Starting phenix.real_space_refine on Sat Mar 7 00:20:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jga_22316/03_2026/7jga_22316.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jga_22316/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jga_22316/03_2026/7jga_22316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jga_22316/03_2026/7jga_22316.map" model { file = "/net/cci-nas-00/data/ceres_data/7jga_22316/03_2026/7jga_22316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jga_22316/03_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-dev-5986/lib/python3.9/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: 9.07, per 1000 atoms: 0.25 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: 3.37 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: 1.21 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: 9.11 Time building geometry restraints manager: 4.32 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: 20086 19.18 - 38.36: 1221 38.36 - 57.55: 275 57.55 - 76.73: 97 76.73 - 95.91: 67 Dihedral angle restraints: 21746 sinusoidal: 8169 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 21743 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 36.420 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 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 : 15.213 95.910 13046 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 covalent geometry : bond 0.00744 (36422) covalent geometry : angle 0.78603 (49490) hydrogen bonds : bond 0.14744 ( 2408) hydrogen bonds : angle 7.35703 ( 6933) Misc. bond : bond 0.83275 ( 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 : 1.218 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: 0.2428 time to fit residues: 333.9639 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 : 1.418 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN D 175 ASN 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 243 GLN d 104 GLN d 116 GLN d 222 HIS d 410 HIS 1 6 ASN 2 71 ASN 3 50 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.112317 restraints weight = 50418.687| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.90 r_work: 0.3196 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 36425 Z= 0.170 Angle : 0.647 10.722 49490 Z= 0.334 Chirality : 0.044 0.223 5810 Planarity : 0.005 0.050 6389 Dihedral : 9.132 113.018 5439 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.55 % Favored : 98.26 % Rotamer: Outliers : 1.89 % Allowed : 10.69 % Favored : 87.42 % 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: 0.19 (0.12), residues: 4774 helix: 0.73 (0.10), residues: 2592 sheet: -0.96 (0.21), residues: 538 loop : -0.26 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 426 TYR 0.027 0.002 TYR a 145 PHE 0.028 0.002 PHE a 213 TRP 0.014 0.001 TRP a 212 HIS 0.005 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00371 (36422) covalent geometry : angle 0.64710 (49490) hydrogen bonds : bond 0.04662 ( 2408) hydrogen bonds : angle 5.12229 ( 6933) Misc. bond : bond 0.00589 ( 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 728 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 662 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 160 THR cc_start: 0.8465 (p) cc_final: 0.8070 (t) REVERT: A 184 ASP cc_start: 0.7760 (m-30) cc_final: 0.7481 (m-30) REVERT: A 200 GLN cc_start: 0.8809 (mt0) cc_final: 0.8436 (mm-40) REVERT: A 310 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7578 (tp30) REVERT: A 372 VAL cc_start: 0.8401 (t) cc_final: 0.8084 (p) REVERT: A 388 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7995 (mt-10) REVERT: A 429 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8192 (mm-30) REVERT: A 473 GLU cc_start: 0.8435 (tp30) cc_final: 0.8041 (tt0) REVERT: A 498 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7574 (mm-30) REVERT: B 194 LEU cc_start: 0.8430 (mt) cc_final: 0.8175 (mt) REVERT: B 466 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7998 (ttp80) REVERT: B 488 GLU cc_start: 0.8082 (tt0) cc_final: 0.7459 (pt0) REVERT: C 41 ILE cc_start: 0.8565 (mm) cc_final: 0.8300 (mt) REVERT: C 44 VAL cc_start: 0.8691 (t) cc_final: 0.8416 (m) REVERT: C 197 ASP cc_start: 0.7889 (t0) cc_final: 0.7513 (m-30) REVERT: C 269 ILE cc_start: 0.8336 (mm) cc_final: 0.8033 (tt) REVERT: C 300 ASP cc_start: 0.8519 (p0) cc_final: 0.8184 (p0) REVERT: C 335 ASN cc_start: 0.8971 (t0) cc_final: 0.8617 (t0) REVERT: C 505 ASN cc_start: 0.8198 (m-40) cc_final: 0.7839 (m110) REVERT: D 67 MET cc_start: 0.8577 (mmp) cc_final: 0.8352 (mmt) REVERT: D 111 TYR cc_start: 0.8387 (t80) cc_final: 0.8183 (t80) REVERT: D 144 VAL cc_start: 0.7984 (t) cc_final: 0.7773 (m) REVERT: D 151 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8506 (t) REVERT: D 185 SER cc_start: 0.8835 (t) cc_final: 0.8584 (m) REVERT: D 222 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8098 (mt-10) REVERT: D 292 GLU cc_start: 0.8091 (tp30) cc_final: 0.7657 (tp30) REVERT: D 314 ASP cc_start: 0.8069 (t0) cc_final: 0.7819 (t70) REVERT: D 342 ILE cc_start: 0.8304 (mm) cc_final: 0.8065 (mt) REVERT: D 447 PHE cc_start: 0.8521 (m-80) cc_final: 0.8092 (m-10) REVERT: D 456 PHE cc_start: 0.8412 (m-80) cc_final: 0.8207 (m-80) REVERT: E 298 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8281 (ttm-80) REVERT: E 315 TYR cc_start: 0.8802 (m-80) cc_final: 0.8374 (m-80) REVERT: E 332 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7846 (mt-10) REVERT: E 453 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8565 (mm-40) REVERT: F 11 ARG cc_start: 0.8346 (ptm-80) cc_final: 0.7556 (ptt-90) REVERT: F 66 SER cc_start: 0.8871 (m) cc_final: 0.8622 (p) REVERT: F 305 MET cc_start: 0.8371 (tpp) cc_final: 0.7865 (tpp) REVERT: F 458 ILE cc_start: 0.8717 (tp) cc_final: 0.8467 (tp) REVERT: G 26 GLU cc_start: 0.7437 (tt0) cc_final: 0.7226 (tt0) REVERT: G 41 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7651 (tm-30) REVERT: G 85 ASP cc_start: 0.7875 (t70) cc_final: 0.7052 (t0) REVERT: G 136 GLU cc_start: 0.8247 (tp30) cc_final: 0.7953 (tp30) REVERT: G 162 MET cc_start: 0.7418 (mtp) cc_final: 0.7189 (mtp) REVERT: H 7 GLU cc_start: 0.7678 (tt0) cc_final: 0.7226 (mt-10) REVERT: a 183 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8483 (pt) REVERT: b 160 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5867 (tt) REVERT: d 34 GLN cc_start: 0.6962 (tt0) cc_final: 0.6301 (tp-100) REVERT: d 132 ILE cc_start: 0.6396 (mt) cc_final: 0.6177 (mt) REVERT: d 141 GLN cc_start: 0.6809 (tp40) cc_final: 0.6581 (tp-100) REVERT: d 298 ARG cc_start: 0.7394 (ttt90) cc_final: 0.6761 (ttm170) REVERT: d 440 GLN cc_start: 0.8225 (tm-30) cc_final: 0.8002 (tm-30) REVERT: 1 21 MET cc_start: 0.7597 (tpp) cc_final: 0.7197 (tpp) REVERT: 1 75 MET cc_start: 0.6968 (ttp) cc_final: 0.6662 (tmm) REVERT: 4 21 MET cc_start: 0.7676 (mmm) cc_final: 0.7465 (tmm) REVERT: 8 21 MET cc_start: 0.8597 (mmm) cc_final: 0.8034 (mmm) REVERT: 8 75 MET cc_start: 0.8234 (ttp) cc_final: 0.7631 (ttp) REVERT: 9 21 MET cc_start: 0.8410 (tpt) cc_final: 0.8163 (tpp) outliers start: 66 outliers final: 35 residues processed: 696 average time/residue: 0.2286 time to fit residues: 260.8314 Evaluate side-chains 600 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 562 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 151 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 13 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 302 ILE 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 174 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 64 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 