Starting phenix.real_space_refine on Tue Aug 26 10:11:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g0e_29655/08_2025/8g0e_29655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g0e_29655/08_2025/8g0e_29655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g0e_29655/08_2025/8g0e_29655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g0e_29655/08_2025/8g0e_29655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g0e_29655/08_2025/8g0e_29655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g0e_29655/08_2025/8g0e_29655.map" } resolution = 2.6 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= 0.013 sd= 0.126 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 13 5.49 5 Mg 4 5.21 5 S 104 5.16 5 C 22946 2.51 5 N 6273 2.21 5 O 6612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 261 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35959 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3837 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 492} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3735 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 8, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3781 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 14, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "D" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3508 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3522 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3512 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2103 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 55 Chain: "H" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 835 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 59 Chain: "b" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 966 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 3, 'TRANS': 137} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 57 Chain: "d" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 2893 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 11, 'TRANS': 420} Chain breaks: 1 Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 32, 'ASP:plan': 20, 'GLN:plan1': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 245 Chain: "9" 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: "1" 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: "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: 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: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "4" 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: "5" 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: "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: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" 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: "8" 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: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1807 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 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: 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: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.12, per 1000 atoms: 0.25 Number of scatterers: 35959 At special positions: 0 Unit cell: (122.57, 132.87, 242.05, 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 104 16.00 P 13 15.00 Mg 4 11.99 O 6612 8.00 N 6273 7.00 C 22946 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=0, symmetry=0 Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8742 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 26 sheets defined 62.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 4.731A 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 138 through 142 removed outlier: 3.519A pdb=" N ARG A 142 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.684A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.539A pdb=" N THR A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 227 through 230 removed outlier: 4.180A pdb=" N GLU A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 262 Proline residue: A 250 - end of helix removed outlier: 3.699A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.687A pdb=" N GLN A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 333 through 336 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: 3.643A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 392 through 404 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.827A pdb=" N ALA A 408 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 432 removed outlier: 3.515A pdb=" N LYS A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 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 Processing helix chain 'A' and resid 479 through 490 removed outlier: 4.327A pdb=" N PHE A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 510 removed outlier: 3.511A pdb=" N LYS A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.919A 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 138 through 142 removed outlier: 3.601A pdb=" N ARG B 142 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.667A pdb=" N THR B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.545A pdb=" N THR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 242 through 262 Proline residue: B 250 - end of helix removed outlier: 3.709A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 298 through 299 No H-bonds generated for 'chain 'B' and resid 298 through 299' Processing helix chain 'B' and resid 300 through 310 removed outlier: 3.599A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 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 Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 479 removed outlier: 3.530A pdb=" N GLU B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 490 removed outlier: 4.442A pdb=" N PHE B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 511 removed outlier: 3.784A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 81 through 85 removed outlier: 4.086A pdb=" N LYS C 84 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.570A pdb=" N PHE C 106 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.796A pdb=" N ARG C 142 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 227 through 230 removed outlier: 3.888A pdb=" N GLU C 230 " --> pdb=" O GLY C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 242 through 262 Proline residue: C 250 - end of helix removed outlier: 3.631A 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 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: 3.557A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 356 through 363 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 407 Processing helix chain 'C' and resid 414 through 432 Processing helix chain 'C' and resid 440 through 453 removed outlier: 3.660A pdb=" N GLY C 451 " --> pdb=" O ALA C 447 " (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 Processing helix chain 'C' and resid 479 through 490 removed outlier: 4.268A pdb=" N PHE C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 removed outlier: 3.779A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 removed outlier: 4.415A pdb=" N VAL D 29 " --> pdb=" O ARG D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 126 through 130 Processing helix chain 'D' and resid 141 through 147 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: 3.729A pdb=" N ARG D 227 " --> pdb=" O PRO D 223 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 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 324 Processing helix chain 'D' and resid 334 through 340 Processing helix chain 'D' and resid 362 through 390 removed outlier: 4.406A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 394 Processing helix chain 'D' and resid 395 through 412 Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 451 through 456 removed outlier: 3.534A pdb=" N PHE D 456 " --> pdb=" O GLN D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 4.263A pdb=" N ASP D 463 " --> pdb=" O GLY D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 29 removed outlier: 4.361A pdb=" N VAL E 29 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'E' and resid 126 through 130 Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 165 through 177 Processing helix chain 'E' and resid 193 through 207 Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 223 through 244 removed outlier: 5.211A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 271 removed outlier: 3.923A pdb=" N PHE E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 292 Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 311 through 314 Processing helix chain 'E' and resid 317 through 324 Processing helix chain 'E' and resid 325 through 327 No H-bonds generated for 'chain 'E' and resid 325 through 327' 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 389 removed outlier: 4.452A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE E 388 " --> pdb=" O ASP E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 394 Processing helix chain 'E' and resid 397 through 412 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 456 Processing helix chain 'E' and resid 461 through 471 Processing helix chain 'F' and resid 25 through 29 removed outlier: 4.120A 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: 4.489A pdb=" N ASP F 114 " --> pdb=" O TYR F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 130 Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'F' and resid 165 through 178 Processing helix chain 'F' and resid 193 through 207 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 223 through 244 removed outlier: 5.262A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 268 removed outlier: 4.041A pdb=" N THR F 260 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 282 through 294 removed outlier: 3.654A pdb=" N LEU F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 314 Processing helix chain 'F' and resid 317 through 325 removed outlier: 4.208A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) 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 390 removed outlier: 4.378A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 394 Processing helix chain 'F' and resid 395 through 413 removed outlier: 3.573A 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 445 Processing helix chain 'F' and resid 451 through 456 Processing helix chain 'F' and resid 460 through 471 Processing helix chain 'G' and