIS B 143 GLN B 188 ASN B 201 GLN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 435 GLN B 465 GLN C 112 ASN D 68 GLN D 377 GLN D 421 GLN E 326 HIS F 326 HIS F 370 GLN F 400 GLN G 93 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN d 104 GLN d 116 GLN d 222 HIS d 410 HIS 1 6 ASN 3 50 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.112351 restraints weight = 50378.785| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.89 r_work: 0.3195 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 36425 Z= 0.173 Angle : 0.641 10.433 49490 Z= 0.332 Chirality : 0.044 0.222 5810 Planarity : 0.005 0.047 6389 Dihedral : 5.875 113.347 5171 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.55 % Favored : 98.26 % Rotamer: Outliers : 1.72 % Allowed : 10.69 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % 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: 0.10 (0.12), residues: 4774 helix: 0.65 (0.10), residues: 2594 sheet: -0.92 (0.21), residues: 529 loop : -0.32 (0.16), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 426 TYR 0.026 0.002 TYR a 145 PHE 0.026 0.002 PHE a 99 TRP 0.014 0.001 TRP a 212 HIS 0.005 0.001 HIS a 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (36422) covalent geometry : angle 0.64125 / 0.33 (49490) hydrogen bonds : bond 0.04832 / 3.25 ( 2408) hydrogen bonds : angle 5.20345 / 3.66 ( 6933) Misc. bond : bond 0.00356 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 650 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7939 (mt-10) REVERT: A 160 THR cc_start: 0.8457 (p) cc_final: 0.8067 (t) REVERT: A 184 ASP cc_start: 0.7751 (m-30) cc_final: 0.7499 (m-30) REVERT: A 200 GLN cc_start: 0.8801 (mt0) cc_final: 0.8450 (mm-40) REVERT: A 336 ASP cc_start: 0.7943 (t0) cc_final: 0.7709 (t0) REVERT: A 372 VAL cc_start: 0.8388 (t) cc_final: 0.8031 (p) REVERT: A 388 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7987 (mt-10) REVERT: A 429 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8173 (mm-30) REVERT: A 473 GLU cc_start: 0.8446 (tp30) cc_final: 0.8063 (tt0) REVERT: A 498 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7559 (mm-30) REVERT: B 194 LEU cc_start: 0.8457 (mt) cc_final: 0.8173 (mt) REVERT: B 488 GLU cc_start: 0.8052 (tt0) cc_final: 0.7441 (pt0) REVERT: C 41 ILE cc_start: 0.8549 (mm) cc_final: 0.8277 (mt) REVERT: C 44 VAL cc_start: 0.8709 (t) cc_final: 0.8438 (m) REVERT: C 197 ASP cc_start: 0.7962 (t0) cc_final: 0.7581 (m-30) REVERT: C 269 ILE cc_start: 0.8337 (mm) cc_final: 0.8030 (tt) REVERT: C 300 ASP cc_start: 0.8530 (p0) cc_final: 0.7868 (p0) REVERT: C 335 ASN cc_start: 0.8979 (t0) cc_final: 0.8616 (t0) REVERT: C 505 ASN cc_start: 0.8194 (m-40) cc_final: 0.7848 (m110) REVERT: D 67 MET cc_start: 0.8582 (mmp) cc_final: 0.8362 (mmt) REVERT: D 144 VAL cc_start: 0.8024 (t) cc_final: 0.7780 (m) REVERT: D 185 SER cc_start: 0.8828 (t) cc_final: 0.8594 (m) REVERT: D 222 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8092 (mt-10) REVERT: D 233 SER cc_start: 0.8522 (t) cc_final: 0.8321 (m) REVERT: D 292 GLU cc_start: 0.8086 (tp30) cc_final: 0.7654 (tp30) REVERT: D 314 ASP cc_start: 0.8114 (t0) cc_final: 0.7856 (t70) REVERT: D 342 ILE cc_start: 0.8297 (mm) cc_final: 0.8058 (mt) REVERT: D 447 PHE cc_start: 0.8521 (m-80) cc_final: 0.8100 (m-10) REVERT: E 279 TYR cc_start: 0.8704 (m-80) cc_final: 0.8398 (m-80) REVERT: E 315 TYR cc_start: 0.8789 (m-80) cc_final: 0.8292 (m-80) REVERT: E 332 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7803 (mt-10) REVERT: E 453 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8556 (mm-40) REVERT: E 457 LEU cc_start: 0.8961 (mt) cc_final: 0.8759 (mp) REVERT: F 11 ARG cc_start: 0.8358 (ptm-80) cc_final: 0.7569 (ptt-90) REVERT: F 66 SER cc_start: 0.8865 (m) cc_final: 0.8620 (p) REVERT: F 458 ILE cc_start: 0.8715 (tp) cc_final: 0.8476 (tp) REVERT: G 26 GLU cc_start: 0.7429 (tt0) cc_final: 0.7220 (tt0) REVERT: G 41 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7612 (tm-30) REVERT: G 85 ASP cc_start: 0.7847 (t70) cc_final: 0.7488 (t0) REVERT: G 136 GLU cc_start: 0.8239 (tp30) cc_final: 0.7947 (tp30) REVERT: G 162 MET cc_start: 0.7419 (mtp) cc_final: 0.7192 (mtp) REVERT: G 193 MET cc_start: 0.8069 (ttp) cc_final: 0.7809 (tpp) REVERT: H 7 GLU cc_start: 0.7661 (tt0) cc_final: 0.7232 (mt-10) REVERT: b 160 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.6041 (tt) REVERT: d 34 GLN cc_start: 0.7022 (tt0) cc_final: 0.6321 (tp-100) REVERT: d 132 ILE cc_start: 0.6427 (mt) cc_final: 0.6210 (mt) REVERT: d 141 GLN cc_start: 0.6810 (tp40) cc_final: 0.6584 (tp-100) REVERT: d 298 ARG cc_start: 0.7394 (ttt90) cc_final: 0.6756 (ttm170) REVERT: d 440 GLN cc_start: 0.8232 (tm-30) cc_final: 0.8011 (tm-30) REVERT: 1 75 MET cc_start: 0.6832 (ttp) cc_final: 0.6574 (tmm) REVERT: 3 21 MET cc_start: 0.7426 (mmm) cc_final: 0.7160 (mmm) REVERT: 4 21 MET cc_start: 0.7661 (mmm) cc_final: 0.7457 (tmm) REVERT: 8 21 MET cc_start: 0.8585 (mmm) cc_final: 0.8106 (mmm) REVERT: 8 75 MET cc_start: 0.8184 (ttp) cc_final: 0.7720 (ttp) REVERT: 9 21 MET cc_start: 0.8398 (tpt) cc_final: 0.8093 (tpp) REVERT: 9 75 MET cc_start: 0.6465 (tmm) cc_final: 0.5216 (tpt) outliers start: 60 outliers final: 35 residues processed: 677 average time/residue: 0.2309 time to fit residues: 258.0416 Evaluate side-chains 599 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 563 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 203 ILE Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 436 LEU Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 99 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 440 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 422 optimal weight: 1.9990 chunk 425 optimal weight: 0.5980 chunk 468 optimal weight: 10.0000 chunk 452 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 346 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 188 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 219 GLN D 421 GLN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** 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 = 0.3801 r_free = 0.3801 target = 0.146446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.108096 restraints weight = 50513.070| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.94 r_work: 0.3144 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 36425 Z= 0.267 Angle : 0.658 9.998 49490 Z= 0.336 Chirality : 0.046 0.240 5810 Planarity : 0.005 0.057 6389 Dihedral : 5.635 112.589 5167 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.12 % Favored : 97.74 % Rotamer: Outliers : 2.49 % Allowed : 12.93 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % 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: 0.62 (0.12), residues: 