Starting phenix.real_space_refine on Tue Sep 15 19:29:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r2k_14245/09_2026/7r2k_14245.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r2k_14245/09_2026/7r2k_14245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7r2k_14245/09_2026/7r2k_14245.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r2k_14245/09_2026/7r2k_14245.cif" model { file = "/net/cci-nas-00/data/ceres_data/7r2k_14245/09_2026/7r2k_14245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r2k_14245/09_2026/7r2k_14245.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r2k_14245/09_2026/7r2k_14245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r2k_14245/09_2026/7r2k_14245.map" } resolution = 3.3 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= -0.002 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ni 2 6.56 5 P 69 5.49 5 S 99 5.16 5 C 27843 2.51 5 N 7529 2.21 5 O 8389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43931 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4304 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 26, 'TRANS': 545} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 5, 'ASN:plan1': 4, 'HIS:plan': 2, 'ARG:plan': 4, 'ASP:plan': 5, 'PHE:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 168 Chain: "C" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "D" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "G" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "H" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "I" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "J" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "K" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2597 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 321} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2603 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 322} 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: "M" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2596 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1822 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 226} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "S" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1936 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 16, 'TRANS': 223} Chain breaks: 2 Chain: "T" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "U" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1215 Classifications: {'RNAv2': 57} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 14, 'rna3p_pur': 15, 'rna3p_pyr': 13} Link IDs: {'rna2p': 27, 'rna3p': 29} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "W" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2350 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "X" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "Y" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2662 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.08, per 1000 atoms: 0.23 Number of scatterers: 43931 At special positions: 0 Unit cell: (143.91, 173.225, 265.167, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ni 2 28.00 S 99 16.00 P 69 15.00 O 8389 8.00 N 7529 7.00 C 27843 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS I 63 " - pdb=" SG CYS I 108 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS Q 65 " distance=2.03 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: 3.88 Conformation dependent library (CDL) restraints added in 1.8 seconds 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10114 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 61 sheets defined 38.5% alpha, 10.4% beta 3 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 4.97 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.980A pdb=" N PHE A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 94 Processing helix chain 'A' and resid 101 through 112 removed outlier: 4.395A pdb=" N GLU A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 140 removed outlier: 3.745A pdb=" N TYR A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 160 removed outlier: 4.190A pdb=" N GLN A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.935A pdb=" N GLU A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.860A pdb=" N MET A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 removed outlier: 3.653A pdb=" N VAL A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 246' Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.930A pdb=" N LYS A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.589A pdb=" N GLU A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLN A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.842A pdb=" N HIS A 370 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 371 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 381 Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.547A pdb=" N ILE A 421 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.911A pdb=" N LEU A 480 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 587 removed outlier: 3.564A pdb=" N TRP A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'C' and resid 5 through 15 removed outlier: 3.908A pdb=" N LEU C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 33 