resid 5 through 43 Processing helix chain 'G' and resid 43 through 61 Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 91 through 110 Processing helix chain 'G' and resid 120 through 130 removed outlier: 3.605A pdb=" N LEU G 124 " --> pdb=" O GLY G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 163 removed outlier: 3.590A pdb=" N ALA G 150 " --> pdb=" O THR G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 303 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 91 through 100 removed outlier: 3.781A pdb=" N ALA H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 118 Processing helix chain 'b' and resid 29 through 48 removed outlier: 3.704A pdb=" N ILE b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 161 removed outlier: 3.745A pdb=" N ALA b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY b 143 " --> pdb=" O GLN b 139 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 4.906A 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 138 Processing helix chain 'd' and resid 139 through 155 Processing helix chain 'd' and resid 173 through 192 removed outlier: 3.898A pdb=" N GLY d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 216 Processing helix chain 'd' and resid 216 through 224 Processing helix chain 'd' and resid 230 through 242 Processing helix chain 'd' and resid 243 through 245 No H-bonds generated for 'chain 'd' and resid 243 through 245' Processing helix chain 'd' and resid 246 through 259 removed outlier: 3.630A pdb=" N LEU d 250 " --> pdb=" O SER d 246 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL d 257 " --> pdb=" O LEU d 253 " (cutoff:3.500A) Processing helix chain 'd' and resid 263 through 287 removed outlier: 3.859A pdb=" N LEU d 267 " --> pdb=" O THR d 263 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU d 279 " --> pdb=" O ALA d 275 " (cutoff:3.500A) Processing helix chain 'd' and resid 288 through 305 Processing helix chain 'd' and resid 306 through 315 removed outlier: 3.583A pdb=" N SER d 310 " --> pdb=" O GLU d 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 319 through 331 Processing helix chain 'd' and resid 338 through 351 Processing helix chain 'd' and resid 356 through 372 removed outlier: 3.704A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 386 through 402 Processing helix chain 'd' and resid 413 through 416 Processing helix chain 'd' and resid 431 through 442 Processing helix chain '9' and resid 6 through 46 Processing helix chain '9' and resid 49 through 80 removed outlier: 4.519A pdb=" N THR 9 55 " --> pdb=" O GLY 9 51 " (cutoff:3.500A) Proline residue: 9 56 - end of helix Processing helix chain '1' and resid 6 through 46 Processing helix chain '1' and resid 49 through 80 removed outlier: 4.080A pdb=" N THR 1 55 " --> pdb=" O GLY 1 51 " (cutoff:3.500A) Proline residue: 1 56 - end of helix Processing helix chain '2' and resid 6 through 46 Processing helix chain '2' and resid 49 through 80 removed outlier: 3.554A pdb=" N PHE 2 54 " --> pdb=" O GLN 2 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR 2 55 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Proline residue: 2 56 - end of helix Processing helix chain '3' and resid 6 through 46 Processing helix chain '3' and resid 49 through 81 removed outlier: 4.195A pdb=" N THR 3 55 " --> pdb=" O GLY 3 51 " (cutoff:3.500A) Proline residue: 3 56 - end of helix Processing helix chain '4' and resid 6 through 46 Processing helix chain '4' and resid 49 through 81 removed outlier: 4.470A pdb=" N THR 4 55 " --> pdb=" O GLY 4 51 " (cutoff:3.500A) Proline residue: 4 56 - end of helix removed outlier: 3.542A pdb=" N ALA 4 67 " --> pdb=" O LEU 4 63 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR 4 68 " --> pdb=" O VAL 4 64 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 46 Processing helix chain '5' and resid 49 through 81 removed outlier: 4.096A pdb=" N THR 5 55 " --> pdb=" O GLY 5 51 " (cutoff:3.500A) Proline residue: 5 56 - end of helix removed outlier: 3.624A pdb=" N TYR 5 68 " --> pdb=" O VAL 5 64 " (cutoff:3.500A) Processing helix chain '6' and resid 6 through 46 Processing helix chain '6' and resid 49 through 80 removed outlier: 3.922A 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: 3.897A 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 46 Processing helix chain '8' and resid 49 through 81 removed outlier: 3.659A pdb=" N PHE 8 54 " --> pdb=" O GLN 8 50 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR 8 55 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) Proline residue: 8 56 - end of helix removed outlier: 3.602A pdb=" N ALA 8 67 " --> pdb=" O LEU 8 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 52 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.687A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.620A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.594A pdb=" N ILE a 160 " --> pdb=" O VAL a 156 " (cutoff:3.500A) 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: 3.573A pdb=" N LEU a 179 " --> pdb=" O ILE a 175 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 3.806A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN a 192 " --> pdb=" O ARG a 188 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET a 205 " --> pdb=" O ALA a 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 246 removed outlier: 3.871A pdb=" N TRP a 212 " --> pdb=" O TRP a 208 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.972A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 38 removed outlier: 5.523A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 41 through 46 current: chain 'A' and resid 63 through 69 removed outlier: 5.707A pdb=" N ALA A 66 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 77 " --> pdb=" O ALA A 66 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 74 through 78 current: chain 'D' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 19 through 23 current: chain 'D' and resid 47 through 58 removed outlier: 6.550A pdb=" N ARG D 63 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N HIS D 56 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU D 61 " --> pdb=" O HIS D 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 61 through 66 current: chain 'd' and resid 405 through 411 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 405 through 411 current: chain 'd' and resid 426 through 429 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 8.644A pdb=" N THR A 233 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 148 removed outlier: 4.883A pdb=" N GLU A 147 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 63 through 69 removed outlier: 4.328A pdb=" N GLU B 54 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU B 55 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL B 34 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU E 78 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU E 39 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA E 35 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN E 34 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG E 63 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N HIS E 56 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU E 61 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU E 23 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 5.739A 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 Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 331 Processing sheet with id=AA9, first strand: chain 'C' and resid 63 through 69 removed outlier: 4.122A pdb=" N GLU C 54 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU C 55 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL C 34 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU C 45 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP C 36 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU C 63 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU F 78 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU F 39 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA F 35 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASN F 34 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG F 63 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N HIS F 56 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU F 61 " --> pdb=" O HIS F 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG F 14 " --> pdb=" O ASP F 21 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU F 23 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL F 12 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AB2, first strand: chain 'C' and resid 110 through 111 removed outlier: 8.527A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.957A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 171 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 534 through 539 removed outlier: 10.843A pdb=" N GLU C 534 " --> pdb=" O PRO G 205 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N GLU G 207 " --> pdb=" O GLU C 534 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU C 536 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLU G 209 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL C 538 " --> pdb=" O GLU G 209 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU G 183 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N THR G 188 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA G 77 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N TYR G 117 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL G 79 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL G 81 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N VAL G 135 " --> pdb=" O PRO G 114 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU G 116 " --> pdb=" O VAL G 135 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER G 137 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL G 118 " --> pdb=" O SER G 137 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 87 through 90 removed outlier: 4.230A pdb=" N GLU D 116 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 98 through 99 current: chain 'D' and resid 213 through 219 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 213 through 219 current: chain 'D' and resid 300 through 307 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 300 through 307 current: chain 'D' and resid 352 through 353 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 