4774 helix: 1.17 (0.10), residues: 2583 sheet: -0.93 (0.21), residues: 546 loop : -0.16 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG a 152 TYR 0.026 0.002 TYR a 145 PHE 0.026 0.002 PHE a 213 TRP 0.015 0.002 TRP a 212 HIS 0.006 0.001 HIS C 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.27 (36422) covalent geometry : angle 0.65834 / 0.34 (49490) hydrogen bonds : bond 0.04615 / 3.10 ( 2408) hydrogen bonds : angle 4.89186 / 3.44 ( 6933) Misc. bond : bond 0.00168 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 601 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8147 (mt-10) REVERT: A 160 THR cc_start: 0.8451 (p) cc_final: 0.8062 (t) REVERT: A 200 GLN cc_start: 0.8917 (mt0) cc_final: 0.8447 (mm-40) REVERT: A 336 ASP cc_start: 0.8012 (t0) cc_final: 0.7772 (t0) REVERT: A 388 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8059 (mt-10) REVERT: A 429 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8108 (mm-30) REVERT: A 473 GLU cc_start: 0.8515 (tp30) cc_final: 0.8134 (tt0) REVERT: A 498 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7617 (mm-30) REVERT: B 194 LEU cc_start: 0.8530 (mt) cc_final: 0.8253 (mt) REVERT: B 229 MET cc_start: 0.8846 (mmm) cc_final: 0.8589 (tpt) REVERT: B 487 ARG cc_start: 0.8296 (ttp-170) cc_final: 0.8095 (ttp80) REVERT: B 488 GLU cc_start: 0.8213 (tt0) cc_final: 0.7619 (pt0) REVERT: C 197 ASP cc_start: 0.7988 (t0) cc_final: 0.7621 (m-30) REVERT: C 229 MET cc_start: 0.9148 (mmm) cc_final: 0.8890 (tpt) REVERT: C 269 ILE cc_start: 0.8396 (mm) cc_final: 0.8103 (tt) REVERT: C 311 ARG cc_start: 0.9045 (mtm-85) cc_final: 0.8830 (mtm-85) REVERT: C 335 ASN cc_start: 0.8993 (t0) cc_final: 0.8592 (t0) REVERT: D 144 VAL cc_start: 0.8145 (t) cc_final: 0.7900 (m) REVERT: D 185 SER cc_start: 0.8840 (t) cc_final: 0.8577 (m) REVERT: D 279 TYR cc_start: 0.8949 (m-80) cc_final: 0.8609 (m-80) REVERT: D 292 GLU cc_start: 0.8076 (tp30) cc_final: 0.7681 (tp30) REVERT: D 314 ASP cc_start: 0.8058 (t0) cc_final: 0.7823 (t0) REVERT: D 333 LEU cc_start: 0.8869 (mt) cc_final: 0.8618 (mp) REVERT: D 442 LEU cc_start: 0.8435 (tp) cc_final: 0.8140 (tt) REVERT: D 446 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7540 (tt0) REVERT: E 332 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7874 (mt-10) REVERT: E 453 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8566 (mm-40) REVERT: F 11 ARG cc_start: 0.8440 (ptm-80) cc_final: 0.7668 (ptt-90) REVERT: F 155 LYS cc_start: 0.8873 (mtpm) cc_final: 0.8669 (mtpt) REVERT: F 254 ASP cc_start: 0.7522 (t0) cc_final: 0.7281 (t70) REVERT: F 458 ILE cc_start: 0.8782 (tp) cc_final: 0.8577 (tp) REVERT: G 41 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7681 (tp30) REVERT: G 85 ASP cc_start: 0.7950 (t70) cc_final: 0.7141 (t0) REVERT: G 121 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7824 (mtm-85) REVERT: G 136 GLU cc_start: 0.8245 (tp30) cc_final: 0.7952 (tp30) REVERT: G 162 MET cc_start: 0.7541 (mtp) cc_final: 0.7277 (mtp) REVERT: H 7 GLU cc_start: 0.7830 (tt0) cc_final: 0.7280 (mt-10) REVERT: a 100 ILE cc_start: 0.6941 (tp) cc_final: 0.6434 (mp) REVERT: a 213 PHE cc_start: 0.7213 (t80) cc_final: 0.6816 (t80) REVERT: d 34 GLN cc_start: 0.6893 (tt0) cc_final: 0.6236 (tp-100) REVERT: d 132 ILE cc_start: 0.6375 (mt) cc_final: 0.6157 (mt) REVERT: d 237 LEU cc_start: 0.8028 (tp) cc_final: 0.7823 (tp) REVERT: d 440 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7990 (tm-30) REVERT: 1 21 MET cc_start: 0.7706 (tpp) cc_final: 0.7170 (tpp) REVERT: 1 75 MET cc_start: 0.6814 (ttp) cc_final: 0.6560 (tmm) REVERT: 2 21 MET cc_start: 0.8233 (tpt) cc_final: 0.7974 (tpp) REVERT: 4 21 MET cc_start: 0.7899 (mmm) cc_final: 0.7534 (tmm) REVERT: 8 21 MET cc_start: 0.8584 (mmm) cc_final: 0.8048 (mmm) REVERT: 8 75 MET cc_start: 0.8246 (ttp) cc_final: 0.7489 (ttp) REVERT: 9 21 MET cc_start: 0.8397 (tpt) cc_final: 0.8128 (tpt) outliers start: 87 outliers final: 54 residues processed: 649 average time/residue: 0.2222 time to fit residues: 240.7997 Evaluate side-chains 607 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 552 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 121 ARG Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 436 LEU Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 49 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 347 optimal weight: 6.9990 chunk 158 optimal weight: 0.8980 chunk 471 optimal weight: 6.9990 chunk 307 optimal weight: 3.9990 chunk 341 optimal weight: 6.9990 chunk 208 optimal weight: 0.8980 chunk 392 optimal weight: 5.9990 chunk 262 optimal weight: 1.9990 chunk 466 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 453 GLN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 143 GLN C 258 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 245 GLN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN d 266 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.145742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.107685 restraints weight = 50043.845| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.91 r_work: 0.3136 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 36425 Z= 0.245 Angle : 0.635 10.355 49490 Z= 0.322 Chirality : 0.045 0.263 5810 Planarity : 0.004 0.056 6389 Dihedral : 5.518 111.387 5167 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.09 % Favored : 97.76 % Rotamer: Outliers : 3.00 % Allowed : 14.10 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % 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: 0.82 (0.12), residues: 4774 helix: 1.39 (0.10), residues: 2581 sheet: -0.91 (0.21), residues: 548 loop : -0.16 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 282 TYR 0.027 0.002 TYR a 145 PHE 0.029 0.002 PHE 7 57 TRP 0.014 0.002 TRP a 212 HIS 0.005 0.001 HIS C 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (36422) covalent geometry : angle 0.63518 / 0.32 (49490) hydrogen bonds : bond 0.04351 / 2.92 ( 2408) hydrogen bonds : angle 4.78887 / 3.37 ( 6933) Misc. bond : bond 0.00098 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 581 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8221 (mt-10) REVERT: A 160 THR cc_start: 0.8451 (p) cc_final: 0.8076 (t) REVERT: A 200 GLN cc_start: 0.8942 (mt0) cc_final: 0.8438 (mm-40) REVERT: A 310 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7382 (mm-30) REVERT: A 336 ASP cc_start: 0.8009 (t0) cc_final: 0.7719 (t0) REVERT: A 388 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8074 (mt-10) REVERT: A 429 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8052 (mm-30) REVERT: A 473 GLU cc_start: 0.8466 (tp30) cc_final: 0.8126 (tt0) REVERT: B 229 MET cc_start: 0.8846 (mmm) cc_final: 0.8600 (tpt) REVERT: C 188 