Processing helix chain 'C' and resid 36 through 49 removed outlier: 4.176A pdb=" N LEU C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 41 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 59 removed outlier: 4.592A pdb=" N GLU C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 83 removed outlier: 3.700A pdb=" N ILE C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 96 removed outlier: 4.185A pdb=" N LYS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 93 " --> pdb=" O ASP C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'E' and resid 5 through 16 removed outlier: 3.576A pdb=" N VAL E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 33 removed outlier: 4.506A pdb=" N VAL E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 removed outlier: 3.924A pdb=" N LEU E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 59 removed outlier: 4.220A pdb=" N GLU E 59 " --> pdb=" O LYS E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 82 removed outlier: 3.866A pdb=" N ILE E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU E 79 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU E 82 " --> pdb=" O GLU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 89 removed outlier: 3.548A pdb=" N ASP E 89 " --> pdb=" O ASN E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 86 through 89' Processing helix chain 'E' and resid 90 through 98 Processing helix chain 'F' and resid 5 through 14 Processing helix chain 'F' and resid 24 through 33 removed outlier: 4.396A pdb=" N VAL F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 50 removed outlier: 3.629A pdb=" N LEU F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 62 Processing helix chain 'F' and resid 70 through 82 removed outlier: 3.750A pdb=" N GLU F 75 " --> pdb=" O PRO F 71 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 101 removed outlier: 3.634A pdb=" N LEU F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU F 93 " --> pdb=" O ASP F 89 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 14 removed outlier: 3.604A pdb=" N ASN G 7 " --> pdb=" O GLY G 3 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR G 14 " --> pdb=" O ARG G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 33 removed outlier: 3.814A pdb=" N VAL G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 50 removed outlier: 3.795A pdb=" N LEU G 50 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 61 removed outlier: 4.102A pdb=" N GLU G 59 " --> pdb=" O LYS G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 84 Processing helix chain 'G' and resid 86 through 100 removed outlier: 4.145A pdb=" N TRP G 100 " --> pdb=" O SER G 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 16 removed outlier: 3.686A pdb=" N LEU H 15 " --> pdb=" O TYR H 11 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 34 removed outlier: 4.001A pdb=" N VAL H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 Processing helix chain 'H' and resid 50 through 62 removed outlier: 4.659A pdb=" N GLU H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER H 60 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 4.014A pdb=" N GLU H 82 " --> pdb=" O GLU H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 100 removed outlier: 3.660A pdb=" N LEU H 90 " --> pdb=" O ASN H 86 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP H 100 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'I' and resid 5 through 15 removed outlier: 3.549A pdb=" N LEU I 15 " --> pdb=" O TYR I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 33 removed outlier: 3.797A pdb=" N VAL I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 49 Processing helix chain 'I' and resid 50 through 61 removed outlier: 3.757A pdb=" N GLU I 59 " --> pdb=" O LYS I 55 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS I 61 " --> pdb=" O LYS I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 84 Processing helix chain 'I' and resid 86 through 98 removed outlier: 3.565A pdb=" N LEU I 90 " --> pdb=" O ASN I 86 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 15 removed outlier: 3.675A pdb=" N LEU J 15 " --> pdb=" O TYR J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 33 removed outlier: 4.437A pdb=" N VAL J 28 " --> pdb=" O ALA J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 49 Processing helix chain 'J' and resid 50 through 59 removed outlier: 4.648A pdb=" N GLU J 59 " --> pdb=" O LYS J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 83 removed outlier: 3.828A pdb=" N LEU J 77 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU J 78 " --> pdb=" O ILE J 74 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU J 79 " --> pdb=" O GLU J 75 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN J 83 " --> pdb=" O GLU J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 100 removed outlier: 3.878A pdb=" N LEU J 90 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS J 92 " --> pdb=" O LYS J 88 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU J 93 " --> pdb=" O ASP J 89 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA J 94 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 70 removed outlier: 3.746A pdb=" N LEU K 55 