135 through 137 removed outlier: 4.756A pdb=" N GLU D 135 " --> pdb=" O ARG D 152 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR D 150 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 87 through 90 removed outlier: 3.967A pdb=" N GLU E 116 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 98 through 99 removed outlier: 6.665A pdb=" N SER E 185 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N VAL E 216 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE E 187 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N TYR E 309 " --> pdb=" O ILE E 253 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS E 155 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N THR E 331 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA E 157 " --> pdb=" O THR E 331 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 136 through 137 removed outlier: 4.259A pdb=" N TYR E 150 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 87 through 90 removed outlier: 4.043A pdb=" N GLU F 116 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 98 through 100 removed outlier: 6.393A pdb=" N PHE F 99 " --> pdb=" O PHE F 217 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER F 185 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL F 216 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE F 187 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLY F 218 " --> pdb=" O PHE F 187 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLY F 189 " --> pdb=" O GLY F 218 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE F 156 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL F 308 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU F 158 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 136 through 137 removed outlier: 4.167A pdb=" N TYR F 150 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 224 through 225 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 224 through 225 current: chain 'H' and resid 14 through 16 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 14 through 16 current: chain 'H' and resid 69 through 72 Processing sheet with id=AC6, first strand: chain 'H' and resid 30 through 34 removed outlier: 4.180A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AC8, first strand: chain 'a' and resid 112 through 114 2383 hydrogen bonds defined for protein. 6840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.88 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 6084 1.31 - 1.47: 14259 1.47 - 1.63: 16038 1.63 - 1.78: 21 1.78 - 1.94: 180 Bond restraints: 36582 Sorted by residual: bond pdb=" CA ARG B 365 " pdb=" C ARG B 365 " ideal model delta sigma weight residual 1.522 1.444 0.079 8.40e-03 1.42e+04 8.76e+01 bond pdb=" CA GLU B 71 " pdb=" C GLU B 71 " ideal model delta sigma weight residual 1.524 1.408 0.115 1.26e-02 6.30e+03 8.38e+01 bond pdb=" CA ASP B 173 " pdb=" C ASP B 173 " ideal model delta sigma weight residual 1.528 1.413 0.114 1.33e-02 5.65e+03 7.41e+01 bond pdb=" CA ASN B 369 " pdb=" C ASN B 369 " ideal model delta sigma weight residual 1.525 1.420 0.104 1.25e-02 6.40e+03 6.95e+01 bond pdb=" C5 ATP B 600 " pdb=" N7 ATP B 600 " ideal model delta sigma weight residual 1.387 1.305 0.082 1.00e-02 1.00e+04 6.78e+01 ... (remaining 36577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 49278 3.61 - 7.22: 392 7.22 - 10.83: 39 10.83 - 14.44: 4 14.44 - 18.05: 1 Bond angle restraints: 49714 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 121.82 18.05 1.00e+00 1.00e+00 3.26e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 122.89 13.94 1.00e+00 1.00e+00 1.94e+02 angle pdb=" N ALA D 359 " pdb=" CA ALA D 359 " pdb=" C ALA D 359 " ideal model delta sigma weight residual 111.28 123.86 -12.58 1.09e+00 8.42e-01 1.33e+02 angle pdb=" N LYS B 178 " pdb=" CA LYS B 178 " pdb=" C LYS B 178 " ideal model delta sigma weight residual 111.28 122.09 -10.81 1.09e+00 8.42e-01 9.83e+01 angle pdb=" N GLU B 71 " pdb=" CA GLU B 71 " pdb=" C GLU B 71 " ideal model delta sigma weight residual 111.14 101.62 9.52 1.08e+00 8.57e-01 7.77e+01 ... (remaining 49709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.64: 20816 24.64 - 49.28: 884 49.28 - 73.92: 165 73.92 - 98.56: 37 98.56 - 123.20: 2 Dihedral angle restraints: 21904 sinusoidal: 8256 harmonic: 13648 Sorted by residual: dihedral pdb=" CA PRO C 366 " pdb=" C PRO C 366 " pdb=" N ALA C 367 " pdb=" CA ALA C 367 " ideal model delta harmonic sigma weight residual 180.00 152.33 27.67 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA GLU D 192 " pdb=" C GLU D 192 " pdb=" N ARG D 193 " pdb=" CA ARG D 193 " ideal model delta harmonic sigma weight residual 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ARG A 365 " pdb=" C ARG A 365 " pdb=" N PRO A 366 " pdb=" CA PRO A 366 " ideal model delta harmonic sigma weight residual 0.00 25.61 -25.61 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 21901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 5767 0.151 - 0.302: 62 0.302 - 0.453: 12 0.453 - 0.604: 2 0.604 - 0.755: 1 Chirality restraints: 5844 Sorted by residual: chirality pdb=" CB VAL B 370 " pdb=" CA VAL B 370 " pdb=" CG1 VAL B 370 " pdb=" CG2 VAL B 370 " both_signs ideal model delta sigma weight residual False -2.63 -1.87 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA LYS B 175 " pdb=" N LYS B 175 " pdb=" C LYS B 175 " pdb=" CB LYS B 175 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.42e+00 chirality pdb=" CA THR B 176 " pdb=" N THR B 176 " pdb=" C THR B 176 " pdb=" CB THR B 176 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.47 2.00e-01 2.50e+01 5.57e+00 ... (remaining 5841 not shown) Planarity restraints: 6397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG 5 45 " 0.026 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C ARG 5 45 " -0.086 2.00e-02 2.50e+03 pdb=" O ARG 5 45 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN 5 46 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN 7 50 " 0.024 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C GLN 7 50 " -0.082 2.00e-02 2.50e+03 pdb=" O GLN 7 50 " 0.030 2.00e-02 2.50e+03 pdb=" N GLY 7 51 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 343 " -0.053 2.00e-02 2.50e+03 3.30e-02 1.90e+01 pdb=" CG PHE D 343 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE D 343 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE D 343 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE D 343 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE D 343 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 343 " -0.035 2.00e-02 2.50e+03 ... (remaining 6394 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 57 2.41 - 3.03: 24057 3.03 - 3.65: 56090 3.65 - 4.28: 87286 4.28 - 4.90: 148133 Nonbonded interactions: 315623 Sorted by model distance: nonbonded pdb=" O2G ATP E 600 " pdb="MG MG E 601 " model vdw 1.784 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.845 2.170 nonbonded pdb=" OG1 THR E 167 " pdb="MG MG E 601 " model vdw 1.849 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.868 2.170 nonbonded pdb=" OG1 THR A 179 " pdb="MG MG A 601 " model vdw 1.897 2.170 ... (remaining 315618 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 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 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 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 '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 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 '6' 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 '7' 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)) selection = (chain '8' 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)) selection = (chain '9' 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)) } ncs_group { reference = (chain 'A' and ((resid 9 through 12 and (name N or name CA or name C or name O o \ r name CB )) or (resid 13 through 17 and (name N or name CA or name C or name O \ or name CB )) or resid 18 or (resid 19 through 22 and (name N or name CA or name \ C or name O or name CB )) or (resid 29 and (name N or name CA or name C or name \ O or name CB )) or resid 30 through 38 or (resid 39 and (name N or name CA or n \ ame C or name O or name CB )) or resid 40 through 69 or (resid 70 and (name N or \ name CA or name C or name O or name CB )) or resid 71 through 172 or (resid 173 \ and (name N or name CA or name C or name O or name CB )) or resid 174 through 2 \ 40 or (resid 241 through 243 and (name N or name CA or name C or name O or name \ CB )) or resid 244 through 272 or (resid 273 and (name N or name CA or name C or \ name O or name CB )) or resid 274 through 278 or (resid 279 through 280 and (na \ me N or name CA or name C or name O or name CB )) or resid 281 through 294 or (r \ esid 295 through 296 and (name N or name CA or name C or name O or name CB )) or \ resid 297 through 299 or (resid 300 and (name N or name CA or name C or name O \ or name CB )) or resid 301 through 316 or (resid 317 through 318 and (name N or \ name CA or name C or name O or name CB )) or resid 319 through 335 or (resid 336 \ and (name N or name CA or name C or name O or name CB )) or resid 337 through 3 \ 55 or (resid 356 and (name N or name CA or name C or name O or name CB )) or res \ id 357 or (resid 358 and (name N or name CA or name C or name O or name CB )) or \ resid 359 through 387 or (resid 388 and (name N or name CA or name C or name O \ or name CB )) or resid 389 through 401 or (resid 402 and (name N or name CA or n \ ame C or name O or name CB )) or resid 403 through 411 or (resid 412 through 416 \ and (name N or name CA or name C or name O or name CB )) or resid 417 through 4 \ 61 or (resid 462 through 463 and (name N or name CA or name C or name O or name \ CB )) or resid 464 through 472 or (resid 473 and (name N or name CA or name C or \ name O or name CB )) or resid 474 through 480 or (resid 481 and (name N or name \ CA or name C or name O or name CB )) or resid 482 through 483 or (resid 484 and \ (name N or name CA or name C or name O or name CB )) or resid 485 through 493 o \ r (resid 494 through 496 and (name N or name CA or name C or name O or name CB ) \ ) or resid 497 or (resid 498 and (name N or name CA or name C or name O or name \ CB )) or resid 499 through 515 or (resid 518 and (name N or name CA or name C or \ name O or name CB )) or resid 519 through 