ASN cc_start: 0.8947 (t0) cc_final: 0.8722 (t0) REVERT: C 197 ASP cc_start: 0.8003 (t0) cc_final: 0.7638 (m-30) REVERT: C 229 MET cc_start: 0.9029 (mmm) cc_final: 0.8739 (tpt) REVERT: C 269 ILE cc_start: 0.8402 (mm) cc_final: 0.8169 (tt) REVERT: C 276 LYS cc_start: 0.8086 (mttp) cc_final: 0.7821 (mttm) REVERT: C 399 GLN cc_start: 0.8255 (mm-40) cc_final: 0.8038 (mm110) REVERT: C 468 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: D 185 SER cc_start: 0.8845 (t) cc_final: 0.8571 (m) REVERT: D 292 GLU cc_start: 0.8092 (tp30) cc_final: 0.7866 (tp30) REVERT: D 314 ASP cc_start: 0.7971 (t0) cc_final: 0.7760 (t0) REVERT: D 333 LEU cc_start: 0.8866 (mt) cc_final: 0.8626 (mp) REVERT: D 446 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7599 (tt0) REVERT: E 45 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8129 (pp) REVERT: E 332 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7898 (mt-10) REVERT: E 453 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8605 (mm-40) REVERT: F 11 ARG cc_start: 0.8476 (ptm-80) cc_final: 0.7781 (ptt-90) REVERT: F 127 PHE cc_start: 0.8314 (t80) cc_final: 0.8112 (t80) REVERT: F 131 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8252 (mt-10) REVERT: F 155 LYS cc_start: 0.8870 (mtpm) cc_final: 0.8660 (mtpt) REVERT: F 254 ASP cc_start: 0.7563 (t0) cc_final: 0.7313 (t70) REVERT: F 420 GLU cc_start: 0.7700 (tp30) cc_final: 0.7287 (tp30) REVERT: F 458 ILE cc_start: 0.8783 (tp) cc_final: 0.8575 (tp) REVERT: F 469 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: G 41 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7693 (tp30) REVERT: G 85 ASP cc_start: 0.7912 (t70) cc_final: 0.7670 (t0) REVERT: G 136 GLU cc_start: 0.8272 (tp30) cc_final: 0.7999 (tp30) REVERT: G 162 MET cc_start: 0.7523 (mtp) cc_final: 0.7301 (mtp) REVERT: H 7 GLU cc_start: 0.7787 (tt0) cc_final: 0.7028 (mm-30) REVERT: a 100 ILE cc_start: 0.6990 (tp) cc_final: 0.6504 (mp) REVERT: d 34 GLN cc_start: 0.6900 (tt0) cc_final: 0.6221 (tp40) REVERT: d 132 ILE cc_start: 0.6374 (mt) cc_final: 0.6150 (mt) REVERT: d 237 LEU cc_start: 0.8097 (tp) cc_final: 0.7834 (tt) REVERT: d 440 GLN cc_start: 0.8255 (tm-30) cc_final: 0.8015 (tm-30) REVERT: 1 21 MET cc_start: 0.7690 (tpp) cc_final: 0.6991 (tpp) REVERT: 1 75 MET cc_start: 0.6979 (ttp) cc_final: 0.6582 (tmm) REVERT: 3 65 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7145 (mm-30) REVERT: 4 21 MET cc_start: 0.7962 (mmm) cc_final: 0.7717 (tmm) REVERT: 5 20 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.7837 (mt) REVERT: 8 21 MET cc_start: 0.8590 (mmm) cc_final: 0.8023 (mmm) REVERT: 8 75 MET cc_start: 0.8216 (ttp) cc_final: 0.7427 (ttp) REVERT: 9 21 MET cc_start: 0.8397 (tpt) cc_final: 0.7942 (tpt) outliers start: 105 outliers final: 71 residues processed: 645 average time/residue: 0.2259 time to fit residues: 242.1991 Evaluate side-chains 627 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 552 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 469 GLU Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 310 SER Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain d residue 436 LEU Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 5 residue 20 ILE Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 405 optimal weight: 6.9990 chunk 361 optimal weight: 8.9990 chunk 451 optimal weight: 0.0030 chunk 438 optimal weight: 1.9990 chunk 383 optimal weight: 0.0870 chunk 201 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 411 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 419 optimal weight: 5.9990 overall best weight: 0.5770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 141 GLN B 258 GLN C 143 GLN C 335 ASN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN d 347 GLN 2 46 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.148403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110636 restraints weight = 49787.154| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.87 r_work: 0.3182 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36425 Z= 0.131 Angle : 0.571 10.956 49490 Z= 0.288 Chirality : 0.042 0.281 5810 Planarity : 0.004 0.054 6389 Dihedral : 5.289 107.668 5167 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.86 % Favored : 98.01 % Rotamer: Outliers : 2.72 % Allowed : 15.76 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % 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: 1.18 (0.12), residues: 4774 helix: 1.70 (0.10), residues: 2575 sheet: -0.79 (0.21), residues: 535 loop : -0.01 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 261 TYR 0.027 0.001 TYR a 145 PHE 0.031 0.001 PHE 7 57 TRP 0.011 0.001 TRP a 212 HIS 0.005 0.001 HIS a 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (36422) covalent geometry : angle 0.57125 / 0.29 (49490) hydrogen bonds : bond 0.03954 / 2.66 ( 2408) hydrogen bonds : angle 4.63524 / 3.26 ( 6933) Misc. bond : bond 0.00081 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 587 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8516 (tp) cc_final: 0.8219 (tp) REVERT: A 71 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8145 (mt-10) REVERT: A 160 THR cc_start: 0.8461 (p) cc_final: 0.8072 (t) REVERT: A 200 GLN cc_start: 0.8876 (mt0) cc_final: 0.8326 (mm-40) REVERT: A 310 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7306 (mm-30) REVERT: A 336 ASP cc_start: 0.7995 (t0) cc_final: 0.7724 (t0) REVERT: A 370 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8255 (t) REVERT: A 388 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8062 (mt-10) REVERT: A 429 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8057 (mm-30) REVERT: A 473 GLU cc_start: 0.8331 (tp30) cc_final: 0.7971 (tt0) REVERT: A 488 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7913 (mm-30) REVERT: B 350 ASP cc_start: 0.8128 (m-30) cc_final: 0.7908 (m-30) REVERT: B 466 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7858 (ttp80) REVERT: B 488 GLU cc_start: 0.8254 (tt0) cc_final: 0.7587 (pt0) REVERT: C 197 ASP cc_start: 0.7893 (t0) cc_final: 0.7511 (m-30) REVERT: C 276 LYS cc_start: 0.7975 (mttp) cc_final: 0.7531 (mttt) REVERT: C 468 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: D 185 SER cc_start: 0.8832 (t) cc_final: 0.8558 (m) REVERT: D 292 GLU cc_start: 0.8036 (tp30) cc_final: 0.7803 (tp30) REVERT: D 314 ASP cc_start: 0.7890 (t0) cc_final: 0.7638 (t0) REVERT: D 333 LEU cc_start: 0.8831 (mt) cc_final: 0.8585 (mp) REVERT: D 446 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7584 (tt0) REVERT: E 247 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8151 (mp10) REVERT: E 298 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8332 (ttm-80) REVERT: E 332 