183 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 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: 0.7980 chunk 440 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 422 optimal weight: 0.9990 chunk 425 optimal weight: 4.9990 chunk 468 optimal weight: 9.9990 chunk 452 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 346 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN 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 258 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN E 55 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108062 restraints weight = 50584.371| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.94 r_work: 0.3143 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 36425 Z= 0.266 Angle : 0.656 10.014 49490 Z= 0.335 Chirality : 0.046 0.248 5810 Planarity : 0.005 0.057 6389 Dihedral : 8.635 109.815 5435 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.03 % Favored : 97.82 % Rotamer: Outliers : 2.49 % Allowed : 13.01 % Favored : 84.50 % 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: 0.63 (0.12), residues: 4774 helix: 1.19 (0.10), residues: 2583 sheet: -0.93 (0.21), residues: 546 loop : -0.18 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 410 TYR 0.026 0.002 TYR a 145 PHE 0.027 0.002 PHE a 213 TRP 0.016 0.002 TRP a 212 HIS 0.006 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00635 (36422) covalent geometry : angle 0.65551 (49490) hydrogen bonds : bond 0.04594 ( 2408) hydrogen bonds : angle 4.87928 ( 6933) Misc. bond : bond 0.00284 ( 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 683 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 596 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8145 (mt-10) REVERT: A 160 THR cc_start: 0.8463 (p) cc_final: 0.8077 (t) REVERT: A 200 GLN cc_start: 0.8920 (mt0) cc_final: 0.8442 (mm-40) REVERT: A 269 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.8006 (mt) REVERT: A 388 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8074 (mt-10) REVERT: A 429 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8118 (mm-30) REVERT: A 473 GLU cc_start: 0.8488 (tp30) cc_final: 0.8127 (tt0) REVERT: A 498 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7626 (mm-30) REVERT: B 194 LEU cc_start: 0.8525 (mt) cc_final: 0.8256 (mt) REVERT: B 488 GLU cc_start: 0.8227 (tt0) cc_final: 0.7613 (pt0) REVERT: C 197 ASP cc_start: 0.7984 (t0) cc_final: 0.7624 (m-30) REVERT: C 229 MET cc_start: 0.9136 (mmm) cc_final: 0.8924 (tpt) REVERT: C 276 LYS cc_start: 0.8046 (mttt) cc_final: 0.7829 (mttt) REVERT: C 335 ASN cc_start: 0.8976 (t0) cc_final: 0.8577 (t0) REVERT: D 144 VAL cc_start: 0.8157 (t) cc_final: 0.7912 (m) REVERT: D 185 SER cc_start: 0.8845 (t) cc_final: 0.8576 (m) REVERT: D 279 TYR cc_start: 0.8956 (m-80) cc_final: 0.8507 (m-10) REVERT: D 292 GLU cc_start: 0.8109 (tp30) cc_final: 0.7719 (tp30) REVERT: D 314 ASP cc_start: 0.8080 (t0) cc_final: 0.7849 (t0) REVERT: D 333 LEU cc_start: 0.8870 (mt) cc_final: 0.8614 (mp) REVERT: D 442 LEU cc_start: 0.8425 (tp) cc_final: 0.8124 (tt) REVERT: D 446 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7568 (tt0) REVERT: E 11 ARG cc_start: 0.8000 (mtp-110) cc_final: 0.7737 (mtm-85) REVERT: E 298 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.8416 (ttm-80) REVERT: E 332 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7909 (mt-10) REVERT: E 453 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8578 (mm-40) REVERT: F 11 ARG cc_start: 0.8434 (ptm-80) cc_final: 0.7671 (ptt-90) REVERT: F 131 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8249 (mt-10) REVERT: F 420 GLU cc_start: 0.7677 (tp30) cc_final: 0.7284 (tp30) REVERT: F 458 ILE cc_start: 0.8808 (tp) cc_final: 0.8607 (tp) REVERT: F 469 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: G 41 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7657 (tp30) REVERT: G 136 GLU cc_start: 0.8228 (tp30) cc_final: 0.7939 (tp30) REVERT: G 162 MET cc_start: 0.7539 (mtp) cc_final: 0.7275 (mtp) REVERT: H 7 GLU cc_start: 0.7830 (tt0) cc_final: 0.7071 (mm-30) REVERT: a 100 ILE cc_start: 0.6965 (tp) cc_final: 0.6469 (mp) REVERT: a 188 ARG cc_start: 0.7719 (ttm110) cc_final: 0.7262 (ttm110) REVERT: a 213 PHE cc_start: 0.7216 (t80) cc_final: 0.6838 (t80) REVERT: b 63 MET cc_start: 0.3902 (ttm) cc_final: 0.3254 (tmm) REVERT: d 34 GLN cc_start: 0.6980 (tt0) cc_final: 0.6272 (tp40) REVERT: d 132 ILE cc_start: 0.6381 (mt) cc_final: 0.6162 (mt) REVERT: d 237 LEU cc_start: 0.7991 (tp) cc_final: 0.7702 (tt) REVERT: d 428 ILE cc_start: 0.7611 (mt) cc_final: 0.7401 (mp) REVERT: d 440 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7955 (tm-30) REVERT: 1 21 MET cc_start: 0.7757 (tpp) cc_final: 0.7171 (tpp) REVERT: 1 75 MET cc_start: 0.6838 (ttp) cc_final: 0.6476 (tmm) REVERT: 2 21 MET cc_start: 0.8247 (tpt) cc_final: 0.7963 (tpp) REVERT: 3 65 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7089 (mm-30) REVERT: 4 21 MET cc_start: 0.7974 (mmm) cc_final: 0.7584 (tmm) REVERT: 8 21 MET cc_start: 0.8606 (mmm) cc_final: 0.8002 (mmm) REVERT: 8 75 MET cc_start: 0.8258 (ttp) cc_final: 0.7458 (ttp) REVERT: 9 21 MET cc_start: 0.8361 (tpt) cc_final: 0.8114 (tpp) outliers start: 87 outliers final: 50 residues processed: 647 average time/residue: 0.2114 time to fit residues: 227.7175 Evaluate side-chains 604 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 552 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 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 B residue 146 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 452 THR 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 E residue 13 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 202 VAL 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 174 ILE Chi-restraints excluded: chain F residue 220 MET 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 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 63 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 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 80 SER 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 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: 0.8980 chunk 206 optimal weight: 0.7980 chunk 347 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 chunk 471 optimal weight: 10.0000 chunk 307 optimal weight: 0.9980 chunk 341 optimal weight: 7.9990 chunk 208 optimal weight: 0.6980 chunk 392 optimal weight: 0.5980 chunk 262 optimal weight: 1.9990 chunk 466 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 GLN C 143 GLN ** 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 266 ASN d 347 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.148435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110360 restraints weight = 49902.036| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.99 r_work: 0.3155 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36425 Z= 0.147 Angle : 0.578 10.786 49490 Z= 0.293 Chirality : 0.042 0.250 5810 Planarity : 0.004 0.053 6389 Dihedral : 8.135 106.526 5435 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.80 % Favored : 98.05 % Rotamer: Outliers : 2.40 % Allowed : 14.30 % Favored : 83.30 % 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: 1.03 (0.12), residues: 4774 helix: 1.56 (0.10), residues: 2586 sheet: -0.81 (0.21), residues: 543 loop : -0.07 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 410 TYR 0.027 0.001 TYR a 145 PHE 0.029 0.001 PHE 7 57 TRP 0.012 0.001 TRP a 212 HIS 0.005 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00330 (36422) covalent geometry : angle 0.57825 (49490) hydrogen bonds : bond 0.04050 ( 2408) hydrogen bonds : angle 4.68271 ( 6933) Misc. bond : bond 0.00109 ( 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: 84 poor density : 602 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8129 (mt-10) REVERT: A 160 THR cc_start: 0.8453 (p) cc_final: 0.8059 (t) REVERT: A 200 GLN cc_start: 0.8887 (mt0) cc_final: 0.8407 (mm-40) REVERT: A 269 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7995 (mt) REVERT: A 388 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8117 (mt-10) REVERT: A 429 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8098 (mm-30) REVERT: A 473 GLU cc_start: 0.8413 (tp30) cc_final: 0.8046 (tt0) REVERT: B 263 ASN cc_start: 0.8791 (t0) cc_final: 0.8285 (m-40) REVERT: B 350 ASP cc_start: 0.8141 (m-30) cc_final: 0.7899 (m-30) REVERT: B 466 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7865 (ttp80) REVERT: B 488 GLU cc_start: 0.8182 (tt0) cc_final: 0.7666 (pt0) REVERT: C 197 ASP cc_start: 0.7912 (t0) cc_final: 0.7526 (m-30) REVERT: C 269 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8153 (tt) REVERT: C 276 LYS cc_start: 0.7947 (mttt) cc_final: 0.7739 (mttt) REVERT: D 111 TYR cc_start: 0.8267 (t80) cc_final: 0.7956 (t80) REVERT: D 120 ILE cc_start: 0.8593 (pt) cc_final: 0.8372 (pt) REVERT: D 185 SER cc_start: 0.8840 (t) cc_final: 0.8572 (m) REVERT: D 292 GLU cc_start: 0.8096 (tp30) cc_final: 0.7666 (tp30) REVERT: D 333 LEU cc_start: 0.8853 (mt) cc_final: 0.8597 (mp) REVERT: D 446 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7593 (tt0) REVERT: E 11 ARG cc_start: 0.7967 (mtp-110) cc_final: 0.7749 (mtm-85) REVERT: E 219 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7692 (mm-40) REVERT: E 298 ARG cc_start: 0.8606 (ttm-80) cc_final: 0.8392 (ttm-80) REVERT: E 332 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7892 (mt-10) REVERT: E 453 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8522 (mm-40) REVERT: F 11 ARG cc_start: 0.8411 (ptm-80) cc_final: 0.7713 (ptt-90) REVERT: F 67 MET cc_start: 0.8633 (mmm) cc_final: 0.7596 (mmm) REVERT: F 131 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8214 (mt-10) REVERT: F 254 ASP cc_start: 0.7537 (t0) cc_final: 0.7329 (t70) REVERT: F 420 GLU cc_start: 0.7696 (tp30) cc_final: 0.7350 (tp30) REVERT: F 458 ILE cc_start: 0.8739 (tp) cc_final: 0.8522 (tp) REVERT: G 41 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7671 (tp30) REVERT: G 136 GLU cc_start: 0.8245 (tp30) cc_final: 0.7971 (tp30) REVERT: G 144 ARG cc_start: 0.7739 (tpp-160) cc_final: 0.7391 (tpt170) REVERT: G 162 MET cc_start: 0.7485 (mtp) cc_final: 0.7235 (mtp) REVERT: H 7 GLU cc_start: 0.7682 (tt0) cc_final: 0.7033 (mm-30) REVERT: a 100 ILE cc_start: 0.7079 (tp) cc_final: 0.6586 (mp) REVERT: a 213 PHE cc_start: 0.7135 (t80) cc_final: 0.6787 (t80) REVERT: b 63 MET cc_start: 0.4188 (ttm) cc_final: 0.3819 (tmm) REVERT: d 132 ILE cc_start: 0.6368 (mt) cc_final: 0.6155 (mt) REVERT: d 147 VAL cc_start: 0.9052 (t) cc_final: 0.8837 (m) REVERT: d 237 LEU cc_start: 0.7984 (tp) cc_final: 0.7780 (tp) REVERT: d 428 ILE cc_start: 0.7588 (mt) cc_final: 0.7348 (mp) REVERT: d 440 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7877 (tm-30) REVERT: 1 21 MET cc_start: 0.7798 (tpp) cc_final: 0.7201 (tpp) REVERT: 5 20 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.7831 (mt) REVERT: 8 21 MET cc_start: 0.8519 (mmm) cc_final: 0.7900 (mmm) REVERT: 8 75 MET cc_start: 0.8200 (ttp) cc_final: 0.7647 (ptt) outliers start: 84 outliers final: 50 residues processed: 647 average time/residue: 0.2117 time to fit residues: 227.7549 Evaluate side-chains 620 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 567 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 269 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 269 ILE 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 E residue 13 VAL 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 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 143 VAL Chi-restraints excluded: chain F residue 220 MET 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 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 a residue 106 LEU Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 131 ILE 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 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 2 residue 75 MET Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 5 residue 20 ILE Chi-restraints excluded: chain 6 residue 21 MET 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: 10.0000 chunk 361 optimal weight: 9.9990 chunk 451 optimal weight: 8.9990 chunk 438 optimal weight: 9.9990 chunk 383 optimal weight: 0.8980 chunk 201 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 411 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 419 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN B 141 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN C 505 ASN E 55 GLN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN 3 46 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.147129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.109138 restraints weight = 49951.746| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.86 r_work: 0.3165 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 36425 Z= 0.193 Angle : 0.597 10.561 49490 Z= 0.301 Chirality : 0.044 0.281 5810 Planarity : 0.004 0.055 6389 Dihedral : 7.927 104.234 5435 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.22 % Favored : 97.63 % Rotamer: Outliers : 3.12 % Allowed : 15.47 % Favored : 81.41 % 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: 1.15 (0.12), residues: 4774 helix: 1.69 (0.10), residues: 2580 sheet: -0.77 (0.21), residues: 545 loop : -0.04 (0.16), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 335 TYR 0.026 0.001 TYR a 145 PHE 0.032 0.002 PHE 7 57 TRP 0.012 0.001 TRP a 212 HIS 0.005 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00453 (36422) covalent geometry : angle 0.59731 (49490) hydrogen bonds : bond 0.04109 ( 2408) hydrogen bonds : angle 4.64580 ( 6933) Misc. bond : bond 0.00101 ( 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 698 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 589 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8146 (mt-10) REVERT: A 160 THR cc_start: 0.8458 (p) cc_final: 0.8076 (t) REVERT: A 200 GLN cc_start: 0.8882 (mt0) cc_final: 0.8354 (mm-40) REVERT: A 370 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8244 (t) REVERT: A 388 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: A 429 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8081 (mm-30) REVERT: A 473 GLU cc_start: 0.8389 (tp30) cc_final: 0.8051 (tt0) REVERT: B 488 GLU cc_start: 0.8248 (tt0) cc_final: 0.7709 (pt0) REVERT: C 197 ASP cc_start: 0.7894 (t0) cc_final: 0.7526 (m-30) REVERT: C 269 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8192 (tt) REVERT: C 276 LYS cc_start: 0.7920 (mttt) cc_final: 0.7645 (mttt) REVERT: C 399 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8080 (mm-40) REVERT: C 421 LEU cc_start: 0.8191 (tp) cc_final: 0.7867 (mp) REVERT: C 468 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: D 111 TYR cc_start: 0.8317 (t80) cc_final: 0.8022 (t80) REVERT: D 120 ILE cc_start: 0.8603 (pt) cc_final: 0.8369 (pt) REVERT: D 185 SER cc_start: 0.8834 (t) cc_final: 0.8559 (m) REVERT: D 292 GLU cc_start: 0.8040 (tp30) cc_final: 0.7818 (tp30) REVERT: D 333 LEU cc_start: 0.8865 (mt) cc_final: 0.8611 (mp) REVERT: D 446 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7504 (tt0) REVERT: E 45 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8042 (pp) REVERT: E 247 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8099 (mp10) REVERT: E 298 ARG cc_start: 0.8633 (ttm-80) cc_final: 0.8381 (ttm-80) REVERT: E 332 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7915 (mt-10) REVERT: E 453 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8690 (mm-40) REVERT: F 11 ARG cc_start: 0.8441 (ptm-80) cc_final: 0.7766 (ptt-90) REVERT: F 67 MET cc_start: 0.8646 (mmm) cc_final: 0.7559 (mmm) REVERT: F 127 PHE cc_start: 0.8295 (t80) cc_final: 0.8090 (t80) REVERT: F 131 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8219 (mt-10) REVERT: F 254 ASP cc_start: 0.7540 (t0) cc_final: 0.7279 (t70) REVERT: F 420 GLU cc_start: 0.7684 (tp30) cc_final: 0.7290 (tp30) REVERT: F 458 ILE cc_start: 0.8773 (tp) cc_final: 0.8570 (tp) REVERT: G 136 GLU cc_start: 0.8264 (tp30) cc_final: 0.7984 (tp30) REVERT: G 144 ARG cc_start: 0.7803 (tpp-160) cc_final: 0.7430 (mtp-110) REVERT: G 162 MET cc_start: 0.7500 (mtp) cc_final: 0.7278 (mtp) REVERT: G 201 ARG cc_start: 0.7432 (mtt-85) cc_final: 0.6563 (mtm110) REVERT: G 243 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7509 (mmt180) REVERT: H 7 GLU cc_start: 0.7659 (tt0) cc_final: 0.7007 (mm-30) REVERT: a 100 ILE cc_start: 0.6960 (tp) cc_final: 0.6472 (mp) REVERT: a 213 PHE cc_start: 0.7082 (t80) cc_final: 0.6505 (m-80) REVERT: b 63 MET cc_start: 0.4028 (ttm) cc_final: 0.3785 (tmm) REVERT: d 132 ILE cc_start: 0.6344 (mt) cc_final: 0.6130 (mt) REVERT: d 428 ILE cc_start: 0.7694 (mt) cc_final: 0.7443 (mp) REVERT: d 440 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7858 (tm-30) REVERT: 4 75 MET cc_start: 0.6903 (ttp) cc_final: 0.6668 (tmm) REVERT: 8 21 MET cc_start: 0.8573 (mmm) cc_final: 0.7924 (mmm) REVERT: 8 75 MET cc_start: 0.8218 (ttp) cc_final: 0.7649 (ptt) outliers start: 109 outliers final: 70 residues processed: 651 average time/residue: 0.2236 time to fit residues: 241.6981 Evaluate side-chains 629 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 554 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 87 GLU 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 370 VAL Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 138 SER 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 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 140 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 468 GLU 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 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 77 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 300 ARG Chi-restraints excluded: chain E residue 316 THR 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 120 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 220 MET 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 470 SER 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 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 131 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 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 422 THR Chi-restraints excluded: chain d residue 436 LEU 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: 6.9990 chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 320 optimal weight: 3.9990 chunk 352 optimal weight: 6.9990 chunk 474 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 289 optimal weight: 0.3980 chunk 131 optimal weight: 1.9990 chunk 460 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3804 r_free = 0.3804 target = 0.146374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108376 restraints weight = 49566.193| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.92 r_work: 0.3130 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: 0.7788 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 36425 Z= 0.213 Angle : 0.607 10.557 49490 Z= 0.305 Chirality : 0.044 0.294 5810 Planarity : 0.004 0.055 6389 Dihedral : 7.822 106.998 5435 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.20 % Favored : 97.65 % Rotamer: Outliers : 3.20 % Allowed : 16.01 % Favored : 80.78 % 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: 1.07 (0.12), residues: 4774 helix: 1.66 (0.10), residues: 2599 sheet: -0.87 (0.22), residues: 539 loop : -0.15 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 335 TYR 0.026 0.002 TYR a 145 PHE 0.033 0.002 PHE 7 57 TRP 0.011 0.001 TRP a 212 HIS 0.005 0.001 HIS D 56 Details of bonding type rmsd covalent geometry : bond 0.00505 (36422) covalent geometry : angle 0.60692 (49490) hydrogen bonds : bond 0.04093 ( 2408) hydrogen bonds : angle 4.64037 ( 6933) Misc. bond : bond 0.00083 ( 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 686 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 574 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8272 (m-30) cc_final: 0.8020 (m-30) REVERT: A 67 LEU cc_start: 0.8534 (tp) cc_final: 0.8213 (tp) REVERT: A 71 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8157 (mt-10) REVERT: A 160 THR cc_start: 0.8447 (p) cc_final: 0.8072 (t) REVERT: A 200 GLN cc_start: 0.8898 (mt0) cc_final: 0.8355 (mm110) REVERT: A 370 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8242 (t) REVERT: A 388 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: A 429 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8071 (mm-30) REVERT: A 473 GLU cc_start: 0.8412 (tp30) cc_final: 0.8042 (tt0) REVERT: B 466 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7965 (ttp80) REVERT: B 487 ARG cc_start: 0.8347 (ttp80) cc_final: 0.8141 (ttp80) REVERT: C 197 ASP cc_start: 0.7932 (t0) cc_final: 0.7582 (m-30) REVERT: C 276 LYS cc_start: 0.7915 (mttt) cc_final: 0.7625 (mttt) REVERT: C 399 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8068 (mm-40) REVERT: C 421 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7871 (mp) REVERT: C 468 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: D 120 ILE cc_start: 0.8607 (pt) cc_final: 0.8380 (pt) REVERT: D 185 SER cc_start: 0.8833 (t) cc_final: 0.8551 (m) REVERT: D 333 LEU cc_start: 0.8878 (mt) cc_final: 0.8628 (mp) REVERT: D 446 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7528 (tt0) REVERT: E 45 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8103 (pp) REVERT: E 172 GLU cc_start: 0.7459 (tp30) cc_final: 0.7013 (tp30) REVERT: E 332 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7917 (mt-10) REVERT: E 453 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8622 (mm-40) REVERT: F 11 ARG cc_start: 0.8475 (ptm-80) cc_final: 0.7811 (ptt-90) REVERT: F 67 MET cc_start: 0.8645 (mmm) cc_final: 0.7565 (mmm) REVERT: F 120 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8144 (tt) REVERT: F 131 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8218 (mt-10) REVERT: F 254 ASP cc_start: 0.7596 (t0) cc_final: 0.7303 (t70) REVERT: F 393 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7012 (tm-30) REVERT: F 420 GLU cc_start: 0.7729 (tp30) cc_final: 0.7365 (tp30) REVERT: G 41 GLU cc_start: 0.8109 (tp30) cc_final: 0.7760 (tp30) REVERT: G 136 GLU cc_start: 0.8290 (tp30) cc_final: 0.7999 (tp30) REVERT: G 144 ARG cc_start: 0.7825 (tpp-160) cc_final: 0.7558 (ttm-80) REVERT: G 162 MET cc_start: 0.7520 (mtp) cc_final: 0.7300 (mtp) REVERT: G 201 ARG cc_start: 0.7554 (mtt-85) cc_final: 0.6663 (mtm110) REVERT: H 7 GLU cc_start: 0.7676 (tt0) cc_final: 0.6963 (mm-30) REVERT: a 100 ILE cc_start: 0.6896 (tp) cc_final: 0.6418 (mp) REVERT: a 213 PHE cc_start: 0.7079 (t80) cc_final: 0.6533 (m-80) REVERT: b 63 MET cc_start: 0.4336 (ttm) cc_final: 0.4050 (tmm) REVERT: d 132 ILE cc_start: 0.6267 (mt) cc_final: 0.6052 (mt) REVERT: d 440 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7737 (tm-30) REVERT: 5 21 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7073 (mmt) REVERT: 8 21 MET cc_start: 0.8595 (mmm) cc_final: 0.8031 (mmm) REVERT: 8 75 MET cc_start: 0.8235 (ttp) cc_final: 0.7659 (ptt) outliers start: 112 outliers final: 75 residues processed: 643 average time/residue: 0.2176 time to fit residues: 232.0320 Evaluate side-chains 636 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 554 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 87 GLU Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 301 VAL 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 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 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 140 VAL 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 D residue 8 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 65 ILE 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 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 48 THR 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 120 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 220 MET 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 470 SER 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 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 131 ILE Chi-restraints excluded: chain a residue 235 LEU 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 80 SER 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 2 residue 46 GLN Chi-restraints excluded: chain 5 residue 21 MET Chi-restraints excluded: chain 9 residue 20 ILE Chi-restraints excluded: chain 9 residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 59 optimal weight: 0.6980 chunk 323 optimal weight: 4.9990 chunk 382 optimal weight: 0.8980 chunk 246 optimal weight: 0.4980 chunk 180 optimal weight: 0.7980 chunk 426 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 213 optimal weight: 0.6980 chunk 475 optimal weight: 0.0870 chunk 299 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN C 89 GLN C 143 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN E 55 GLN E 245 GLN d 141 GLN d 273 HIS 4 46 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.148449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110519 restraints weight = 49664.834| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.94 r_work: 0.3186 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36425 Z= 0.131 Angle : 0.577 11.611 49490 Z= 0.289 Chirality : 0.042 0.308 5810 Planarity : 0.004 0.054 6389 Dihedral : 7.501 107.087 5435 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.01 % Favored : 97.86 % Rotamer: Outliers : 2.57 % Allowed : 16.96 % Favored : 80.47 % 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: 1.34 (0.12), residues: 4774 helix: 1.86 (0.10), residues: 2581 sheet: -0.80 (0.22), residues: 532 loop : 0.03 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 261 TYR 0.022 0.001 TYR a 145 PHE 0.035 0.001 PHE 7 57 TRP 0.010 0.001 TRP a 212 HIS 0.005 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00294 (36422) covalent geometry : angle 0.57723 (49490) hydrogen bonds : bond 0.03836 ( 2408) hydrogen bonds : angle 4.53819 ( 6933) Misc. bond : bond 0.00069 ( 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 675 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 585 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8473 (tp) cc_final: 0.8271 (tp) REVERT: A 71 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8162 (mt-10) REVERT: A 160 THR cc_start: 0.8461 (p) cc_final: 0.8089 (t) REVERT: A 200 GLN cc_start: 0.8868 (mt0) cc_final: 0.8301 (mm110) REVERT: A 310 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7390 (mm-30) REVERT: A 370 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8165 (t) REVERT: A 388 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: A 429 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8116 (mm-30) REVERT: A 473 GLU cc_start: 0.8339 (tp30) cc_final: 0.7984 (tt0) REVERT: A 488 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7911 (mm-30) REVERT: B 39 ASP cc_start: 0.6738 (m-30) cc_final: 0.6277 (m-30) REVERT: B 54 GLU cc_start: 0.8177 (tt0) cc_final: 0.7860 (tt0) REVERT: B 487 ARG cc_start: 0.8297 (ttp80) cc_final: 0.8078 (ttp80) REVERT: C 197 ASP cc_start: 0.7872 (t0) cc_final: 0.7517 (m-30) REVERT: C 269 ILE cc_start: 0.8400 (mm) cc_final: 0.8172 (tt) REVERT: C 276 LYS cc_start: 0.7910 (mttt) cc_final: 0.7645 (mttt) REVERT: C 421 LEU cc_start: 0.8102 (tp) cc_final: 0.7799 (mp) REVERT: C 468 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: D 39 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8287 (mm-30) REVERT: D 120 ILE cc_start: 0.8606 (pt) cc_final: 0.8382 (pt) REVERT: D 185 SER cc_start: 0.8822 (t) cc_final: 0.8551 (m) REVERT: D 221 ASP cc_start: 0.8324 (m-30) cc_final: 0.8051 (m-30) REVERT: D 333 LEU cc_start: 0.8872 (mt) cc_final: 0.8604 (mp) REVERT: D 446 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7563 (tt0) REVERT: E 45 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7976 (pp) REVERT: E 219 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7704 (mm110) REVERT: E 332 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7934 (mt-10) REVERT: E 412 LEU cc_start: 0.8283 (mt) cc_final: 0.7914 (mm) REVERT: E 444 LYS cc_start: 0.8204 (mmtp) cc_final: 0.7994 (mmtp) REVERT: E 453 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8590 (mm-40) REVERT: E 457 LEU cc_start: 0.8706 (mt) cc_final: 0.8504 (mt) REVERT: F 11 ARG cc_start: 0.8437 (ptm-80) cc_final: 0.7821 (ptt-90) REVERT: F 67 MET cc_start: 0.8550 (mmm) cc_final: 0.7429 (mmm) REVERT: F 131 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8208 (mt-10) REVERT: F 254 ASP cc_start: 0.7552 (t0) cc_final: 0.7242 (t70) REVERT: F 378 ARG cc_start: 0.8123 (tpt170) cc_final: 0.7900 (tpt-90) REVERT: F 393 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6943 (tm-30) REVERT: F 420 GLU cc_start: 0.7718 (tp30) cc_final: 0.7402 (tp30) REVERT: G 136 GLU cc_start: 0.8308 (tp30) cc_final: 0.8014 (tp30) REVERT: G 144 ARG cc_start: 0.7843 (tpp-160) cc_final: 0.7450 (mtp-110) REVERT: G 162 MET cc_start: 0.7454 (mtp) cc_final: 0.7229 (mtp) REVERT: G 201 ARG cc_start: 0.7444 (mtt-85) cc_final: 0.6654 (mtm110) REVERT: G 263 MET cc_start: 0.7818 (mmp) cc_final: 0.7590 (mmt) REVERT: H 7 GLU cc_start: 0.7678 (tt0) cc_final: 0.6973 (mm-30) REVERT: a 83 MET cc_start: 0.5054 (mtp) cc_final: 0.4790 (mtp) REVERT: a 100 ILE cc_start: 0.7052 (tp) cc_final: 0.6605 (mp) REVERT: a 213 PHE cc_start: 0.7059 (t80) cc_final: 0.6595 (m-80) REVERT: b 63 MET cc_start: 0.4396 (ttm) cc_final: 0.3934 (tmm) REVERT: d 132 ILE cc_start: 0.6192 (mt) cc_final: 0.5990 (mt) REVERT: d 147 VAL cc_start: 0.9019 (t) cc_final: 0.8815 (m) REVERT: d 241 LEU cc_start: 0.8021 (mt) cc_final: 0.7761 (mt) REVERT: 1 21 MET cc_start: 0.7615 (tpp) cc_final: 0.7146 (tpp) REVERT: 2 75 MET cc_start: 0.6820 (ppp) cc_final: 0.6608 (tmm) REVERT: 8 21 MET cc_start: 0.8598 (mmm) cc_final: 0.7968 (mmm) REVERT: 8 75 MET cc_start: 0.8272 (ttp) cc_final: 0.7652 (ptt) outliers start: 90 outliers final: 62 residues processed: 639 average time/residue: 0.2234 time to fit residues: 236.2430 Evaluate side-chains 612 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 546 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 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 123 ASP Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 430 LEU 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 