601)) selection = (chain 'B' 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 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 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 240 or \ (resid 241 through 243 and (name N or name CA or name C or name O or name CB )) \ or resid 244 through 272 or (resid 273 and (name N or name CA or name C or name \ O or name CB )) or resid 274 through 278 or (resid 279 through 280 and (name N \ or name CA or name C or name O or name CB )) or resid 281 through 294 or (resid \ 295 through 296 and (name N or name CA or name C or name O or name CB )) or resi \ d 297 through 316 or (resid 317 through 318 and (name N or name CA or name C or \ name O or name CB )) or resid 319 through 335 or (resid 336 and (name N or name \ CA or name C or name O or name CB )) or resid 337 through 387 or (resid 388 and \ (name N or name CA or name C or name O or name CB )) or resid 389 through 403 or \ (resid 404 through 405 and (name N or name CA or name C or name O or name CB )) \ or resid 406 through 461 or (resid 462 through 463 and (name N or name CA or na \ me C or name O or name CB )) or resid 464 through 493 or (resid 494 through 496 \ and (name N or name CA or name C or name O or name CB )) or resid 497 or (resid \ 498 and (name N or name CA or name C or name O or name CB )) or resid 499 throug \ h 515 or resid 518 through 601)) selection = (chain 'C' and (resid 9 through 38 or (resid 39 and (name N or name CA or name C \ or name O or name CB )) or resid 40 through 69 or (resid 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 122 or (resid 123 and \ (name N or name CA or name C or name O or name CB )) or resid 124 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 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 o \ r name C or name O or name CB )) or resid 403 or (resid 404 through 405 and (nam \ e N or name CA or name C or name O or name CB )) or resid 406 through 412 or (re \ sid 413 through 416 and (name N or name CA or name C or name O or name CB )) or \ resid 417 through 421 or (resid 422 and (name N or name CA or name C or name O o \ r name CB )) or resid 423 through 505 or (resid 506 and (name N or name CA or na \ me C or name O or name CB )) or resid 507 through 515 or (resid 537 and (name N \ or name CA or name C or name O or name CB )) or resid 538 or resid 540 or resid \ 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 191 or (resid 192 and (name N or na \ me CA or name C or name O or name CB )) or resid 193 through 198 or (resid 199 a \ nd (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 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 n \ ame O or name CB )) or resid 208 through 211 or (resid 212 and (name N or name C \ A or name C or name O or name CB )) or resid 213 through 284 or (resid 285 and ( \ name N or name CA or name C or name O or name CB )) or resid 286 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 396 or (resid 397 through 398 and (name N or name CA or \ name C or name O or name CB )) or resid 399 through 436 or (resid 437 through 4 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 439 through \ 471)) selection = (chain 'E' and (resid 8 through 198 or (resid 199 and (name N or name CA or name \ C or name O or name CB )) or resid 200 through 253 or (resid 254 and (name N or \ name CA or name C or name O or name CB )) or resid 255 through 312 or (resid 31 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 314 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 391 or (resid 392 through 393 and (name N or name CA \ or name C or name O or name CB )) or resid 394 through 395 or (resid 396 throug \ h 398 and (name N or name CA or name C or name O or name CB )) or resid 399 thro \ ugh 436 or (resid 437 through 438 and (name N or name CA or name C or name O or \ name CB )) or resid 439 through 447 or (resid 448 and (name N or name CA or name \ C or name O or name CB )) or resid 449 through 452 or (resid 453 through 454 an \ d (name N or name CA or name C or name O or name CB )) or resid 455 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 471)) selection = (chain 'F' and (resid 8 through 58 or (resid 59 through 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 211 or (resid 212 and (n \ ame N or name CA or name C or name O or name CB )) or resid 213 through 253 or ( \ resid 254 and (name N or name CA or name C or name O or name CB )) or resid 255 \ 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 na \ me O or name CB )) or resid 293 through 312 or (resid 313 and (name N or name CA \ or name C or name O or name CB )) or resid 314 through 391 or (resid 392 throug \ h 393 and (name N or name CA or name C or name O or name CB )) or resid 394 thro \ ugh 397 or (resid 398 and (name N or name CA or name C or name O or name CB )) o \ r resid 399 through 447 or (resid 448 and (name N or name CA or name C or name O \ or name CB )) or resid 449 through 452 or (resid 453 through 454 and (name N or \ name CA or name C or name O or name CB )) or resid 455 through 462 or (resid 46 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 464 through \ 471)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 36.790 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 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:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 : 0.008 0.120 36582 Z= 0.507 Angle : 0.801 18.052 49714 Z= 0.501 Chirality : 0.052 0.755 5844 Planarity : 0.005 0.085 6397 Dihedral : 14.351 123.201 13162 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Rotamer: Outliers : 1.18 % Allowed : 0.92 % Favored : 97.90 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 4.12 % 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 aren not related in a simple way. whole: 0.70 (0.12), residues: 4804 helix: 1.11 (0.10), residues: 2622 sheet: -0.95 (0.22), residues: 517 loop : 0.11 (0.16), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 144 TYR 0.020 0.001 TYR E 315 PHE 0.053 0.002 PHE D 343 TRP 0.011 0.001 TRP F 118 HIS 0.005 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00789 (36582) covalent geometry : angle 0.80056 (49714) hydrogen bonds : bond 0.14460 ( 2383) hydrogen bonds : angle 6.86284 ( 6840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 338 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 358 PRO cc_start: 0.9079 (OUTLIER) cc_final: 0.8871 (Cg_exo) REVERT: G 155 ASP cc_start: 0.8000 (t0) cc_final: 0.7781 (t0) outliers start: 41 outliers final: 9 residues processed: 372 average time/residue: 0.8233 time to fit residues: 363.7038 Evaluate side-chains 204 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 358 PRO Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain b residue 55 LYS Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 242 SER Chi-restraints excluded: chain 5 residue 52 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 470 optimal weight: 8.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS A 512 GLN D 425 GLN E 175 ASN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 HIS F 175 ASN F 326 HIS b 136 GLN d 34 GLN 1 6 ASN ** 3 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 71 ASN a 15 HIS a 76 GLN a 243 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.071806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.044587 restraints weight = 122559.057| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.60 r_work: 0.2757 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 36582 Z= 0.184 Angle : 0.613 11.885 49714 Z= 0.313 Chirality : 0.043 0.245 5844 Planarity : 0.004 0.048 6397 Dihedral : 8.491 118.264 5587 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.75 % Favored : 98.23 % Rotamer: Outliers : 1.35 % Allowed : 7.50 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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 aren not related in a simple way. whole: 1.44 (0.12), residues: 4804 helix: 1.79 (0.10), residues: 2646 sheet: -0.84 (0.22), residues: 529 loop : 0.35 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 9 45 TYR 0.026 0.001 TYR a 145 PHE 0.024 0.002 PHE 3 74 TRP 0.016 0.001 TRP d 21 HIS 0.006 0.001 HIS a 12 Details of bonding type rmsd covalent geometry : bond 0.00408 (36582) covalent geometry : angle 0.61319 (49714) hydrogen bonds : bond 0.04694 ( 2383) hydrogen bonds : angle 5.02952 ( 6840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 227 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 403 ASN cc_start: 0.9100 (m-40) cc_final: 0.8872 (m-40) REVERT: G 155 ASP cc_start: 0.9208 (t0) cc_final: 0.8864 (t0) REVERT: H 7 GLU cc_start: 0.9010 (pt0) cc_final: 0.8266 (pm20) REVERT: H 31 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7347 (mm-30) REVERT: b 45 ILE cc_start: 0.7874 (mm) cc_final: 0.7572 (tp) REVERT: b 59 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8890 (pp20) REVERT: b 82 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8924 (tp-100) REVERT: b 89 MET cc_start: 0.8512 (mmp) cc_final: 0.8259 (mmm) REVERT: d 68 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8615 (tm-30) REVERT: 9 39 LEU cc_start: 0.9128 (tp) cc_final: 0.8918 (mp) REVERT: 9 63 LEU cc_start: 0.9049 (mm) cc_final: 0.8636 (tt) REVERT: 9 74 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8404 (t80) REVERT: 2 21 MET cc_start: 0.8127 (ttt) cc_final: 0.7773 (ttt) REVERT: 3 32 ASP cc_start: 0.8913 (m-30) cc_final: 0.8275 (t0) REVERT: 3 65 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6743 (tm-30) REVERT: 3 74 PHE cc_start: 0.8327 (t80) cc_final: 0.7906 (t80) REVERT: 4 32 ASP cc_start: 0.9193 (m-30) cc_final: 0.8908 (p0) REVERT: 4 63 LEU cc_start: 0.9042 (mt) cc_final: 0.8673 (tm) REVERT: 4 72 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9195 (mp) REVERT: 4 75 MET cc_start: 0.8940 (ppp) cc_final: 0.8541 (ppp) REVERT: 6 65 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7631 (tp30) REVERT: 6 69 PHE cc_start: 0.8823 (t80) cc_final: 0.8571 (t80) REVERT: 7 75 MET cc_start: 0.8195 (ppp) cc_final: 0.7847 (ppp) REVERT: 8 75 MET cc_start: 0.8317 (tmm) cc_final: 0.6814 (tmm) REVERT: a 74 ARG cc_start: 0.9482 (ttp-110) cc_final: 0.9282 (ttp-110) REVERT: a 229 GLN cc_start: 0.9565 (mm-40) cc_final: 0.9150 (mm-40) REVERT: a 240 TYR cc_start: 0.9218 (m-80) cc_final: 0.8899 (m-80) outliers start: 47 outliers final: 11 residues processed: 257 average