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7859 (mt-10) REVERT: F 11 ARG cc_start: 0.8395 (ptm-80) cc_final: 0.7708 (ptt-90) REVERT: F 67 MET cc_start: 0.8588 (mmm) cc_final: 0.7437 (mmm) REVERT: F 120 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8097 (tt) REVERT: F 131 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8236 (mt-10) REVERT: F 254 ASP cc_start: 0.7522 (t0) cc_final: 0.7246 (t70) REVERT: F 420 GLU cc_start: 0.7662 (tp30) cc_final: 0.7300 (tp30) REVERT: F 458 ILE cc_start: 0.8719 (tp) cc_final: 0.8514 (tp) REVERT: F 469 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: G 41 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7721 (tp30) REVERT: G 136 GLU cc_start: 0.8228 (tp30) cc_final: 0.7922 (tp30) REVERT: G 144 ARG cc_start: 0.7730 (tpp-160) cc_final: 0.7390 (tpt170) REVERT: G 162 MET cc_start: 0.7477 (mtp) cc_final: 0.7237 (mtp) REVERT: H 7 GLU cc_start: 0.7674 (tt0) cc_final: 0.7018 (mm-30) REVERT: a 100 ILE cc_start: 0.7088 (tp) cc_final: 0.6600 (mp) REVERT: d 34 GLN cc_start: 0.6867 (tt0) cc_final: 0.6157 (tp40) REVERT: d 440 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7848 (tm-30) REVERT: 1 21 MET cc_start: 0.7713 (tpp) cc_final: 0.7308 (tpp) REVERT: 4 21 MET cc_start: 0.7961 (mmm) cc_final: 0.7423 (tmm) REVERT: 8 21 MET cc_start: 0.8621 (mmm) cc_final: 0.8001 (mmm) REVERT: 8 75 MET cc_start: 0.8212 (ttp) cc_final: 0.7680 (ptt) REVERT: 9 21 MET cc_start: 0.8404 (tpt) cc_final: 0.8185 (tpp) outliers start: 95 outliers final: 57 residues processed: 642 average time/residue: 0.2191 time to fit residues: 234.8390 Evaluate side-chains 612 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 550 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 469 GLU Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain d residue 436 LEU Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 458 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 320 optimal weight: 2.9990 chunk 352 optimal weight: 9.9990 chunk 474 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 289 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 460 optimal weight: 0.0770 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 HIS C 143 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN C 505 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN 2 46 GLN 3 46 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.108600 restraints weight = 49568.497| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.85 r_work: 0.3139 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 36425 Z= 0.222 Angle : 0.609 10.532 49490 Z= 0.306 Chirality : 0.044 0.296 5810 Planarity : 0.004 0.056 6389 Dihedral : 5.272 106.866 5167 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.03 % Favored : 97.82 % Rotamer: Outliers : 3.29 % Allowed : 16.04 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % 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: 1.17 (0.12), residues: 4774 helix: 1.72 (0.10), residues: 2582 sheet: -0.83 (0.22), residues: 529 loop : -0.07 (0.16), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 335 TYR 0.026 0.002 TYR a 145 PHE 0.032 0.002 PHE 7 57 TRP 0.011 0.001 TRP a 212 HIS 0.004 0.001 HIS a 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 (36422) covalent geometry : angle 0.60878 / 0.31 (49490) hydrogen bonds : bond 0.04115 / 2.77 ( 2408) hydrogen bonds : angle 4.64439 / 3.27 ( 6933) Misc. bond : bond 0.00082 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 564 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8250 (m-30) cc_final: 0.7953 (m-30) REVERT: A 67 LEU cc_start: 0.8545 (tp) cc_final: 0.8223 (tp) REVERT: A 71 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8129 (mt-10) REVERT: A 160 THR cc_start: 0.8444 (p) cc_final: 0.8068 (t) REVERT: A 200 GLN cc_start: 0.8876 (mt0) cc_final: 0.8329 (mm110) REVERT: A 310 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7404 (mm-30) REVERT: A 336 ASP cc_start: 0.8058 (t0) cc_final: 0.7782 (t0) REVERT: A 388 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: A 429 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 473 GLU cc_start: 0.8412 (tp30) cc_final: 0.8031 (tt0) REVERT: A 488 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7892 (mm-30) REVERT: C 197 ASP cc_start: 0.7932 (t0) cc_final: 0.7577 (m-30) REVERT: C 276 LYS cc_start: 0.8028 (mttp) cc_final: 0.7528 (mttt) REVERT: C 399 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8026 (mm-40) REVERT: C 468 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: D 120 ILE cc_start: 0.8610 (pt) cc_final: 0.8377 (pt) REVERT: D 185 SER cc_start: 0.8833 (t) cc_final: 0.8546 (m) REVERT: D 221 ASP cc_start: 0.8361 (m-30) cc_final: 0.8095 (m-30) REVERT: D 292 GLU cc_start: 0.8074 (tp30) cc_final: 0.7719 (tp30) REVERT: D 314 ASP cc_start: 0.7978 (t0) cc_final: 0.7757 (t0) REVERT: D 333 LEU cc_start: 0.8851 (mt) cc_final: 0.8609 (mp) REVERT: D 446 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7638 (tt0) REVERT: D 447 PHE cc_start: 0.8625 (m-80) cc_final: 0.8375 (m-10) REVERT: E 45 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8087 (pp) REVERT: E 247 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8110 (mp10) REVERT: E 332 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7914 (mt-10) REVERT: F 11 ARG cc_start: 0.8459 (ptm-80) cc_final: 0.7770 (ptt-90) REVERT: F 67 MET cc_start: 0.8626 (mmm) cc_final: 0.7525 (mmm) REVERT: F 131 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8205 (mt-10) REVERT: F 254 ASP cc_start: 0.7605 (t0) cc_final: 0.7313 (t70) REVERT: F 315 TYR cc_start: 0.8891 (m-80) cc_final: 0.8684 (m-80) REVERT: F 420 GLU cc_start: 0.7674 (tp30) cc_final: 0.7265 (tp30) REVERT: F 458 ILE cc_start: 0.8759 (tp) cc_final: 0.8554 (tp) REVERT: F 469 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: G 41 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7737 (tp30) REVERT: G 136 GLU cc_start: 0.8269 (tp30) cc_final: 0.7964 (tp30) REVERT: G 144 ARG cc_start: 0.7792 (tpp-160) cc_final: 0.7417 (mtp-110) REVERT: G 162 MET cc_start: 0.7495 (mtp) cc_final: 0.7271 (mtp) REVERT: H 7 GLU cc_start: 0.7710 (tt0) cc_final: 0.7014 (mm-30) REVERT: a 100 ILE cc_start: 0.6887 (tp) cc_final: 0.6395 (mp) REVERT: a 213 PHE cc_start: 0.7104 (t80) cc_final: 0.6556 (m-80) REVERT: d 440 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7758 (tm-30) REVERT: 1 21 MET cc_start: 0.7546 (tpp) cc_final: 0.7215 (tpp) REVERT: 4 21 MET cc_start: 0.8024 (mmm) cc_final: 0.7599 (tmm) REVERT: 5 20 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.7957 (mt) REVERT: 6 75 MET cc_start: 0.7627 (tpt) cc_final: 0.7359 (tpp) REVERT: 8 21 MET cc_start: 0.8615 (mmm) cc_final: 0.7980 (mmm) REVERT: 8 