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR K 69 " --> pdb=" O ASP K 65 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR K 70 " --> pdb=" O TYR K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 75 removed outlier: 4.278A pdb=" N VAL K 74 " --> pdb=" O PRO K 71 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN K 75 " --> pdb=" O TYR K 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 71 through 75' Processing helix chain 'K' and resid 77 through 82 removed outlier: 3.690A pdb=" N LEU K 81 " --> pdb=" O THR K 77 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 77 through 82' Processing helix chain 'K' and resid 107 through 115 Processing helix chain 'K' and resid 116 through 122 Processing helix chain 'K' and resid 144 through 152 Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 227 through 242 removed outlier: 3.786A pdb=" N LEU K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 301 removed outlier: 3.510A pdb=" N ALA K 289 " --> pdb=" O ASP K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 333 Processing helix chain 'L' and resid 51 through 69 removed outlier: 3.723A pdb=" N LEU L 55 " --> pdb=" O THR L 51 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR L 69 " --> pdb=" O ASP L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 75 removed outlier: 4.422A pdb=" N VAL L 74 " --> pdb=" O PRO L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 82 removed outlier: 3.675A pdb=" N ARG L 82 " --> pdb=" O GLU L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 115 Processing helix chain 'L' and resid 116 through 121 Processing helix chain 'L' and resid 144 through 152 Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 227 through 241 Processing helix chain 'L' and resid 242 through 243 No H-bonds generated for 'chain 'L' and resid 242 through 243' Processing helix chain 'L' and resid 244 through 248 removed outlier: 3.600A pdb=" N SER L 247 " --> pdb=" O PRO L 244 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY L 248 " --> pdb=" O MET L 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 244 through 248' Processing helix chain 'L' and resid 285 through 301 removed outlier: 3.592A pdb=" N ALA L 289 " --> pdb=" O ASP L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 334 Processing helix chain 'M' and resid 51 through 69 removed outlier: 3.564A pdb=" N LEU M 55 " --> pdb=" O THR M 51 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR M 69 " --> pdb=" O ASP M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 75 removed outlier: 4.488A pdb=" N VAL M 74 " --> pdb=" O PRO M 71 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN M 75 " --> pdb=" O TYR M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 82 removed outlier: 3.600A pdb=" N LEU M 81 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG M 82 " --> pdb=" O GLU M 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 77 through 82' Processing helix chain 'M' and resid 107 through 115 Processing helix chain 'M' and resid 115 through 122 Processing helix chain 'M' and resid 144 through 152 Processing helix chain 'M' and resid 227 through 241 Processing helix chain 'M' and resid 242 through 247 Processing helix chain 'M' and resid 286 through 300 Processing helix chain 'M' and resid 324 through 335 removed outlier: 3.915A pdb=" N MET M 335 " --> pdb=" O ASN M 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 68 removed outlier: 3.506A pdb=" N LYS N 68 " --> pdb=" O VAL N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 75 removed outlier: 4.431A pdb=" N VAL N 74 " --> pdb=" O PRO N 71 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN N 75 " --> pdb=" O TYR N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 removed outlier: 3.501A pdb=" N LEU N 81 " --> pdb=" O THR N 77 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG N 82 " --> pdb=" O GLU N 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 77 through 82' Processing helix chain 'N' and resid 107 through 115 Processing helix chain 'N' and resid 115 through 122 Processing helix chain 'N' and resid 144 through 151 Processing helix chain 'N' and resid 227 through 241 Processing helix chain 'N' and resid 283 through 285 No H-bonds generated for 'chain 'N' and resid 283 through 285' Processing helix chain 'N' and resid 286 through 301 Processing helix chain 'N' and resid 324 through 335 removed outlier: 3.900A pdb=" N MET N 335 " --> pdb=" O ASN N 331 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 69 removed outlier: 3.752A pdb=" N LEU O 55 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR O 69 " --> pdb=" O ASP O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 75 removed outlier: 4.182A pdb=" N VAL O 74 " --> pdb=" O PRO O 71 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN O 75 " --> pdb=" O TYR O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 removed outlier: 3.689A pdb=" N LEU O 81 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 77 through 82' Processing helix chain 'O' and resid 107 through 115 removed outlier: 3.690A pdb=" N ILE O 111 " --> pdb=" O ASP O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 122 Processing helix chain 'O' and resid 144 