468 GLU 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 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 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 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 220 MET Chi-restraints excluded: chain F residue 251 LEU 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 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 G residue 236 LEU Chi-restraints excluded: chain G residue 293 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 111 VAL Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 80 SER 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 2 residue 46 GLN 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: 20.0000 chunk 452 optimal weight: 5.9990 chunk 384 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 436 optimal weight: 0.5980 chunk 341 optimal weight: 3.9990 chunk 311 optimal weight: 0.5980 chunk 438 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN D 421 GLN E 247 GLN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 GLN d 273 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.146894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.109034 restraints weight = 49528.568| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.93 r_work: 0.3164 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36425 Z= 0.188 Angle : 0.601 11.926 49490 Z= 0.303 Chirality : 0.044 0.330 5810 Planarity : 0.004 0.055 6389 Dihedral : 7.388 105.562 5435 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.22 % Favored : 97.63 % Rotamer: Outliers : 2.63 % Allowed : 17.90 % Favored : 79.47 % 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: 1.32 (0.12), residues: 4774 helix: 1.87 (0.10), residues: 2569 sheet: -0.81 (0.22), residues: 529 loop : 0.01 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 335 TYR 0.025 0.001 TYR a 145 PHE 0.036 0.001 PHE 7 57 TRP 0.012 0.001 TRP a 212 HIS 0.005 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00444 (36422) covalent geometry : angle 0.60072 (49490) hydrogen bonds : bond 0.03971 ( 2408) hydrogen bonds : angle 4.54319 ( 6933) Misc. bond : bond 0.00071 ( 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 647 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 555 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8484 (tp) cc_final: 0.8231 (tp) REVERT: A 71 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8064 (mt-10) REVERT: A 83 GLU cc_start: 0.8200 (pt0) cc_final: 0.7893 (tm-30) REVERT: A 84 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8743 (mtpt) REVERT: A 160 THR cc_start: 0.8460 (p) cc_final: 0.8104 (t) REVERT: A 200 GLN cc_start: 0.8905 (mt0) cc_final: 0.8345 (mm-40) REVERT: A 310 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7486 (mm-30) REVERT: A 370 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8211 (t) REVERT: A 388 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8087 (mt-10) REVERT: A 429 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8096 (mm-30) REVERT: A 473 GLU cc_start: 0.8385 (tp30) cc_final: 0.8016 (tt0) REVERT: B 279 ASP cc_start: 0.8053 (t0) cc_final: 0.7813 (t0) REVERT: B 319 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8788 (mm) REVERT: B 466 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7938 (ttp80) REVERT: C 194 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8567 (mt) REVERT: C 197 ASP cc_start: 0.7881 (t0) cc_final: 0.7527 (m-30) REVERT: C 269 ILE cc_start: 0.8472 (mm) cc_final: 0.8211 (tt) REVERT: C 276 LYS cc_start: 0.7923 (mttt) cc_final: 0.7642 (mttt) REVERT: C 335 ASN cc_start: 0.8844 (t0) cc_final: 0.8542 (t0) REVERT: C 399 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7922 (mm110) REVERT: C 421 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7839 (mp) REVERT: C 468 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: C 535 LYS cc_start: 0.8811 (mttp) cc_final: 0.8267 (mmtp) REVERT: D 39 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8298 (mm-30) REVERT: D 120 ILE cc_start: 0.8616 (pt) cc_final: 0.8389 (pt) REVERT: D 139 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7981 (p) REVERT: D 185 SER cc_start: 0.8834 (t) cc_final: 0.8555 (m) REVERT: D 221 ASP cc_start: 0.8328 (m-30) cc_final: 0.8053 (m-30) REVERT: D 333 LEU cc_start: 0.8887 (mt) cc_final: 0.8624 (mp) REVERT: D 446 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7515 (tt0) REVERT: E 45 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8030 (pp) REVERT: E 173 MET cc_start: 0.8475 (mmt) cc_final: 0.8183 (mmt) REVERT: E 219 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7719 (mm110) REVERT: E 332 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7943 (mt-10) REVERT: E 444 LYS cc_start: 0.8228 (mmtp) cc_final: 0.8020 (mmtp) REVERT: E 453 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8603 (mm-40) REVERT: F 11 ARG cc_start: 0.8489 (ptm-80) cc_final: 0.7859 (ptt-90) REVERT: F 67 MET cc_start: 0.8597 (mmm) cc_final: 0.7504 (mmm) REVERT: F 131 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8250 (mt-10) REVERT: F 254 ASP cc_start: 0.7569 (t0) cc_final: 0.7257 (t70) REVERT: F 393 GLU cc_start: 0.7303 (tm-30) cc_final: 0.7055 (tm-30) REVERT: F 420 GLU cc_start: 0.7779 (tp30) cc_final: 0.7457 (tp30) REVERT: G 136 GLU cc_start: 0.8337 (tp30) cc_final: 0.8039 (tp30) REVERT: G 144 ARG cc_start: 0.7976 (tpp-160) cc_final: 0.7593 (mtp-110) REVERT: G 162 MET cc_start: 0.7559 (mtp) cc_final: 0.7337 (mtp) REVERT: G 201 ARG cc_start: 0.7481 (mtt-85) cc_final: 0.6687 (mtm110) REVERT: G 230 THR cc_start: 0.8227 (m) cc_final: 0.7946 (t) REVERT: G 263 MET cc_start: 0.7937 (mmp) cc_final: 0.7685 (mmt) REVERT: H 7 GLU cc_start: 0.7690 (tt0) cc_final: 0.7001 (mm-30) REVERT: a 83 MET cc_start: 0.4988 (mtp) cc_final: 0.4726 (mtp) REVERT: a 100 ILE cc_start: 0.6979 (tp) cc_final: 0.6510 (mp) REVERT: a 233 PHE cc_start: 0.7904 (t80) cc_final: 0.7301 (t80) REVERT: b 63 MET cc_start: 0.4498 (ttm) cc_final: 0.4041 (tmm) REVERT: d 132 ILE cc_start: 0.6200 (mt) cc_final: 0.5993 (mt) REVERT: d 147 VAL cc_start: 0.9038 (t) cc_final: 0.8822 (m) REVERT: 2 75 MET cc_start: 0.6881 (ppp) cc_final: 0.6470 (tmm) REVERT: 8 21 MET cc_start: 0.8643 (mmm) cc_final: 0.8009 (mmm) REVERT: 8 75 MET cc_start: 0.8238 (ttp) cc_final: 0.7664 (ptt) outliers start: 92 outliers final: 71 residues processed: 614 average time/residue: 0.2137 time to fit residues: 217.1855 Evaluate side-chains 623 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 545 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 197 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 123 ASP 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 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 194 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 468 GLU 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 139 THR 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 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 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 220 MET Chi-restraints excluded: chain F residue 251 LEU 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 13 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 97 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 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 80 SER 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 2 residue 46 GLN 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: 0.5980 chunk 239 optimal weight: 0.8980 chunk 416 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 385 optimal weight: 6.9990 chunk 