75 MET cc_start: 0.8233 (ttp) cc_final: 0.7678 (ptt) REVERT: 9 21 MET cc_start: 0.8399 (tpt) cc_final: 0.8171 (tpp) outliers start: 115 outliers final: 82 residues processed: 634 average time/residue: 0.2190 time to fit residues: 232.7500 Evaluate side-chains 637 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 550 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 469 GLU Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 310 SER Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain d residue 436 LEU Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 5 residue 20 ILE Chi-restraints excluded: chain 5 residue 21 MET Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 59 optimal weight: 1.9990 chunk 323 optimal weight: 4.9990 chunk 382 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 426 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 475 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN C 143 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN D 365 HIS a 112 GLN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.145778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107973 restraints weight = 49699.717| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.93 r_work: 0.3129 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 36425 Z= 0.219 Angle : 0.612 10.505 49490 Z= 0.308 Chirality : 0.044 0.305 5810 Planarity : 0.004 0.056 6389 Dihedral : 5.220 109.590 5167 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.16 % Favored : 97.70 % Rotamer: Outliers : 3.09 % Allowed : 17.27 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % 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: 1.16 (0.12), residues: 4774 helix: 1.73 (0.10), residues: 2589 sheet: -0.83 (0.22), residues: 524 loop : -0.12 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 261 TYR 0.026 0.002 TYR a 145 PHE 0.036 0.002 PHE 7 57 TRP 0.012 0.001 TRP a 212 HIS 0.006 0.001 HIS F 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (36422) covalent geometry : angle 0.61208 / 0.31 (49490) hydrogen bonds : bond 0.04103 / 2.77 ( 2408) hydrogen bonds : angle 4.63255 / 3.26 ( 6933) Misc. bond : bond 0.00072 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 562 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8537 (tp) cc_final: 0.8279 (tp) REVERT: A 71 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8135 (mt-10) REVERT: A 160 THR cc_start: 0.8430 (p) cc_final: 0.8069 (t) REVERT: A 200 GLN cc_start: 0.8893 (mt0) cc_final: 0.8334 (mm110) REVERT: A 310 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7417 (mm-30) REVERT: A 388 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: A 429 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8058 (mm-30) REVERT: A 473 GLU cc_start: 0.8436 (tp30) cc_final: 0.8060 (tt0) REVERT: B 319 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8829 (mm) REVERT: B 466 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7964 (ttp80) REVERT: C 197 ASP cc_start: 0.7956 (t0) cc_final: 0.7605 (m-30) REVERT: C 276 LYS cc_start: 0.8048 (mttp) cc_final: 0.7547 (mttt) REVERT: C 399 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8055 (mm-40) REVERT: C 421 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7863 (mp) REVERT: C 468 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: D 39 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8282 (mm-30) REVERT: D 120 ILE cc_start: 0.8621 (pt) cc_final: 0.8408 (pt) REVERT: D 185 SER cc_start: 0.8843 (t) cc_final: 0.8567 (m) REVERT: D 221 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8022 (m-30) REVERT: D 279 TYR cc_start: 0.8966 (m-80) cc_final: 0.8731 (m-80) REVERT: D 333 LEU cc_start: 0.8871 (mt) cc_final: 0.8628 (mp) REVERT: D 446 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7664 (tt0) REVERT: D 447 PHE cc_start: 0.8652 (m-80) cc_final: 0.8431 (m-10) REVERT: E 45 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8074 (pp) REVERT: E 332 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7950 (mt-10) REVERT: F 11 ARG cc_start: 0.8489 (ptm-80) cc_final: 0.7860 (ptt-90) REVERT: F 67 MET cc_start: 0.8570 (mmm) cc_final: 0.7517 (mmm) REVERT: F 131 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8242 (mt-10) REVERT: F 173 MET cc_start: 0.8299 (tpp) cc_final: 0.7770 (mmt) REVERT: F 254 ASP cc_start: 0.7628 (t0) cc_final: 0.7329 (t70) REVERT: F 420 GLU cc_start: 0.7710 (tp30) cc_final: 0.7340 (tp30) REVERT: G 136 GLU cc_start: 0.8352 (tp30) cc_final: 0.8049 (tp30) REVERT: G 144 ARG cc_start: 0.7871 (tpp-160) cc_final: 0.7633 (ttm-80) REVERT: G 162 MET cc_start: 0.7551 (mtp) cc_final: 0.7338 (mtp) REVERT: H 7 GLU cc_start: 0.7748 (tt0) cc_final: 0.7023 (mm-30) REVERT: H 23 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.8037 (p) REVERT: a 100 ILE cc_start: 0.6921 (tp) cc_final: 0.6433 (mp) REVERT: b 25 LEU cc_start: 0.4844 (tt) cc_final: 0.4381 (mp) REVERT: d 440 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7720 (tm-30) REVERT: 1 21 MET cc_start: 0.7556 (tpp) cc_final: 0.7198 (tpp) REVERT: 4 21 MET cc_start: 0.8129 (mmm) cc_final: 0.7603 (tmm) REVERT: 5 20 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.7917 (mt) REVERT: 5 21 MET cc_start: 0.7458 (tpp) cc_final: 0.6937 (mmp) REVERT: 5 65 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: 6 21 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.6102 (mmm) REVERT: 8 21 MET cc_start: 0.8597 (mmm) cc_final: 0.7978 (mmm) REVERT: 8 75 MET cc_start: 0.8259 (ttp) cc_final: 0.7715 (ptt) REVERT: 9 21 MET cc_start: 0.8373 (tpt) cc_final: 0.7881 (tpt) outliers start: 108 outliers final: 78 residues processed: 628 average time/residue: 0.2141 time to fit residues: 225.1640 Evaluate side-chains 630 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 542 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 175 ILE Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 310 SER Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain d residue 436 LEU Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 5 residue 20 ILE Chi-restraints excluded: chain 5 residue 65 GLU Chi-restraints excluded: chain 6 residue 21 MET Chi-restraints excluded: chain 9 residue 20 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 368 optimal weight: 5.9990 chunk 452 optimal weight: 1.9990 chunk 384 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 chunk 436 optimal weight: 10.0000 chunk 341 optimal weight: 0.9980 chunk 311 optimal weight: 2.9990 chunk 438 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 GLN C 352 GLN C 505 ASN E 247 GLN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN d 273 HIS 4 46 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108273 restraints