through 149 Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 227 through 241 Processing helix chain 'O' and resid 242 through 247 removed outlier: 3.743A pdb=" N SER O 247 " --> pdb=" O ILE O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 285 through 301 removed outlier: 3.545A pdb=" N ALA O 289 " --> pdb=" O ASP O 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 324 through 335 removed outlier: 3.951A pdb=" N MET O 335 " --> pdb=" O ASN O 331 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 69 removed outlier: 3.745A pdb=" N LEU P 55 " --> pdb=" O THR P 51 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 82 removed outlier: 3.674A pdb=" N LEU P 81 " --> pdb=" O THR P 77 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG P 82 " --> pdb=" O GLU P 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 77 through 82' Processing helix chain 'P' and resid 107 through 115 removed outlier: 3.780A pdb=" N ILE P 111 " --> pdb=" O ASP P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 122 Processing helix chain 'P' and resid 144 through 150 Processing helix chain 'P' and resid 203 through 205 No H-bonds generated for 'chain 'P' and resid 203 through 205' Processing helix chain 'P' and resid 227 through 241 Processing helix chain 'P' and resid 285 through 301 Processing helix chain 'P' and resid 324 through 335 removed outlier: 3.898A pdb=" N LEU P 328 " --> pdb=" O SER P 324 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET P 335 " --> pdb=" O ASN P 331 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 41 removed outlier: 4.167A pdb=" N ALA Q 17 " --> pdb=" O GLU Q 13 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE Q 24 " --> pdb=" O ALA Q 20 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN Q 27 " --> pdb=" O GLU Q 23 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS Q 28 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) Proline residue: Q 31 - end of helix removed outlier: 4.325A pdb=" N THR Q 39 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL Q 40 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY Q 41 " --> pdb=" O MET Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 60 Processing helix chain 'Q' and resid 68 through 75 Processing helix chain 'Q' and resid 83 through 101 removed outlier: 4.374A pdb=" N VAL Q 87 " --> pdb=" O ARG Q 83 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS Q 101 " --> pdb=" O LYS Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 116 removed outlier: 3.610A pdb=" N PHE Q 107 " --> pdb=" O GLU Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 145 Processing helix chain 'Q' and resid 151 through 164 Processing helix chain 'Q' and resid 175 through 191 Processing helix chain 'Q' and resid 196 through 207 Processing helix chain 'Q' and resid 211 through 216 Processing helix chain 'Q' and resid 222 through 227 Processing helix chain 'Q' and resid 228 through 230 No H-bonds generated for 'chain 'Q' and resid 228 through 230' Processing helix chain 'R' and resid 19 through 23 removed outlier: 3.687A pdb=" N GLY R 23 " --> pdb=" O GLY R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 68 removed outlier: 3.776A pdb=" N LEU R 55 " --> pdb=" O THR R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 82 removed outlier: 3.583A pdb=" N LEU R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG R 82 " --> pdb=" O GLU R 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 77 through 82' Processing helix chain 'R' and resid 107 through 115 removed outlier: 3.643A pdb=" N ILE R 111 " --> pdb=" O ASP R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 122 Processing helix chain 'R' and resid 144 through 150 Processing helix chain 'R' and resid 203 through 205 No H-bonds generated for 'chain 'R' and resid 203 through 205' Processing helix chain 'R' and resid 227 through 241 Processing helix chain 'R' and resid 285 through 301 removed outlier: 3.750A pdb=" N ALA R 289 " --> pdb=" O ASP R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 335 removed outlier: 3.961A pdb=" N MET R 335 " --> pdb=" O ASN R 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 46 removed outlier: 3.548A pdb=" N LEU S 38 " --> pdb=" O LEU S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 70 Processing helix chain 'S' and resid 129 through 141 removed outlier: 4.569A pdb=" N LEU S 135 " --> pdb=" O GLU S 131 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET S 141 " --> pdb=" O LEU S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 177 through 182 removed outlier: 3.875A pdb=" N SER S 181 " --> pdb=" O THR S 177 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 23 removed outlier: 4.213A pdb=" N GLY T 22 " --> pdb=" O GLN T 19 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 69 removed outlier: 3.799A pdb=" N LEU T 55 " --> pdb=" O THR T 51 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR T 69 " --> pdb=" O ASP T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 82 removed outlier: 3.619A pdb=" N LEU T 81 " --> pdb=" O THR T 77 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG T 82 " --> pdb=" O GLU T 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 77 through 