time/residue: 0.7962 time to fit residues: 245.4153 Evaluate side-chains 213 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain 9 residue 74 PHE Chi-restraints excluded: chain 3 residue 65 GLU Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 6 residue 65 GLU Chi-restraints excluded: chain 6 residue 72 LEU Chi-restraints excluded: chain 7 residue 32 ASP Chi-restraints excluded: chain 7 residue 74 PHE Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain a residue 181 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 49 optimal weight: 1.9990 chunk 328 optimal weight: 50.0000 chunk 127 optimal weight: 0.8980 chunk 86 optimal weight: 0.0020 chunk 178 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 HIS G 131 GLN b 136 GLN ** 1 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 71 ASN a 76 GLN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.071912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.045235 restraints weight = 121419.794| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.56 r_work: 0.2780 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36582 Z= 0.140 Angle : 0.560 10.211 49714 Z= 0.284 Chirality : 0.042 0.245 5844 Planarity : 0.004 0.050 6397 Dihedral : 7.671 110.960 5569 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.69 % Favored : 98.29 % Rotamer: Outliers : 1.58 % Allowed : 9.05 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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 aren not related in a simple way. whole: 1.64 (0.12), residues: 4804 helix: 1.98 (0.10), residues: 2668 sheet: -0.91 (0.22), residues: 525 loop : 0.41 (0.17), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 9 52 TYR 0.025 0.001 TYR a 145 PHE 0.025 0.001 PHE 8 54 TRP 0.010 0.001 TRP d 21 HIS 0.005 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00303 (36582) covalent geometry : angle 0.56048 (49714) hydrogen bonds : bond 0.04186 ( 2383) hydrogen bonds : angle 4.75961 ( 6840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 217 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 403 ASN cc_start: 0.9089 (m-40) cc_final: 0.8847 (m-40) REVERT: F 343 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: F 416 MET cc_start: 0.9421 (mtm) cc_final: 0.8951 (mtm) REVERT: G 155 ASP cc_start: 0.9214 (t0) cc_final: 0.8864 (t0) REVERT: H 7 GLU cc_start: 0.8986 (pt0) cc_final: 0.8301 (pm20) REVERT: H 31 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7429 (mm-30) REVERT: b 45 ILE cc_start: 0.7779 (mm) cc_final: 0.7419 (tp) REVERT: b 82 GLN cc_start: 0.9003 (tp-100) cc_final: 0.8577 (tp-100) REVERT: 9 19 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8099 (tm) REVERT: 9 63 LEU cc_start: 0.9185 (mm) cc_final: 0.8907 (tt) REVERT: 9 74 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8227 (t80) REVERT: 2 21 MET cc_start: 0.8172 (ttt) cc_final: 0.7348 (ttt) REVERT: 3 32 ASP cc_start: 0.9082 (m-30) cc_final: 0.8360 (t0) REVERT: 3 65 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6476 (tm-30) REVERT: 3 74 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7665 (t80) REVERT: 4 63 LEU cc_start: 0.8994 (mt) cc_final: 0.8685 (tm) REVERT: 4 75 MET cc_start: 0.8913 (ppp) cc_final: 0.8616 (ppp) REVERT: 5 46 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8718 (tm-30) REVERT: 5 72 LEU cc_start: 0.9311 (mt) cc_final: 0.9099 (mt) REVERT: 6 32 ASP cc_start: 0.8364 (m-30) cc_final: 0.8107 (m-30) REVERT: 6 65 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7777 (tp30) REVERT: 6 69 PHE cc_start: 0.8780 (t80) cc_final: 0.8542 (t80) REVERT: 7 75 MET cc_start: 0.8041 (ppp) cc_final: 0.7809 (ppp) REVERT: a 177 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8305 (mp0) REVERT: a 240 TYR cc_start: 0.9245 (m-80) cc_final: 0.8945 (m-80) outliers start: 55 outliers final: 12 residues processed: 247 average time/residue: 0.6022 time to fit residues: 181.8248 Evaluate side-chains 217 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain F residue 343 PHE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain 9 residue 19 LEU Chi-restraints excluded: chain 9 residue 74 PHE Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 3 residue 65 GLU Chi-restraints excluded: chain 3 residue 74 PHE Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 6 residue 65 GLU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 74 PHE Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain a residue 181 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 429 optimal weight: 30.0000 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 450 optimal weight: 40.0000 chunk 333 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 353 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 GLN b 136 GLN ** 2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN ** 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 = 0.3678 r_free = 0.3678 target = 0.070586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.043610 restraints weight = 122538.800| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.55 r_work: 0.2724 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 36582 Z= 0.245 Angle : 0.601 10.281 49714 Z= 0.302 Chirality : 0.043 0.226 5844 Planarity : 0.004 0.049 6397 Dihedral : 7.317 114.174 5568 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.81 % Favored : 98.17 % Rotamer: Outliers : 1.81 % Allowed : 10.26 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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 aren not related in a simple way. whole: 1.75 (0.12), residues: 4804 helix: 2.08 (0.10), residues: 2658 sheet: -0.94 (0.22), residues: 518 loop : 0.49 (0.17), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 141 TYR 0.024 0.001 TYR a 145 PHE 0.020 0.001 PHE E 257 TRP 0.010 0.001 TRP b 48 HIS 0.005 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00551 (36582) covalent geometry : angle 0.60149 (49714) hydrogen bonds : bond 0.04242 ( 2383) hydrogen bonds : angle 4.67941 ( 6840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 324 MET cc_start: 0.9562 (ttm) cc_final: 0.9351 (ttp) REVERT: D 403 ASN cc_start: 0.9080 (m-40) cc_final: 0.8869 (m-40) REVERT: F 343 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8634 (m-80) REVERT: F 355 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9199 (tp) REVERT: F 416 MET cc_start: 0.9428 (mtm) cc_final: 0.9002 (mtm) REVERT: G 155 ASP cc_start: 0.9216 (t0) cc_final: 0.8882 (t0) REVERT: H 7 GLU cc_start: 0.9019 (pt0) cc_final: 0.8352 (pm20) REVERT: H 31 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7111 (mp0) REVERT: b 45 ILE cc_start: 0.7861 (mm) cc_final: 0.7479 (tp) REVERT: d 68 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9084 (tm-30) REVERT: d 72 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8408 (p) REVERT: 9 19 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8151 (tm) REVERT: 9 63 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8959 (tt) REVERT: 9 74 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8345 (t80) REVERT: 1 32 ASP cc_start: 0.8777 (m-30) cc_final: 0.8270 (m-30) REVERT: 2 21 MET cc_start: 0.8148 (ttt) cc_final: 0.7302 (ttt) REVERT: 2 75 MET cc_start: 0.7955 (tmm) cc_final: 0.7736 (tmm) REVERT: 3 32 ASP cc_start: 0.9063 (m-30) cc_final: 0.8332 (t0) REVERT: 3 53 LEU cc_start: 0.9100 (mm) cc_final: 0.8730 (pp) REVERT: 3 65 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6537 (tm-30) REVERT: 3 74 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7688 (t80) REVERT: 3 75 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8085 (ppp) REVERT: 4 32 ASP cc_start: 0.9232 (m-30) cc_final: 0.8963 (p0) REVERT: 4 63 LEU cc_start: 0.8972 (mt) cc_final: 0.8685 (tm) REVERT: 4 75 MET cc_start: 0.8987 (ppp) cc_final: 0.8508 (ppp) REVERT: 5 52 ARG cc_start: 0.7282 (ttp-170) cc_final: 0.7059 (ptt180) REVERT: 6 65 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7584 (tp30) REVERT: 6 69 PHE cc_start: 0.8754 (t80) cc_final: 0.8512 (t80) REVERT: 8 74 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8743 (t80) REVERT: 8 75 MET cc_start: 0.8235 (tmm) cc_final: 0.6064 (tmm) REVERT: a 12 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.7045 (t70) REVERT: a 205 MET cc_start: 0.8462 (mpm) cc_final: 0.8201 (mpm) outliers start: 63 outliers final: 20 residues processed: 249 average time/residue: 0.7265 time to fit residues: 220.3015 Evaluate side-chains 223 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain F residue 343 PHE Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 274 THR Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 9 residue 19 LEU Chi-restraints excluded: chain 9 residue 63 LEU Chi-restraints excluded: chain 9 residue 74 PHE Chi-restraints excluded: chain 3 residue 65 GLU Chi-restraints excluded: chain 3 residue 74 PHE Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 6 residue 19 LEU Chi-restraints excluded: chain 6 residue 65 GLU Chi-restraints excluded: chain 7 residue 32 ASP Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 8 residue 53 LEU Chi-restraints excluded: chain 8 residue 57 PHE Chi-restraints excluded: chain 8 residue 74 PHE Chi-restraints excluded: chain a residue 12 HIS Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain a residue 181 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 143 optimal weight: 0.0470 chunk 112 optimal weight: 6.9990 chunk 336 optimal weight: 6.9990 chunk 391 optimal weight: 50.0000 chunk 475 optimal weight: 5.9990 chunk 410 optimal weight: 40.0000 chunk 341 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 478 optimal weight: 30.0000 chunk 462 optimal weight: 7.9990 overall best weight: 4.