weight = 49372.549| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.91 r_work: 0.3152 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 36425 Z= 0.204 Angle : 0.611 12.007 49490 Z= 0.308 Chirality : 0.044 0.330 5810 Planarity : 0.004 0.055 6389 Dihedral : 5.157 109.159 5167 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.22 % Favored : 97.63 % Rotamer: Outliers : 3.09 % Allowed : 17.53 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % 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: 1.19 (0.12), residues: 4774 helix: 1.77 (0.10), residues: 2582 sheet: -0.86 (0.22), residues: 521 loop : -0.10 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 122 TYR 0.022 0.002 TYR a 145 PHE 0.036 0.002 PHE 7 57 TRP 0.012 0.001 TRP a 212 HIS 0.004 0.001 HIS a 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (36422) covalent geometry : angle 0.61102 / 0.31 (49490) hydrogen bonds : bond 0.04046 / 2.73 ( 2408) hydrogen bonds : angle 4.59824 / 3.23 ( 6933) Misc. bond : bond 0.00069 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 569 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8512 (tp) cc_final: 0.8231 (tp) REVERT: A 71 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8101 (mt-10) REVERT: A 84 LYS cc_start: 0.9164 (mtmm) cc_final: 0.8900 (mtpt) REVERT: A 160 THR cc_start: 0.8460 (p) cc_final: 0.8089 (t) REVERT: A 200 GLN cc_start: 0.8885 (mt0) cc_final: 0.8302 (mm110) REVERT: A 310 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7419 (mm-30) REVERT: A 388 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: A 429 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 473 GLU cc_start: 0.8423 (tp30) cc_final: 0.8064 (tt0) REVERT: B 466 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7930 (ttp80) REVERT: C 197 ASP cc_start: 0.7951 (t0) cc_final: 0.7600 (m-30) REVERT: C 276 LYS cc_start: 0.8049 (mttp) cc_final: 0.7556 (mttt) REVERT: C 335 ASN cc_start: 0.8939 (t0) cc_final: 0.8558 (t0) REVERT: C 399 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7930 (mm110) REVERT: C 421 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7868 (mp) REVERT: C 468 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: D 39 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8242 (mm-30) REVERT: D 120 ILE cc_start: 0.8617 (pt) cc_final: 0.8413 (pt) REVERT: D 139 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.8070 (p) REVERT: D 185 SER cc_start: 0.8838 (t) cc_final: 0.8568 (m) REVERT: D 221 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: D 333 LEU cc_start: 0.8884 (mt) cc_final: 0.8638 (mp) REVERT: D 446 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7652 (tt0) REVERT: D 447 PHE cc_start: 0.8640 (m-80) cc_final: 0.8425 (m-10) REVERT: E 45 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8086 (pp) REVERT: E 332 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7940 (mt-10) REVERT: F 11 ARG cc_start: 0.8511 (ptm-80) cc_final: 0.7869 (ptt-90) REVERT: F 67 MET cc_start: 0.8542 (mmm) cc_final: 0.7467 (mmm) REVERT: F 131 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8243 (mt-10) REVERT: F 254 ASP cc_start: 0.7617 (t0) cc_final: 0.7310 (t70) REVERT: F 420 GLU cc_start: 0.7717 (tp30) cc_final: 0.7356 (tp30) REVERT: G 41 GLU cc_start: 0.8116 (tp30) cc_final: 0.7788 (tp30) REVERT: G 136 GLU cc_start: 0.8322 (tp30) cc_final: 0.8009 (tp30) REVERT: G 144 ARG cc_start: 0.7815 (tpp-160) cc_final: 0.7465 (mtp-110) REVERT: G 162 MET cc_start: 0.7594 (mtp) cc_final: 0.7381 (mtp) REVERT: G 230 THR cc_start: 0.8247 (m) cc_final: 0.7958 (t) REVERT: H 7 GLU cc_start: 0.7728 (tt0) cc_final: 0.7207 (mm-30) REVERT: a 100 ILE cc_start: 0.6963 (tp) cc_final: 0.6485 (mp) REVERT: a 233 PHE cc_start: 0.7946 (t80) cc_final: 0.7384 (t80) REVERT: d 241 LEU cc_start: 0.8000 (mt) cc_final: 0.7774 (mt) REVERT: d 440 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7703 (tm-30) REVERT: 1 21 MET cc_start: 0.7563 (tpp) cc_final: 0.7209 (tpp) REVERT: 2 21 MET cc_start: 0.8127 (mmt) cc_final: 0.7886 (mmp) REVERT: 5 65 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: 8 21 MET cc_start: 0.8621 (mmm) cc_final: 0.8000 (mmm) REVERT: 8 75 MET cc_start: 0.8286 (ttp) cc_final: 0.7713 (ptt) REVERT: 9 21 MET cc_start: 0.8384 (tpt) cc_final: 0.7883 (tpt) outliers start: 108 outliers final: 88 residues processed: 636 average time/residue: 0.2225 time to fit residues: 236.0360 Evaluate side-chains 644 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 549 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 247 GLN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 175 ILE Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 111 VAL Chi-restraints excluded: chain b residue 112 ASP Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain d residue 436 LEU Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 5 residue 65 GLU Chi-restraints excluded: chain 9 residue 20 ILE Chi-restraints excluded: chain 9 residue 72 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 204 optimal weight: 0.2980 chunk 239 optimal weight: 1.9990 chunk 416 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 385 optimal weight: 2.9990 chunk 354 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 473 optimal weight: 6.9990 chunk 443 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 305 HIS C 143 GLN C 505 ASN H 119 GLN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.146843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.109439 restraints weight = 49037.242| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.84 r_work: 0.3158 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 36425 Z= 0.159 Angle : 0.592 12.131 49490 Z= 0.298 Chirality : 0.043 0.348 5810 Planarity : 0.004 0.055 6389 Dihedral : 5.078 108.874 5167 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.16 % Favored : 97.70 % Rotamer: Outliers : 3.00 % Allowed : 17.96 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % 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: 1.31 (0.12), residues: 4774 helix: 1.88 (0.10), residues: 2576 sheet: -0.85 (0.22), residues: 521 loop : -0.04 (0.16), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 122 TYR 0.024 0.001 TYR a 145 PHE 0.036 0.001 PHE 7 57 TRP 0.011 0.001 TRP a 212 HIS 0.006 0.001 HIS d 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (36422) covalent geometry : angle 0.59160 / 0.30 (49490) hydrogen bonds : bond 0.03925 / 2.65 ( 2408) hydrogen bonds : angle 4.54533 / 3.19 ( 6933) Misc. bond : bond 0.00060 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 573 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8488 (tp) cc_final: 0.8250 (tp) REVERT: A 71 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 