82' Processing helix chain 'T' and resid 107 through 115 removed outlier: 3.756A pdb=" N ILE T 111 " --> pdb=" O ASP T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 116 through 122 Processing helix chain 'T' and resid 144 through 152 removed outlier: 3.797A pdb=" N GLU T 152 " --> pdb=" O ILE T 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 227 through 241 Processing helix chain 'T' and resid 285 through 301 removed outlier: 3.953A pdb=" N ALA T 289 " --> pdb=" O ASP T 285 " (cutoff:3.500A) Processing helix chain 'T' and resid 325 through 335 removed outlier: 4.306A pdb=" N MET T 335 " --> pdb=" O ASN T 331 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 69 removed outlier: 4.245A pdb=" N THR V 69 " --> pdb=" O ASP V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 82 removed outlier: 4.027A pdb=" N LEU V 81 " --> pdb=" O THR V 77 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG V 82 " --> pdb=" O GLU V 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 77 through 82' Processing helix chain 'V' and resid 107 through 114 Processing helix chain 'V' and resid 116 through 122 Processing helix chain 'V' and resid 144 through 152 removed outlier: 3.501A pdb=" N ILE V 148 " --> pdb=" O THR V 144 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU V 150 " --> pdb=" O ASP V 146 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU V 152 " --> pdb=" O ILE V 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 227 through 241 Processing helix chain 'V' and resid 285 through 301 removed outlier: 3.868A pdb=" N ALA V 289 " --> pdb=" O ASP V 285 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA V 297 " --> pdb=" O ILE V 293 " (cutoff:3.500A) Processing helix chain 'V' and resid 325 through 334 Processing helix chain 'W' and resid 20 through 24 removed outlier: 3.513A pdb=" N GLY W 23 " --> pdb=" O GLY W 20 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR W 24 " --> pdb=" O GLY W 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 20 through 24' Processing helix chain 'W' and resid 51 through 68 removed outlier: 3.583A pdb=" N LEU W 55 " --> pdb=" O THR W 51 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS W 68 " --> pdb=" O VAL W 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 70 through 75 removed outlier: 3.927A pdb=" N VAL W 74 " --> pdb=" O PRO W 71 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN W 75 " --> pdb=" O TYR W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 82 removed outlier: 3.722A pdb=" N LEU W 81 " --> pdb=" O THR W 77 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG W 82 " --> pdb=" O GLU W 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 77 through 82' Processing helix chain 'W' and resid 107 through 115 removed outlier: 3.671A pdb=" N ILE W 111 " --> pdb=" O ASP W 107 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS W 113 " --> pdb=" O ALA W 109 " (cutoff:3.500A) Processing helix chain 'W' and resid 116 through 122 Processing helix chain 'W' and resid 144 through 152 removed outlier: 4.029A pdb=" N GLU W 152 " --> pdb=" O ILE W 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 205 Processing helix chain 'W' and resid 227 through 241 Processing helix chain 'W' and resid 242 through 247 removed outlier: 3.939A pdb=" N LEU W 246 " --> pdb=" O LEU W 242 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER W 247 " --> pdb=" O ILE W 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 242 through 247' Processing helix chain 'W' and resid 285 through 301 removed outlier: 3.978A pdb=" N ALA W 289 " --> pdb=" O ASP W 285 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY W 301 " --> pdb=" O ALA W 297 " (cutoff:3.500A) Processing helix chain 'W' and resid 325 through 333 Processing helix chain 'Y' and resid 13 through 28 removed outlier: 4.450A pdb=" N VAL Y 23 " --> pdb=" O ALA Y 19 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL Y 24 " --> pdb=" O TYR Y 20 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG Y 28 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 71 removed outlier: 3.624A pdb=" N PHE Y 54 " --> pdb=" O SER Y 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 116 removed outlier: 3.538A pdb=" N TRP Y 100 " --> pdb=" O ASN Y 96 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP Y 101 " --> pdb=" O ASN Y 97 " (cutoff:3.500A) Proline residue: Y 104 - end of helix removed outlier: 4.300A pdb=" N LYS Y 116 " --> pdb=" O LYS Y 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 154 through 167 Processing helix chain 'Y' and resid 193 through 204 removed outlier: 3.685A pdb=" N LEU Y 203 " --> pdb=" O SER Y 199 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS Y 204 " --> pdb=" O LEU Y 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 219 removed outlier: 3.729A pdb=" N LEU Y 218 " --> pdb=" O LEU Y 215 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE Y 219 " --> pdb=" O ASP Y 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 215 through 219' Processing helix chain 'Y' and resid 220 through 231 removed outlier: 3.676A pdb=" N HIS Y 231 " --> pdb=" O TYR Y 227 " (cutoff:3.500A) Processing helix chain 'Y' and resid 236 through 240 