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 56 HIS E 255 ASN G 131 GLN ** b 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 136 GLN a 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.070108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.043148 restraints weight = 122803.084| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.53 r_work: 0.2711 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 36582 Z= 0.276 Angle : 0.615 10.953 49714 Z= 0.309 Chirality : 0.044 0.251 5844 Planarity : 0.004 0.051 6397 Dihedral : 7.178 103.313 5568 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.95 % Allowed : 11.01 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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 aren not related in a simple way. whole: 1.78 (0.12), residues: 4804 helix: 2.11 (0.10), residues: 2657 sheet: -0.96 (0.22), residues: 528 loop : 0.50 (0.17), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 141 TYR 0.023 0.001 TYR a 145 PHE 0.037 0.001 PHE 7 74 TRP 0.010 0.001 TRP b 48 HIS 0.006 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00620 (36582) covalent geometry : angle 0.61471 (49714) hydrogen bonds : bond 0.04195 ( 2383) hydrogen bonds : angle 4.68284 ( 6840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 202 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 324 MET cc_start: 0.9626 (ttm) cc_final: 0.9306 (ttp) REVERT: D 403 ASN cc_start: 0.9095 (m-40) cc_final: 0.8886 (m-40) REVERT: E 227 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.8782 (mtp-110) REVERT: E 255 ASN cc_start: 0.9345 (OUTLIER) cc_final: 0.9073 (p0) REVERT: F 136 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.9215 (ttt) REVERT: F 343 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8671 (m-80) REVERT: F 355 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9194 (tp) REVERT: F 416 MET cc_start: 0.9425 (mtm) cc_final: 0.8948 (mtm) REVERT: G 155 ASP cc_start: 0.9222 (t0) cc_final: 0.8887 (t0) REVERT: H 7 GLU cc_start: 0.9050 (pt0) cc_final: 0.8420 (pm20) REVERT: H 31 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7473 (mm-30) REVERT: b 45 ILE cc_start: 0.7913 (mm) cc_final: 0.7668 (tp) REVERT: b 136 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7674 (tp40) REVERT: d 68 GLU cc_start: 0.9472 (mm-30) cc_final: 0.9199 (tm-30) REVERT: d 72 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8525 (p) REVERT: d 371 ARG cc_start: 0.9412 (OUTLIER) cc_final: 0.9134 (tpp80) REVERT: 9 19 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8174 (tm) REVERT: 9 57 PHE cc_start: 0.9468 (t80) cc_final: 0.9257 (t80) REVERT: 9 74 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8337 (t80) REVERT: 2 21 MET cc_start: 0.8144 (ttt) cc_final: 0.7557 (OUTLIER) REVERT: 3 21 MET cc_start: 0.9142 (tpt) cc_final: 0.8837 (tpt) REVERT: 3 32 ASP cc_start: 0.9061 (m-30) cc_final: 0.8351 (t0) REVERT: 3 53 LEU cc_start: 0.9075 (mm) cc_final: 0.8765 (pp) REVERT: 3 65 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6648 (tm-30) REVERT: 3 74 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7956 (t80) REVERT: 3 75 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8191 (ppp) REVERT: 4 32 ASP cc_start: 0.9240 (m-30) cc_final: 0.8971 (p0) REVERT: 4 63 LEU cc_start: 0.9002 (mt) cc_final: 0.8728 (tm) REVERT: 4 75 MET cc_start: 0.8885 (ppp) cc_final: 0.8308 (ppp) REVERT: 5 46 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8664 (tm-30) REVERT: 6 65 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7806 (tp30) REVERT: 8 74 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8684 (t80) REVERT: 8 75 MET cc_start: 0.8093 (tmm) cc_final: 0.7207 (tmm) REVERT: a 12 HIS cc_start: 0.7668 (OUTLIER) cc_final: 0.7100 (t70) REVERT: a 83 MET cc_start: 0.8123 (mmt) cc_final: 0.7870 (mmt) REVERT: a 177 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8815 (mp0) REVERT: a 205 MET cc_start: 0.8609 (mpm) cc_final: 0.8324 (mpm) outliers start: 68 outliers final: 17 residues processed: 248 average time/residue: 0.7584 time to fit residues: 227.3840 Evaluate side-chains 223 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 343 PHE Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain b residue 136 GLN Chi-restraints excluded: chain b residue 159 ILE Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 274 THR Chi-restraints excluded: chain d residue 371 ARG Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 9 residue 19 LEU Chi-restraints excluded: chain 9 residue 74 PHE Chi-restraints excluded: chain 3 residue 65 GLU Chi-restraints excluded: chain 3 residue 74 PHE Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 6 residue 65 GLU Chi-restraints excluded: chain 8 residue 53 LEU Chi-restraints excluded: chain 8 residue 55 THR Chi-restraints excluded: chain 8 residue 57 PHE Chi-restraints excluded: chain 8 residue 74 PHE Chi-restraints excluded: chain a residue 12 HIS Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 243 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 436 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 446 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 460 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 454 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN E 255 ASN 3 50 GLN a 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.070568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.043617 restraints weight = 121103.551| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.53 r_work: 0.2725 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 36582 Z= 0.212 Angle : 0.592 11.681 49714 Z= 0.297 Chirality : 0.043 0.204 5844 Planarity : 0.004 0.056 6397 Dihedral : 6.867 91.461 5564 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.75 % Allowed : 11.99 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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 aren not related in a simple way. whole: 1.82 (0.12), residues: 4804 helix: 2.15 (0.10), residues: 2655 sheet: -1.00 (0.22), residues: 530 loop : 0.55 (0.17), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG b 141 TYR 0.024 0.001 TYR a 240 PHE 0.036 0.001 PHE 7 74 TRP 0.011 0.001 TRP b 48 HIS 0.005 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00475 (36582) covalent geometry : angle 0.59158 (49714) hydrogen bonds : bond 0.04044 ( 2383) hydrogen bonds : angle 4.64256 ( 6840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 201 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 324 MET cc_start: 0.9606 (ttm) cc_final: 0.9305 (ttp) REVERT: D 403 ASN cc_start: 0.9091 (m-40) cc_final: 0.8870 (m-40) REVERT: E 227 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8767 (mtp-110) REVERT: F 136 MET cc_start: 0.9486 (OUTLIER) cc_final: 0.9204 (ttt) REVERT: F 343 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8660 (m-80) REVERT: F 355 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9187 (tp) REVERT: F 416 MET cc_start: 0.9407 (mtm) cc_final: 0.9016 (mtm) REVERT: G 155 ASP cc_start: 0.9230 (t0) cc_final: 0.8892 (t0) REVERT: H 7 GLU cc_start: 0.9047 (pt0) cc_final: 0.8413 (pm20) REVERT: H 31 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7188 (mp0) REVERT: b 45 ILE cc_start: 0.7903 (mm) cc_final: 0.7659 (tp) REVERT: d 68 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9086 (tm-30) REVERT: d 371 ARG cc_start: 0.9426 (OUTLIER) cc_final: 0.9139 (tpp80) REVERT: 9 19 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8184 (tm) REVERT: 9 57 PHE cc_start: 0.9438 (t80) cc_final: 0.9206 (t80) REVERT: 9 65 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6753 (tm-30) REVERT: 9 74 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8311 (t80) REVERT: 2 21 MET cc_start: 0.8149 (ttt) cc_final: 0.7258 (ttt) REVERT: 3 21 MET cc_start: 0.9140 (tpt) cc_final: 0.8882 (tpt) REVERT: 3 32 ASP cc_start: 0.9066 (m-30) cc_final: 0.8348 (t70) REVERT: 3 53 LEU cc_start: 0.9095 (mm) cc_final: 0.8783 (pp) REVERT: 3 65 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: 3 74 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7809 (t80) REVERT: 3 75 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8059 (ppp) REVERT: 4 32 ASP cc_start: 0.9259 (m-30) cc_final: 0.8938 (p0) REVERT: 4 63 LEU cc_start: 0.9015 (mt) cc_final: 0.8686 (tm) REVERT: 4 75 MET cc_start: 0.8946 (ppp) cc_final: 0.8546 (ppp) REVERT: 5 46 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8610 (tm-30) REVERT: 6 32 ASP cc_start: 0.8535 (m-30) cc_final: 0.8292 (m-30) REVERT: 6 65 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7571 (tp30) REVERT: 8 32 ASP cc_start: 0.8660 (t0) cc_final: 0.8405 (t0) REVERT: 8 75 MET cc_start: 0.8103 (tmm) cc_final: 0.7243 (tmm) REVERT: a 12 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.7128 (t70) REVERT: a 104 ASN cc_start: 0.9177 (t0) cc_final: 0.8930 (m-40) REVERT: a 205 MET cc_start: 0.8647 (mpm) cc_final: 0.8337 (mpm) outliers start: 61 outliers final: 23 residues processed: 242 average time/residue: 0.7606 time to fit residues: 222.2998 Evaluate side-chains 224 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 343 PHE Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain b residue 159 ILE Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 371 ARG Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 9 residue 19 LEU Chi-restraints excluded: chain 9 residue 65 GLU Chi-restraints excluded: chain 9 residue 74 PHE Chi-restraints excluded: chain 9 residue 78 PHE Chi-restraints excluded: chain 3 residue 65 GLU Chi-restraints excluded: chain 3 residue 74 PHE Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 6 residue 65 GLU Chi-restraints excluded: chain 7 residue 32 ASP Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 8 residue 53 LEU Chi-restraints excluded: chain 8 residue 55 THR Chi-restraints excluded: chain 8 residue 57 PHE Chi-restraints excluded: chain 8 residue 64 VAL Chi-restraints excluded: chain a residue 12 HIS Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 243 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 340 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 445 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 304 optimal weight: 6.9990 chunk 309 optimal weight: 20.0000 chunk 398 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 416 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN 3 50 GLN a 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.070213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.043227 restraints weight = 122249.007| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.53 r_work: 0.2714 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 36582 Z= 0.243 Angle : 0.612 13.670 49714 Z= 0.306 Chirality : 0.043 0.244 5844 Planarity : 0.004 0.059 6397 Dihedral : 6.666 86.928 5564 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.85 % Favored : 98.13 % Rotamer: Outliers : 1.75 % Allowed : 12.53 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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 aren not related in a simple way. whole: 1.85 (0.13), residues: 4804 helix: 2.21 (0.10), residues: 2630 sheet: -0.94 (0.22), residues: 