84 LYS cc_start: 0.9133 (mtmm) cc_final: 0.8858 (mtpt) REVERT: A 160 THR cc_start: 0.8460 (p) cc_final: 0.8077 (t) REVERT: A 200 GLN cc_start: 0.8866 (mt0) cc_final: 0.8285 (mm110) REVERT: A 310 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7457 (mm-30) REVERT: A 324 MET cc_start: 0.8549 (tpp) cc_final: 0.8281 (ttt) REVERT: A 388 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: A 429 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8004 (mm-30) REVERT: A 473 GLU cc_start: 0.8351 (tp30) cc_final: 0.7956 (tt0) REVERT: B 319 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8772 (mm) REVERT: B 466 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7926 (ttp80) REVERT: C 194 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8657 (mt) REVERT: C 197 ASP cc_start: 0.7895 (t0) cc_final: 0.7555 (m-30) REVERT: C 276 LYS cc_start: 0.7989 (mttp) cc_final: 0.7528 (mttt) REVERT: C 335 ASN cc_start: 0.8895 (t0) cc_final: 0.8596 (t0) REVERT: C 399 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7911 (mm110) REVERT: C 421 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7823 (mp) REVERT: C 468 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: D 39 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8213 (mm-30) REVERT: D 120 ILE cc_start: 0.8621 (pt) cc_final: 0.8402 (pt) REVERT: D 139 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.8065 (p) REVERT: D 185 SER cc_start: 0.8825 (t) cc_final: 0.8544 (m) REVERT: D 221 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: D 333 LEU cc_start: 0.8867 (mt) cc_final: 0.8619 (mp) REVERT: D 446 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7659 (tt0) REVERT: D 447 PHE cc_start: 0.8611 (m-80) cc_final: 0.8330 (m-10) REVERT: E 45 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8022 (pp) REVERT: E 219 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7758 (mm110) REVERT: E 247 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8019 (mt0) REVERT: E 332 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7912 (mt-10) REVERT: E 393 GLU cc_start: 0.7760 (tp30) cc_final: 0.7549 (tm-30) REVERT: F 11 ARG cc_start: 0.8487 (ptm-80) cc_final: 0.7835 (ptt-90) REVERT: F 59 ASP cc_start: 0.8327 (t0) cc_final: 0.8127 (t0) REVERT: F 67 MET cc_start: 0.8519 (mmm) cc_final: 0.7400 (mmm) REVERT: F 120 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8048 (tt) REVERT: F 131 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8228 (mt-10) REVERT: F 173 MET cc_start: 0.8091 (mmt) cc_final: 0.7767 (mmt) REVERT: F 254 ASP cc_start: 0.7606 (t0) cc_final: 0.7269 (t70) REVERT: F 378 ARG cc_start: 0.8118 (tpt170) cc_final: 0.7899 (mmm160) REVERT: F 420 GLU cc_start: 0.7721 (tp30) cc_final: 0.7367 (tp30) REVERT: G 13 ARG cc_start: 0.7883 (mmm160) cc_final: 0.7411 (ttp80) REVERT: G 41 GLU cc_start: 0.8087 (tp30) cc_final: 0.7758 (tp30) REVERT: G 136 GLU cc_start: 0.8311 (tp30) cc_final: 0.7985 (tp30) REVERT: G 144 ARG cc_start: 0.7909 (tpp-160) cc_final: 0.7549 (mtp-110) REVERT: G 162 MET cc_start: 0.7518 (mtp) cc_final: 0.7289 (mtp) REVERT: G 201 ARG cc_start: 0.7396 (mtt-85) cc_final: 0.6639 (mtm110) REVERT: G 206 MET cc_start: 0.8828 (mtp) cc_final: 0.8075 (mtp) REVERT: G 230 THR cc_start: 0.8207 (m) cc_final: 0.7971 (t) REVERT: H 7 GLU cc_start: 0.7684 (tt0) cc_final: 0.7140 (mt-10) REVERT: H 63 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8051 (mm) REVERT: a 100 ILE cc_start: 0.6871 (tp) cc_final: 0.6383 (mp) REVERT: a 233 PHE cc_start: 0.7938 (t80) cc_final: 0.7352 (t80) REVERT: d 241 LEU cc_start: 0.7917 (mt) cc_final: 0.7666 (mt) REVERT: d 440 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7662 (tm-30) REVERT: 1 21 MET cc_start: 0.7555 (tpp) cc_final: 0.7188 (tpp) REVERT: 2 21 MET cc_start: 0.8088 (mmt) cc_final: 0.7796 (mmp) REVERT: 2 75 MET cc_start: 0.6886 (ppp) cc_final: 0.6334 (tmm) REVERT: 5 65 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: 8 21 MET cc_start: 0.8607 (mmm) cc_final: 0.8020 (mmm) REVERT: 8 75 MET cc_start: 0.8293 (ttp) cc_final: 0.7775 (ptt) REVERT: 9 21 MET cc_start: 0.8375 (tpt) cc_final: 0.7877 (tpt) outliers start: 105 outliers final: 83 residues processed: 641 average time/residue: 0.2241 time to fit residues: 238.8158 Evaluate side-chains 649 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 554 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 247 GLN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 175 ILE Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 112 ASP Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 310 SER Chi-restraints excluded: chain d residue 362 ILE Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain d residue 436 LEU Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 5 residue 65 GLU Chi-restraints excluded: chain 9 residue 20 ILE Chi-restraints excluded: chain 9 residue 72 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 311 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 473 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 99 optimal weight: 0.0270 chunk 461 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 182 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 340 optimal weight: 30.0000 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 GLN C 505 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.147441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110092 restraints weight = 49171.832| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.84 r_work: 0.3185 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 36425 Z= 0.150 Angle : 0.582 12.011 49490 Z= 0.292 Chirality : 0.043 0.340 5810 Planarity : 0.004 0.054 6389 Dihedral : 4.980 106.649 5167 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.16 % Favored : 97.72 % Rotamer: Outliers : 2.83 % Allowed : 18.36 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % 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: 1.40 (0.12), residues: 4774 helix: 1.98 (0.10), residues: 2566 sheet: -0.85 (0.22), residues: 526 loop : -0.03 (0.16), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 122 TYR 0.020 0.001 TYR a 145 PHE 0.037 0.001 PHE 7 57 TRP 0.014 0.001 TRP a 212 HIS 0.007 0.001 HIS d 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (36422) covalent geometry : angle 0.58154 / 0.29 (49490) hydrogen bonds : bond 0.03818 / 2.57 ( 2408) hydrogen bonds : angle 4.47275 / 3.13 ( 6933) Misc. bond : bond 0.00059 / 0.