354 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 473 optimal weight: 4.9990 chunk 443 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN C 352 GLN C 505 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 273 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.145745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.107956 restraints weight = 49380.263| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.91 r_work: 0.3150 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 36425 Z= 0.238 Angle : 0.629 12.170 49490 Z= 0.317 Chirality : 0.045 0.352 5810 Planarity : 0.004 0.056 6389 Dihedral : 7.349 107.096 5435 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.26 % Favored : 97.59 % Rotamer: Outliers : 2.77 % Allowed : 18.22 % Favored : 79.01 % 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: 1.21 (0.12), residues: 4774 helix: 1.80 (0.10), residues: 2570 sheet: -0.87 (0.22), residues: 529 loop : -0.09 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 335 TYR 0.025 0.002 TYR a 145 PHE 0.037 0.002 PHE 7 57 TRP 0.013 0.001 TRP a 212 HIS 0.005 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00567 (36422) covalent geometry : angle 0.62898 (49490) hydrogen bonds : bond 0.04076 ( 2408) hydrogen bonds : angle 4.58095 ( 6933) Misc. bond : bond 0.00081 ( 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 653 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 556 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8512 (tp) cc_final: 0.8248 (tp) REVERT: A 71 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8091 (mt-10) REVERT: A 83 GLU cc_start: 0.8218 (pt0) cc_final: 0.7959 (tm-30) REVERT: A 84 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8848 (mtpt) REVERT: A 160 THR cc_start: 0.8459 (p) cc_final: 0.8096 (t) REVERT: A 200 GLN cc_start: 0.8907 (mt0) cc_final: 0.8365 (mm-40) REVERT: A 310 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7505 (mm-30) REVERT: A 388 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: A 429 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8078 (mm-30) REVERT: A 473 GLU cc_start: 0.8431 (tp30) cc_final: 0.8072 (tt0) REVERT: B 279 ASP cc_start: 0.8028 (t0) cc_final: 0.7791 (t0) REVERT: B 319 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8808 (mm) REVERT: B 466 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7945 (ttp80) REVERT: C 194 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8582 (mt) REVERT: C 197 ASP cc_start: 0.7904 (t0) cc_final: 0.7541 (m-30) REVERT: C 269 ILE cc_start: 0.8503 (mm) cc_final: 0.8214 (tt) REVERT: C 276 LYS cc_start: 0.7944 (mttt) cc_final: 0.7614 (mttt) REVERT: C 335 ASN cc_start: 0.8831 (t0) cc_final: 0.8528 (t0) REVERT: C 421 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7871 (mp) REVERT: C 429 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7903 (mm-30) REVERT: C 468 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: C 535 LYS cc_start: 0.8850 (mttp) cc_final: 0.8310 (mmtp) REVERT: D 39 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8269 (mm-30) REVERT: D 120 ILE cc_start: 0.8618 (pt) cc_final: 0.8416 (pt) REVERT: D 139 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8191 (p) REVERT: D 185 SER cc_start: 0.8849 (t) cc_final: 0.8569 (m) REVERT: D 221 ASP cc_start: 0.8381 (m-30) cc_final: 0.8103 (m-30) REVERT: D 333 LEU cc_start: 0.8903 (mt) cc_final: 0.8650 (mp) REVERT: D 446 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7586 (tt0) REVERT: D 447 PHE cc_start: 0.8592 (m-80) cc_final: 0.8321 (m-10) REVERT: E 45 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8106 (pp) REVERT: E 192 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7435 (mm-30) REVERT: E 219 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7796 (mm110) REVERT: E 247 GLN cc_start: 0.8551 (mp10) cc_final: 0.8218 (mp10) REVERT: E 444 LYS cc_start: 0.8265 (mmtp) cc_final: 0.8051 (mmtp) REVERT: E 453 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8640 (mm-40) REVERT: F 11 ARG cc_start: 0.8557 (ptm-80) cc_final: 0.7911 (ptt-90) REVERT: F 67 MET cc_start: 0.8585 (mmm) cc_final: 0.7516 (mmm) REVERT: F 131 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8278 (mt-10) REVERT: F 254 ASP cc_start: 0.7566 (t0) cc_final: 0.7255 (t70) REVERT: F 393 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7138 (tm-30) REVERT: F 420 GLU cc_start: 0.7754 (tp30) cc_final: 0.7406 (tp30) REVERT: G 136 GLU cc_start: 0.8351 (tp30) cc_final: 0.8053 (tp30) REVERT: G 144 ARG cc_start: 0.7908 (tpp-160) cc_final: 0.7580 (mtp-110) REVERT: G 162 MET cc_start: 0.7612 (mtp) cc_final: 0.7374 (mtp) REVERT: G 201 ARG cc_start: 0.7516 (mtt-85) cc_final: 0.6707 (mtm110) REVERT: G 230 THR cc_start: 0.8247 (m) cc_final: 0.8002 (t) REVERT: G 263 MET cc_start: 0.7985 (mmp) cc_final: 0.7744 (mmt) REVERT: H 7 GLU cc_start: 0.7717 (tt0) cc_final: 0.7039 (mm-30) REVERT: a 83 MET cc_start: 0.5034 (mtp) cc_final: 0.4771 (mtp) REVERT: a 100 ILE cc_start: 0.6884 (tp) cc_final: 0.6416 (mp) REVERT: a 206 PHE cc_start: 0.5632 (m-80) cc_final: 0.5303 (m-10) REVERT: a 233 PHE cc_start: 0.7947 (t80) cc_final: 0.7355 (t80) REVERT: b 63 MET cc_start: 0.4530 (ttm) cc_final: 0.4065 (tmm) REVERT: d 132 ILE cc_start: 0.6157 (mt) cc_final: 0.5947 (mt) REVERT: d 147 VAL cc_start: 0.9049 (t) cc_final: 0.8838 (m) REVERT: 8 21 MET cc_start: 0.8623 (mmm) cc_final: 0.8034 (mmm) REVERT: 8 75 MET cc_start: 0.8267 (ttp) cc_final: 0.7684 (ptt) outliers start: 97 outliers final: 80 residues processed: 617 average time/residue: 0.2163 time to fit residues: 220.7346 Evaluate side-chains 631 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 544 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 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 388 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 123 ASP 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 B residue 442 GLU 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 194 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 85 SER 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 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 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 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 143 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 277 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 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 97 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 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 112 ASP Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 80 SER 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 2 residue 46 GLN 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: 0.6980 chunk 126 optimal weight: 0.5980 chunk 473 optimal weight: 7.9990 chunk 236 optimal weight: 3.9990 chunk 99 optimal weight: 0.0020 chunk 461 optimal weight: 4.9990 chunk 239 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 182 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 340 optimal weight: 40.0000 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.148491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.111004 restraints weight = 49222.609| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.87 r_work: 0.3198 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 36425 Z= 0.131 Angle : 0.588 12.310 49490 Z= 0.295 Chirality : 0.042 0.354 5810 Planarity : 0.004 0.053 6389 Dihedral : 7.106 105.504 5435 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.99 % Favored : 97.88 % Rotamer: Outliers : 2.17 % Allowed : 