534 loop : 0.49 (0.17), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG b 141 TYR 0.023 0.001 TYR a 145 PHE 0.018 0.001 PHE 3 74 TRP 0.011 0.001 TRP b 48 HIS 0.005 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00547 (36582) covalent geometry : angle 0.61171 (49714) hydrogen bonds : bond 0.04046 ( 2383) hydrogen bonds : angle 4.63147 ( 6840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 324 MET cc_start: 0.9630 (ttm) cc_final: 0.9318 (ttp) REVERT: D 403 ASN cc_start: 0.9102 (m-40) cc_final: 0.8881 (m-40) REVERT: E 135 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: E 227 ARG cc_start: 0.9311 (OUTLIER) cc_final: 0.8776 (mtp-110) REVERT: F 136 MET cc_start: 0.9491 (OUTLIER) cc_final: 0.9209 (ttt) REVERT: F 343 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8668 (m-80) REVERT: F 355 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9196 (tp) REVERT: F 416 MET cc_start: 0.9414 (mtm) cc_final: 0.9038 (mtm) REVERT: G 155 ASP cc_start: 0.9240 (t0) cc_final: 0.8896 (t0) REVERT: H 7 GLU cc_start: 0.9035 (pt0) cc_final: 0.8404 (pm20) REVERT: H 31 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7093 (mp0) REVERT: b 45 ILE cc_start: 0.7942 (mm) cc_final: 0.7686 (tp) REVERT: b 59 GLU cc_start: 0.9324 (mm-30) cc_final: 0.8985 (pp20) REVERT: d 68 GLU cc_start: 0.9474 (mm-30) cc_final: 0.9145 (tm-30) REVERT: d 72 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8547 (p) REVERT: d 371 ARG cc_start: 0.9428 (OUTLIER) cc_final: 0.9134 (tpp80) REVERT: 9 19 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8244 (tm) REVERT: 9 57 PHE cc_start: 0.9431 (t80) cc_final: 0.9070 (t80) REVERT: 9 65 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6475 (tm-30) REVERT: 9 74 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8298 (t80) REVERT: 2 21 MET cc_start: 0.8205 (ttt) cc_final: 0.7371 (ttt) REVERT: 3 21 MET cc_start: 0.9146 (tpt) cc_final: 0.8844 (tpt) REVERT: 3 32 ASP cc_start: 0.9054 (m-30) cc_final: 0.8313 (t70) REVERT: 3 53 LEU cc_start: 0.9090 (mm) cc_final: 0.8776 (pp) REVERT: 3 74 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7766 (t80) REVERT: 3 75 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8047 (ppp) REVERT: 4 32 ASP cc_start: 0.9296 (m-30) cc_final: 0.8972 (p0) REVERT: 4 63 LEU cc_start: 0.9047 (mt) cc_final: 0.8751 (tm) REVERT: 4 75 MET cc_start: 0.8927 (ppp) cc_final: 0.8459 (ppp) REVERT: 5 46 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8662 (tm-30) REVERT: 6 65 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7712 (tp30) REVERT: 6 75 MET cc_start: 0.7622 (tmm) cc_final: 0.7421 (tmm) REVERT: 8 74 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8727 (t80) REVERT: a 104 ASN cc_start: 0.9225 (t0) cc_final: 0.8950 (m-40) REVERT: a 205 MET cc_start: 0.8642 (mpm) cc_final: 0.8429 (mpm) REVERT: a 240 TYR cc_start: 0.9352 (m-80) cc_final: 0.9136 (m-80) outliers start: 61 outliers final: 27 residues processed: 244 average time/residue: 0.7453 time to fit residues: 220.4627 Evaluate side-chains 226 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 343 PHE Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain b residue 159 ILE Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 274 THR Chi-restraints excluded: chain d residue 371 ARG Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 9 residue 19 LEU Chi-restraints excluded: chain 9 residue 65 GLU Chi-restraints excluded: chain 9 residue 74 PHE Chi-restraints excluded: chain 9 residue 78 PHE Chi-restraints excluded: chain 3 residue 65 GLU Chi-restraints excluded: chain 3 residue 74 PHE Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 6 residue 65 GLU Chi-restraints excluded: chain 7 residue 39 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 8 residue 53 LEU Chi-restraints excluded: chain 8 residue 55 THR Chi-restraints excluded: chain 8 residue 74 PHE Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 243 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 83 optimal weight: 0.0070 chunk 374 optimal weight: 20.0000 chunk 430 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 474 optimal weight: 30.0000 chunk 304 optimal weight: 2.9990 chunk 424 optimal weight: 4.9990 chunk 361 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 50 GLN a 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.071006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.044216 restraints weight = 120899.123| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.53 r_work: 0.2753 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36582 Z= 0.146 Angle : 0.581 14.443 49714 Z= 0.288 Chirality : 0.041 0.250 5844 Planarity : 0.004 0.060 6397 Dihedral : 6.302 88.342 5564 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.85 % Favored : 98.13 % Rotamer: Outliers : 1.52 % Allowed : 13.22 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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 aren not related in a simple way. whole: 1.92 (0.13), residues: 4804 helix: 2.26 (0.10), residues: 2647 sheet: -0.91 (0.22), residues: 536 loop : 0.53 (0.17), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG b 141 TYR 0.023 0.001 TYR a 145 PHE 0.017 0.001 PHE a 142 TRP 0.012 0.001 TRP b 48 HIS 0.004 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00322 (36582) covalent geometry : angle 0.58062 (49714) hydrogen bonds : bond 0.03841 ( 2383) hydrogen bonds : angle 4.53613 ( 6840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 403 ASN cc_start: 0.9103 (m-40) cc_final: 0.8874 (m-40) REVERT: E 227 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8733 (mtp-110) REVERT: F 136 MET cc_start: 0.9451 (OUTLIER) cc_final: 0.9171 (ttt) REVERT: F 343 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8699 (m-80) REVERT: F 355 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9189 (tp) REVERT: F 416 MET cc_start: 0.9394 (mtm) cc_final: 0.9022 (mtm) REVERT: G 155 ASP cc_start: 0.9240 (t0) cc_final: 0.8928 (t0) REVERT: G 232 PHE cc_start: 0.9036 (t80) cc_final: 0.8828 (t80) REVERT: H 7 GLU cc_start: 0.9005 (pt0) cc_final: 0.8379 (pm20) REVERT: H 31 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7013 (mp0) REVERT: b 45 ILE cc_start: 0.7866 (mm) cc_final: 0.7593 (tp) REVERT: b 59 GLU cc_start: 0.9342 (mm-30) cc_final: 0.9050 (pp20) REVERT: b 82 GLN cc_start: 0.8933 (tp-100) cc_final: 0.8692 (tp-100) REVERT: d 57 MET cc_start: 0.8746 (ttp) cc_final: 0.8470 (tmm) REVERT: d 68 GLU cc_start: 0.9475 (mm-30) cc_final: 0.9160 (tm-30) REVERT: d 72 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8573 (p) REVERT: d 371 ARG cc_start: 0.9415 (OUTLIER) cc_final: 0.9112 (tpp80) REVERT: 9 19 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8165 (tm) REVERT: 9 57 PHE cc_start: 0.9331 (t80) cc_final: 0.9096 (t80) REVERT: 9 65 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6658 (tm-30) REVERT: 9 74 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8422 (t80) REVERT: 9 78 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.5758 (m-80) REVERT: 2 21 MET cc_start: 0.8241 (ttt) cc_final: 0.7453 (ttt) REVERT: 3 32 ASP cc_start: 0.9043 (m-30) cc_final: 0.8295 (t70) REVERT: 3 53 LEU cc_start: 0.9107 (mm) cc_final: 0.8788 (pp) REVERT: 3 65 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6517 (tm-30) REVERT: 3 74 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7808 (t80) REVERT: 3 75 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8116 (ppp) REVERT: 4 32 ASP cc_start: 0.9306 (m-30) cc_final: 0.8990 (p0) REVERT: 4 63 LEU cc_start: 0.9069 (mt) cc_final: 0.8778 (tm) REVERT: 4 72 LEU cc_start: 0.9406 (pp) cc_final: 0.9023 (pt) REVERT: 4 75 MET cc_start: 0.8898 (ppp) cc_final: 0.8401 (ppp) REVERT: 5 46 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8626 (tm-30) REVERT: 8 75 MET cc_start: 0.8631 (tmm) cc_final: 0.8273 (tmm) REVERT: a 12 HIS cc_start: 0.7659 (OUTLIER) cc_final: 0.7099 (t70) REVERT: a 74 ARG cc_start: 0.9716 (ptm160) cc_final: 0.9415 (ttp-110) REVERT: a 104 ASN cc_start: 0.9226 (t0) cc_final: 0.8918 (m-40) REVERT: a 205 MET cc_start: 0.8710 (mpm) cc_final: 0.8322 (mpm) REVERT: a 240 TYR cc_start: 0.9416 (m-80) cc_final: 0.9039 (m-80) outliers start: 53 outliers final: 22 residues processed: 238 average time/residue: 0.7642 time to fit residues: 219.5660 Evaluate side-chains 223 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 343 PHE Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 222 TYR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain b residue 159 ILE Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 274 THR Chi-restraints excluded: chain d residue 371 ARG Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 9 residue 19 LEU Chi-restraints excluded: chain 9 residue 65 GLU Chi-restraints excluded: chain 9 residue 74 PHE Chi-restraints excluded: chain 9 residue 78 PHE Chi-restraints excluded: chain 3 residue 65 GLU Chi-restraints excluded: chain 3 residue 74 PHE Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 4 residue 21 MET Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 5 residue 75 MET Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 7 residue 39 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 8 residue 55 THR Chi-restraints excluded: chain a residue 12 HIS Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 243 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 387 optimal weight: 20.0000 chunk 157 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 461 optimal weight: 50.0000 chunk 113 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 427 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 306 GLN G 131 GLN ** 2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 50 GLN a 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.069718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.043440 restraints weight = 122292.913| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.66 r_work: 0.2759 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36582 Z= 0.133 Angle : 0.580 13.692 49714 Z= 0.288 Chirality : 0.042 0.276 5844 Planarity : 0.004 0.068 6397 Dihedral : 6.095 87.973 5564 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.79 % Favored : 98.19 % Rotamer: Outliers : 1.72 % Allowed : 13.37 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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 aren not related in a simple way. whole: 1.97 (0.13), residues: 