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 571 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8443 (tp) cc_final: 0.8241 (tp) REVERT: A 71 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8053 (mt-10) REVERT: A 84 LYS cc_start: 0.9105 (mtmm) cc_final: 0.8824 (mtpt) REVERT: A 160 THR cc_start: 0.8486 (p) cc_final: 0.8113 (t) REVERT: A 200 GLN cc_start: 0.8871 (mt0) cc_final: 0.8329 (mm-40) REVERT: A 308 LEU cc_start: 0.8188 (tp) cc_final: 0.7976 (tt) REVERT: A 310 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7455 (mm-30) REVERT: A 324 MET cc_start: 0.8520 (tpp) cc_final: 0.8284 (ttt) REVERT: A 388 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: A 429 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8051 (mm-30) REVERT: A 473 GLU cc_start: 0.8338 (tp30) cc_final: 0.7965 (tt0) REVERT: B 54 GLU cc_start: 0.8240 (tt0) cc_final: 0.7920 (tt0) REVERT: B 65 VAL cc_start: 0.8425 (t) cc_final: 0.8153 (m) REVERT: B 279 ASP cc_start: 0.7993 (t0) cc_final: 0.7751 (t0) REVERT: B 319 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8776 (mm) REVERT: B 466 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7917 (ttp80) REVERT: B 487 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7987 (ttp-110) REVERT: C 194 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8565 (mt) REVERT: C 197 ASP cc_start: 0.7757 (t0) cc_final: 0.7316 (m-30) REVERT: C 276 LYS cc_start: 0.7987 (mttp) cc_final: 0.7528 (mttt) REVERT: C 421 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7816 (mp) REVERT: C 468 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: D 39 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8227 (mm-30) REVERT: D 120 ILE cc_start: 0.8628 (pt) cc_final: 0.8414 (pt) REVERT: D 139 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.8047 (p) REVERT: D 185 SER cc_start: 0.8829 (t) cc_final: 0.8554 (m) REVERT: D 221 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: D 287 MET cc_start: 0.8466 (tpt) cc_final: 0.8152 (tpp) REVERT: D 333 LEU cc_start: 0.8871 (mt) cc_final: 0.8618 (mp) REVERT: D 446 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7639 (tt0) REVERT: D 447 PHE cc_start: 0.8589 (m-80) cc_final: 0.8320 (m-10) REVERT: E 45 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7995 (pp) REVERT: E 179 ARG cc_start: 0.8651 (mtp85) cc_final: 0.8427 (tpp80) REVERT: E 219 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7777 (mm110) REVERT: E 332 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7891 (mt-10) REVERT: E 393 GLU cc_start: 0.7747 (tp30) cc_final: 0.7526 (tm-30) REVERT: E 407 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8145 (mtt-85) REVERT: E 412 LEU cc_start: 0.8260 (mt) cc_final: 0.7931 (mm) REVERT: F 11 ARG cc_start: 0.8515 (ptm-80) cc_final: 0.7902 (ptt-90) REVERT: F 67 MET cc_start: 0.8510 (mmm) cc_final: 0.7394 (mmm) REVERT: F 131 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8213 (mt-10) REVERT: F 152 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8266 (ttm170) REVERT: F 254 ASP cc_start: 0.7588 (t0) cc_final: 0.7261 (t70) REVERT: F 315 TYR cc_start: 0.8953 (m-80) cc_final: 0.8737 (m-80) REVERT: F 393 GLU cc_start: 0.7273 (tm-30) cc_final: 0.7049 (tm-30) REVERT: F 420 GLU cc_start: 0.7748 (tp30) cc_final: 0.7437 (tp30) REVERT: G 13 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7451 (ttp80) REVERT: G 136 GLU cc_start: 0.8339 (tp30) cc_final: 0.8019 (tp30) REVERT: G 144 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.7563 (mtp-110) REVERT: G 162 MET cc_start: 0.7535 (mtp) cc_final: 0.7307 (mtp) REVERT: G 201 ARG cc_start: 0.7355 (mtt-85) cc_final: 0.6575 (mtm110) REVERT: G 206 MET cc_start: 0.8809 (mtp) cc_final: 0.8159 (mtp) REVERT: G 230 THR cc_start: 0.8200 (m) cc_final: 0.7969 (t) REVERT: H 7 GLU cc_start: 0.7690 (tt0) cc_final: 0.6978 (mm-30) REVERT: H 63 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.8039 (mm) REVERT: a 100 ILE cc_start: 0.6853 (tp) cc_final: 0.6365 (mp) REVERT: a 206 PHE cc_start: 0.5533 (m-80) cc_final: 0.5312 (m-10) REVERT: a 233 PHE cc_start: 0.7953 (t80) cc_final: 0.7418 (t80) REVERT: 2 75 MET cc_start: 0.6944 (ppp) cc_final: 0.6614 (tmm) REVERT: 6 75 MET cc_start: 0.7531 (tpt) cc_final: 0.7227 (tpt) REVERT: 8 21 MET cc_start: 0.8632 (mmm) cc_final: 0.8068 (mmm) REVERT: 8 75 MET cc_start: 0.8263 (ttp) cc_final: 0.7758 (ptt) REVERT: 9 21 MET cc_start: 0.8364 (tpt) cc_final: 0.7873 (tpt) outliers start: 99 outliers final: 77 residues processed: 633 average time/residue: 0.2219 time to fit residues: 232.7486 Evaluate side-chains 651 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 563 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 407 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 421 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 112 ASP Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 89 GLU Chi-restraints excluded: chain d residue 249 THR Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 310 SER Chi-restraints excluded: chain d residue 362 ILE Chi-restraints excluded: chain d residue 422 THR Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain d residue 436 LEU Chi-restraints excluded: chain 9 residue 20 ILE Chi-restraints excluded: chain 9 residue 72 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 79 optimal weight: 0.9980 chunk 256 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 331 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 416 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 378 optimal weight: 0.3980 chunk 325 optimal weight: 0.0060 chunk 149 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 GLN C 505 ASN E 55 GLN E 421 GLN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.148035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110775 restraints weight = 48816.398| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.84 r_work: 0.3197 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36425 Z= 0.139 Angle : 0.580 12.190 49490 Z= 0.291 Chirality : 0.042 0.330 5810 Planarity : 0.004 0.054 6389 Dihedral : 4.904 104.050 5167 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.07 % Favored : 97.80 % Rotamer: Outliers : 2.77 % Allowed : 18.64 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.13 % 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: 1.49 (0.12), residues: 4774 helix: 2.05 (0.10), residues: 2568 sheet: -0.84 (0.23), residues: 523 loop : 0.02 (0.16), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 272 TYR 0.023 0.001 TYR a 145 PHE 0.037 0.001 PHE 7 57 TRP 0.022 0.001 TRP a 212 HIS 0.005 0.001 HIS d 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (36422) covalent geometry : angle 0.57952 / 0.29 (49490) hydrogen bonds : bond 0.03760 / 2.53 ( 2408) hydrogen bonds : angle 4.43559 / 3.11 ( 6933) Misc. bond : bond 0.00058 / 0.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10930.51 seconds wall clock time: 187 minutes 15.05 seconds (11235.05 seconds total)