removed outlier: 3.795A pdb=" N THR Y 239 " --> pdb=" O GLU Y 236 " (cutoff:3.500A) Processing helix chain 'Y' and resid 267 through 278 removed outlier: 3.598A pdb=" N MET Y 271 " --> pdb=" O ILE Y 267 " (cutoff:3.500A) Processing helix chain 'Y' and resid 285 through 295 Processing helix chain 'Y' and resid 296 through 310 Processing helix chain 'Y' and resid 311 through 326 removed outlier: 4.174A pdb=" N PHE Y 315 " --> pdb=" O ARG Y 311 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR Y 316 " --> pdb=" O LEU Y 312 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA Y 325 " --> pdb=" O LEU Y 321 " (cutoff:3.500A) Processing helix chain 'Y' and resid 330 through 342 removed outlier: 3.560A pdb=" N VAL Y 334 " --> pdb=" O SER Y 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.853A pdb=" N ILE A 197 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 39 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER A 199 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL A 196 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 164 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU A 69 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR A 131 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N TYR A 71 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 236 removed outlier: 6.528A pdb=" N LYS A 233 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ILE A 361 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ARG A 235 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 332 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 258 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 2 through 14 current: chain 'K' and resid 184 through 201 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 184 through 201 current: chain 'K' and resid 305 through 309 Processing sheet with id=AA5, first strand: chain 'K' and resid 31 through 37 Processing sheet with id=AA6, first strand: chain 'K' and resid 94 through 96 Processing sheet with id=AA7, first strand: chain 'K' and resid 123 through 125 removed outlier: 6.914A pdb=" N PHE K 123 " --> pdb=" O ARG K 131 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ARG K 131 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA K 125 " --> pdb=" O GLY K 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 2 through 14 current: chain 'L' and resid 184 through 201 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 184 through 201 current: chain 'L' and resid 305 through 309 removed outlier: 7.008A pdb=" N VAL L 306 " --> pdb=" O THR L 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'L' and resid 31 through 36 Processing sheet with id=AB1, first strand: chain 'L' and resid 94 through 96 Processing sheet with id=AB2, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AB3, first strand: chain 'M' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 2 through 14 current: chain 'M' and resid 184 through 201 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 184 through 201 current: chain 'M' and resid 304 through 309 removed outlier: 9.172A pdb=" N THR M 320 " --> pdb=" O ILE M 304 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL M 306 " --> pdb=" O THR M 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'M' and resid 31 through 36 Processing sheet with id=AB5, first strand: chain 'M' and resid 94 through 96 Processing sheet with id=AB6, first strand: chain 'M' and resid 123 through 124 Processing sheet with id=AB7, first strand: chain 'N' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 2 through 14 current: chain 'N' and resid 183 through 196 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 183 through 196 current: chain 'N' and resid 305 through 309 removed outlier: 6.825A pdb=" N VAL N 306 " --> pdb=" O THR N 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'N' and resid 31 through 36 Processing sheet with id=AB9, first strand: chain 'N' and resid 94 through 96 Processing sheet with id=AC1, first strand: chain 'N' and resid 123 through 124 removed outlier: 3.745A pdb=" N ARG N 132 " --> pdb=" O PHE N 123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 2 through 14 current: chain 'O' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 190 through 196 current: chain 'O' and resid 306 through 309 Processing sheet with id=AC3, first strand: chain 'O' and resid 31 through 36 Processing sheet with id=AC4, first strand: chain 'O' and resid 94 through 96 Processing sheet with id=AC5, first strand: chain 'O' and resid 123 through 124 removed outlier: 3.669A pdb=" N PHE O 123 " --> pdb=" O ARG O 132 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG O 132 " --> pdb=" O PHE O 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'O' and resid 160 through 161 Processing sheet with id=AC7, first strand: chain 'O' and resid 213 through 215 Processing sheet with id=AC8, first strand: chain 'P' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 2 through 14 current: chain 'P' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 190 through 196 current: chain 'P' and resid 306 through 309 Processing sheet with id=AC9, first strand: chain 'P' and resid 26 through 27 Processing sheet with