4804 helix: 2.27 (0.10), residues: 2659 sheet: -0.78 (0.22), residues: 527 loop : 0.53 (0.17), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG b 141 TYR 0.023 0.001 TYR a 145 PHE 0.030 0.001 PHE 7 74 TRP 0.013 0.001 TRP b 48 HIS 0.004 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00291 (36582) covalent geometry : angle 0.58008 (49714) hydrogen bonds : bond 0.03727 ( 2383) hydrogen bonds : angle 4.49865 ( 6840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 201 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 403 ASN cc_start: 0.9087 (m-40) cc_final: 0.8863 (m-40) REVERT: F 136 MET cc_start: 0.9442 (OUTLIER) cc_final: 0.9174 (ttt) REVERT: F 343 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8729 (m-80) REVERT: F 416 MET cc_start: 0.9370 (mtm) cc_final: 0.9015 (mtm) REVERT: G 155 ASP cc_start: 0.9233 (t0) cc_final: 0.8972 (t0) REVERT: H 7 GLU cc_start: 0.8969 (pt0) cc_final: 0.8364 (pm20) REVERT: H 31 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7009 (mp0) REVERT: b 45 ILE cc_start: 0.7812 (mm) cc_final: 0.7532 (tp) REVERT: b 59 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9089 (pp20) REVERT: b 82 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8689 (tp-100) REVERT: b 86 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8623 (mm-30) REVERT: d 57 MET cc_start: 0.8707 (ttp) cc_final: 0.8454 (tmm) REVERT: d 68 GLU cc_start: 0.9462 (mm-30) cc_final: 0.9157 (tm-30) REVERT: d 72 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8522 (p) REVERT: d 371 ARG cc_start: 0.9433 (OUTLIER) cc_final: 0.9129 (tpp80) REVERT: 9 19 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8200 (tm) REVERT: 9 57 PHE cc_start: 0.9293 (t80) cc_final: 0.9055 (t80) REVERT: 9 78 PHE cc_start: 0.6775 (OUTLIER) cc_final: 0.5717 (m-80) REVERT: 2 21 MET cc_start: 0.8234 (ttt) cc_final: 0.7469 (ttt) REVERT: 3 21 MET cc_start: 0.9095 (tpt) cc_final: 0.8851 (tpt) REVERT: 3 32 ASP cc_start: 0.9044 (m-30) cc_final: 0.8316 (t70) REVERT: 3 53 LEU cc_start: 0.9097 (mm) cc_final: 0.8778 (pp) REVERT: 3 63 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8600 (tp) REVERT: 3 65 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6521 (tm-30) REVERT: 3 74 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7803 (t80) REVERT: 3 75 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8188 (ppp) REVERT: 4 32 ASP cc_start: 0.9302 (m-30) cc_final: 0.9004 (p0) REVERT: 4 63 LEU cc_start: 0.9087 (mt) cc_final: 0.8782 (tm) REVERT: 4 75 MET cc_start: 0.8926 (ppp) cc_final: 0.8435 (ppp) REVERT: 5 46 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8614 (tm-30) REVERT: a 12 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.7131 (t70) REVERT: a 74 ARG cc_start: 0.9722 (ptm160) cc_final: 0.9437 (ttp-110) REVERT: a 104 ASN cc_start: 0.9259 (t0) cc_final: 0.8951 (m-40) REVERT: a 205 MET cc_start: 0.8701 (mpm) cc_final: 0.8335 (mpm) REVERT: a 240 TYR cc_start: 0.9445 (m-80) cc_final: 0.9046 (m-80) outliers start: 60 outliers final: 24 residues processed: 246 average time/residue: 0.7331 time to fit residues: 218.9027 Evaluate side-chains 222 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 343 PHE Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 222 TYR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 274 THR Chi-restraints excluded: chain d residue 371 ARG Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 9 residue 19 LEU Chi-restraints excluded: chain 9 residue 78 PHE Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 65 GLU Chi-restraints excluded: chain 3 residue 74 PHE Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 4 residue 21 MET Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 7 residue 39 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 8 residue 55 THR Chi-restraints excluded: chain a residue 12 HIS Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 243 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 467 optimal weight: 40.0000 chunk 344 optimal weight: 4.9990 chunk 430 optimal weight: 5.9990 chunk 432 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 chunk 368 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 299 optimal weight: 0.9980 chunk 439 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 306 GLN ** 2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.068947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.041885 restraints weight = 123922.658| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.58 r_work: 0.2732 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 36582 Z= 0.200 Angle : 0.615 15.206 49714 Z= 0.306 Chirality : 0.043 0.274 5844 Planarity : 0.004 0.048 6397 Dihedral : 6.086 89.175 5564 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.44 % Allowed : 13.85 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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 aren not related in a simple way. whole: 1.97 (0.13), residues: 4804 helix: 2.29 (0.10), residues: 2646 sheet: -0.87 (0.22), residues: 535 loop : 0.56 (0.17), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG b 141 TYR 0.022 0.001 TYR a 145 PHE 0.055 0.001 PHE 7 74 TRP 0.015 0.001 TRP a 105 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00450 (36582) covalent geometry : angle 0.61476 (49714) hydrogen bonds : bond 0.03912 ( 2383) hydrogen bonds : angle 4.54611 ( 6840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9608 Ramachandran restraints generated. 4804 Oldfield, 0 Emsley, 4804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 512 GLN cc_start: 0.9139 (mt0) cc_final: 0.8583 (pp30) REVERT: D 403 ASN cc_start: 0.9105 (m-40) cc_final: 0.8889 (m-40) REVERT: F 136 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.9228 (ttt) REVERT: F 416 MET cc_start: 0.9402 (mtm) cc_final: 0.9174 (mtm) REVERT: G 155 ASP cc_start: 0.9241 (t0) cc_final: 0.8989 (t0) REVERT: H 7 GLU cc_start: 0.9000 (pt0) cc_final: 0.8357 (pm20) REVERT: H 31 GLU cc_start: 0.7681 (mm-30) cc_final: 0.6907 (mp0) REVERT: b 45 ILE cc_start: 0.7959 (mm) cc_final: 0.7669 (tp) REVERT: b 82 GLN cc_start: 0.8936 (tp-100) cc_final: 0.8712 (tp-100) REVERT: d 57 MET cc_start: 0.8674 (ttp) cc_final: 0.8468 (tmm) REVERT: d 68 GLU cc_start: 0.9487 (mm-30) cc_final: 0.9167 (tm-30) REVERT: d 72 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8580 (p) REVERT: d 371 ARG cc_start: 0.9449 (OUTLIER) cc_final: 0.9135 (tpp80) REVERT: 9 19 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8241 (tm) REVERT: 9 57 PHE cc_start: 0.9316 (t80) cc_final: 0.9101 (t80) REVERT: 2 21 MET cc_start: 0.8232 (ttt) cc_final: 0.7439 (ttt) REVERT: 3 21 MET cc_start: 0.9084 (tpt) cc_final: 0.8842 (tpt) REVERT: 3 32 ASP cc_start: 0.9074 (m-30) cc_final: 0.8373 (t70) REVERT: 3 53 LEU cc_start: 0.9125 (mm) cc_final: 0.8801 (pp) REVERT: 3 65 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6246 (tm-30) REVERT: 3 74 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7803 (t80) REVERT: 3 75 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8094 (ppp) REVERT: 4 32 ASP cc_start: 0.9346 (m-30) cc_final: 0.9037 (p0) REVERT: 4 63 LEU cc_start: 0.9093 (mt) cc_final: 0.8794 (tm) REVERT: 4 72 LEU cc_start: 0.9413 (pp) cc_final: 0.9044 (pt) REVERT: 4 75 MET cc_start: 0.8876 (ppp) cc_final: 0.8380 (ppp) REVERT: 5 46 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8595 (tm-30) REVERT: a 12 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7203 (t70) REVERT: a 74 ARG cc_start: 0.9730 (ptm160) cc_final: 0.9466 (ttp-110) REVERT: a 76 GLN cc_start: 0.9269 (mm110) cc_final: 0.8995 (mp10) REVERT: a 104 ASN cc_start: 0.9265 (t0) cc_final: 0.8968 (m-40) REVERT: a 205 MET cc_start: 0.8792 (mpm) cc_final: 0.8501 (mpm) REVERT: a 240 TYR cc_start: 0.9444 (m-80) cc_final: 0.9024 (m-80) outliers start: 50 outliers final: 27 residues processed: 231 average time/residue: 0.7414 time to fit residues: 208.2388 Evaluate side-chains 224 residues out of total 3782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 222 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 274 THR Chi-restraints excluded: chain d residue 371 ARG Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 9 residue 19 LEU Chi-restraints excluded: chain 9 residue 78 PHE Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 65 GLU Chi-restraints excluded: chain 3 residue 74 PHE Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 4 residue 21 MET Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 5 residue 46 GLN Chi-restraints excluded: chain 5 residue 78 PHE Chi-restraints excluded: chain 7 residue 39 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 8 residue 55 THR Chi-restraints excluded: chain a residue 12 HIS Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 243 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 251 optimal weight: 0.8980 chunk 277 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 290 optimal weight: 2.9990 chunk 303 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 324 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 461 optimal weight: 0.3980 chunk 456 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 306 GLN G 131 GLN 9 71 ASN ** 2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.069925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.043137 restraints weight = 122965.273| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.56 r_work: 0.2774 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36582 Z= 0.125 Angle : 0.596 14.363 49714 Z= 0.296 Chirality : 0.042 0.263 5844 Planarity : 0.004 0.059 6397 Dihedral : 5.949 85.369 5564 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.12 % Allowed : 14.11 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.12 % 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 aren not related in a simple way. whole: 1.98 (0.13), residues: 4804 helix: 2.27 (0.10), residues: 2657 sheet: -0.75 (0.22), residues: 525 loop : 0.55 (0.17), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG 6 52 TYR 0.023 0.001 TYR a 145 PHE 0.054 0.001 PHE 7 74 TRP 0.022 0.001 TRP a 105 HIS 0.004 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00270 (36582) covalent geometry : angle 0.59551 (49714) hydrogen bonds : bond 0.03741 ( 2383) hydrogen bonds : angle 4.48824 ( 6840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20027.54 seconds wall clock time: 340 minutes 49.98 seconds (20449.98 seconds total)