18.96 % Favored : 78.87 % 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: 1.99 (0.10), residues: 2563 sheet: -0.81 (0.22), residues: 536 loop : -0.04 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 122 TYR 0.025 0.001 TYR a 145 PHE 0.036 0.001 PHE 7 57 TRP 0.012 0.001 TRP a 212 HIS 0.004 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00294 (36422) covalent geometry : angle 0.58795 (49490) hydrogen bonds : bond 0.03781 ( 2408) hydrogen bonds : angle 4.49769 ( 6933) Misc. bond : bond 0.00069 ( 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 652 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 576 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8015 (mt-10) REVERT: A 83 GLU cc_start: 0.8194 (pt0) cc_final: 0.7917 (tm-30) REVERT: A 84 LYS cc_start: 0.9044 (mtmm) cc_final: 0.8727 (mtpt) REVERT: A 160 THR cc_start: 0.8479 (p) cc_final: 0.8105 (t) REVERT: A 200 GLN cc_start: 0.8877 (mt0) cc_final: 0.8293 (mm-40) REVERT: A 310 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7360 (mm-30) REVERT: A 348 ILE cc_start: 0.8437 (mt) cc_final: 0.8185 (tp) REVERT: A 388 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8049 (mt-10) REVERT: A 429 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8117 (mm-30) REVERT: A 473 GLU cc_start: 0.8326 (tp30) cc_final: 0.7961 (tt0) REVERT: B 54 GLU cc_start: 0.8236 (tt0) cc_final: 0.7892 (tt0) REVERT: B 65 VAL cc_start: 0.8425 (t) cc_final: 0.8148 (m) REVERT: B 279 ASP cc_start: 0.7990 (t0) cc_final: 0.7748 (t0) REVERT: B 466 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7930 (ttp80) REVERT: C 194 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8523 (mt) REVERT: C 197 ASP cc_start: 0.7740 (t0) cc_final: 0.7391 (m-30) REVERT: C 269 ILE cc_start: 0.8420 (mm) cc_final: 0.8205 (tt) REVERT: C 276 LYS cc_start: 0.7881 (mttt) cc_final: 0.7607 (mttt) REVERT: C 347 SER cc_start: 0.8720 (p) cc_final: 0.8513 (p) REVERT: C 399 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7889 (mm110) REVERT: C 429 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7852 (mm-30) REVERT: C 468 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: C 506 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7381 (mt-10) REVERT: C 535 LYS cc_start: 0.8813 (mttp) cc_final: 0.8288 (mmtp) REVERT: D 39 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8269 (mm-30) REVERT: D 120 ILE cc_start: 0.8627 (pt) cc_final: 0.8387 (pt) REVERT: D 139 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7929 (p) REVERT: D 185 SER cc_start: 0.8826 (t) cc_final: 0.8554 (m) REVERT: D 216 VAL cc_start: 0.8689 (t) cc_final: 0.8386 (m) REVERT: D 221 ASP cc_start: 0.8270 (m-30) cc_final: 0.7992 (m-30) REVERT: D 287 MET cc_start: 0.8425 (tpt) cc_final: 0.8149 (tpp) REVERT: D 333 LEU cc_start: 0.8873 (mt) cc_final: 0.8603 (mp) REVERT: D 349 LEU cc_start: 0.8984 (mm) cc_final: 0.8770 (mt) REVERT: D 446 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7542 (tt0) REVERT: D 447 PHE cc_start: 0.8488 (m-80) cc_final: 0.8183 (m-10) REVERT: E 45 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7951 (pp) REVERT: E 123 LYS cc_start: 0.9101 (mtmm) cc_final: 0.8741 (mmmm) REVERT: E 192 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7409 (mm-30) REVERT: E 219 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7767 (mm110) REVERT: E 315 TYR cc_start: 0.8611 (m-80) cc_final: 0.8317 (m-80) REVERT: E 330 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8294 (p) REVERT: E 393 GLU cc_start: 0.7742 (tp30) cc_final: 0.7519 (tm-30) REVERT: E 412 LEU cc_start: 0.8226 (mt) cc_final: 0.7867 (mm) REVERT: E 453 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8571 (mm-40) REVERT: F 11 ARG cc_start: 0.8491 (ptm-80) cc_final: 0.7867 (ptt-90) REVERT: F 67 MET cc_start: 0.8486 (mmm) cc_final: 0.7355 (mmm) REVERT: F 131 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8253 (mt-10) REVERT: F 152 ARG cc_start: 0.8445 (ttm-80) cc_final: 0.8198 (ttm170) REVERT: F 254 ASP cc_start: 0.7522 (t0) cc_final: 0.7183 (t70) REVERT: F 420 GLU cc_start: 0.7730 (tp30) cc_final: 0.7418 (tp30) REVERT: G 136 GLU cc_start: 0.8326 (tp30) cc_final: 0.8023 (tp30) REVERT: G 144 ARG cc_start: 0.7915 (tpp-160) cc_final: 0.7562 (mtp-110) REVERT: G 162 MET cc_start: 0.7545 (mtp) cc_final: 0.7321 (mtp) REVERT: G 201 ARG cc_start: 0.7407 (mtt-85) cc_final: 0.6659 (mtm110) REVERT: G 230 THR cc_start: 0.8198 (m) cc_final: 0.7959 (t) REVERT: G 263 MET cc_start: 0.7904 (mmp) cc_final: 0.7687 (mmt) REVERT: H 7 GLU cc_start: 0.7663 (tt0) cc_final: 0.6965 (mm-30) REVERT: a 83 MET cc_start: 0.4968 (mtp) cc_final: 0.4679 (mtp) REVERT: a 100 ILE cc_start: 0.6909 (tp) cc_final: 0.6452 (mp) REVERT: a 233 PHE cc_start: 0.7942 (t80) cc_final: 0.7370 (t80) REVERT: b 63 MET cc_start: 0.4530 (ttm) cc_final: 0.4080 (tmm) REVERT: 8 21 MET cc_start: 0.8651 (mmm) cc_final: 0.8058 (mmm) REVERT: 8 75 MET cc_start: 0.8296 (ttp) cc_final: 0.7664 (ptt) outliers start: 76 outliers final: 62 residues processed: 626 average time/residue: 0.2187 time to fit residues: 224.6741 Evaluate side-chains 625 residues out of total 3763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 558 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 269 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 468 GLU 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 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 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 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 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 330 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 143 VAL Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 251 LEU 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 13 ARG Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 236 LEU 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 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 80 SER 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 2 residue 46 GLN 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: 0.8980 chunk 256 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 416 optimal weight: 0.0370 chunk 83 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 378 optimal weight: 0.9990 chunk 325 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 HIS C 143 GLN C 505 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.148211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110484 restraints weight = 48933.208| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.91 r_work: 0.3180 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 36425 Z= 0.147 Angle : 0.596 12.187 49490 Z= 0.298 Chirality : 0.043 0.344 5810 Planarity : 0.004 0.054 6389 Dihedral : 7.003 103.371 5435 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.18 % Favored : 97.70 % Rotamer: Outliers : 2.09 % Allowed : 19.27 % Favored : 78.64 % 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: 1.39 (0.12), residues: 4774 helix: 1.98 (0.10), residues: 2583 sheet: -0.85 (0.22), residues: 529 loop : -0.07 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 261 TYR 0.021 0.001 TYR a 145 PHE 0.037 0.001 PHE 7 57 TRP 0.013 0.001 TRP a 212 HIS 0.005 0.001 HIS d 273 Details of bonding type rmsd covalent geometry : bond 0.00339 (36422) covalent geometry : angle 0.59622 (49490) hydrogen bonds : bond 0.03793 ( 2408) hydrogen bonds : angle 4.45616 ( 6933) Misc. bond : bond 0.00072 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10628.48 seconds wall clock time: 181 minutes 58.87 seconds (10918.87 seconds total)