id=AD1, first strand: chain 'P' and resid 31 through 36 Processing sheet with id=AD2, first strand: chain 'P' and resid 94 through 96 Processing sheet with id=AD3, first strand: chain 'P' and resid 123 through 124 removed outlier: 3.675A pdb=" N PHE P 123 " --> pdb=" O ARG P 132 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 213 through 215 Processing sheet with id=AD5, first strand: chain 'R' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 2 through 14 current: chain 'R' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 190 through 196 current: chain 'R' and resid 306 through 309 Processing sheet with id=AD6, first strand: chain 'R' and resid 31 through 36 Processing sheet with id=AD7, first strand: chain 'R' and resid 94 through 96 Processing sheet with id=AD8, first strand: chain 'R' and resid 123 through 124 Processing sheet with id=AD9, first strand: chain 'R' and resid 213 through 215 Processing sheet with id=AE1, first strand: chain 'S' and resid 77 through 79 removed outlier: 3.639A pdb=" N LEU S 120 " --> pdb=" O ALA S 79 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE S 3 " --> pdb=" O PHE S 160 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE S 160 " --> pdb=" O ILE S 3 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU S 5 " --> pdb=" O ALA S 158 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA S 158 " --> pdb=" O LEU S 5 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N CYS S 7 " --> pdb=" O VAL S 156 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 12 through 13 Processing sheet with id=AE3, first strand: chain 'S' and resid 168 through 169 removed outlier: 3.652A pdb=" N ALA S 168 " --> pdb=" O VAL S 240 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 174 through 175 removed outlier: 4.135A pdb=" N ALA S 174 " --> pdb=" O TYR S 218 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 242 through 246 removed outlier: 3.996A pdb=" N LYS S 242 " --> pdb=" O ILE S 253 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 2 through 14 current: chain 'T' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 190 through 196 current: chain 'T' and resid 306 through 309 removed outlier: 6.998A pdb=" N VAL T 306 " --> pdb=" O THR T 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'T' and resid 31 through 36 Processing sheet with id=AE8, first strand: chain 'T' and resid 94 through 96 Processing sheet with id=AE9, first strand: chain 'T' and resid 123 through 124 removed outlier: 3.632A pdb=" N PHE T 123 " --> pdb=" O ARG T 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 160 through 161 Processing sheet with id=AF2, first strand: chain 'T' and resid 213 through 215 Processing sheet with id=AF3, first strand: chain 'V' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 2 through 14 current: chain 'V' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 190 through 196 current: chain 'V' and resid 306 through 309 Processing sheet with id=AF4, first strand: chain 'V' and resid 26 through 27 removed outlier: 3.909A pdb=" N ARG V 187 " --> pdb=" O ILE V 160 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE V 160 " --> pdb=" O ARG V 187 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 31 through 36 Processing sheet with id=AF6, first strand: chain 'V' and resid 95 through 96 Processing sheet with id=AF7, first strand: chain 'V' and resid 123 through 124 removed outlier: 3.640A pdb=" N PHE V 123 " --> pdb=" O ARG V 132 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG V 132 " --> pdb=" O PHE V 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'V' and resid 213 through 215 Processing sheet with id=AF9, first strand: chain 'W' and resid 3 through 12 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 3 through 12 current: chain 'W' and resid 306 through 309 Processing sheet with id=AG1, first strand: chain 'W' and resid 31 through 36 Processing sheet with id=AG2, first strand: chain 'W' and resid 95 through 96 Processing sheet with id=AG3, first strand: chain 'W' and resid 123 through 124 Processing sheet with id=AG4, first strand: chain 'W' and resid 213 through 215 Processing sheet with id=AG5, first strand: chain 'Y' and resid 35 through 37 Processing sheet with id=AG6, first strand: chain 'Y' and resid 123 through 124 Processing sheet with id=AG7, first strand: chain 'Y' and resid 170 through 173 removed outlier: 3.833A pdb=" N ALA Y 258 " --> pdb=" O GLU Y 251 " (cutoff:3.500A) 1330 hydrogen bonds defined for protein. 3807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 9.09 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13568 1.34 - 1.46: 8279 1.46 - 1.58: 22763 1.58 - 1.70: 136 1.70 - 1.82: 178 Bond restraints: 44924 Sorted by residual: bond pdb=" N VAL Y 98 " pdb=" CA VAL Y 98 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.30e-02 5.92e+03 7.76e+00 bond pdb=" N THR Y 125 " pdb=" CA THR Y 125 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.30e-02 5.92e+03 5.18e+00 bond pdb=" O3' DG D 48 " pdb=" P DG D 49 " ideal model delta sigma weight residual 1.607 1.633 -0.026 1.20e-02 6.94e+03 4.84e+00 bond pdb=" N GLY A 611 " pdb=" CA GLY A 611 " ideal model delta sigma weight residual 1.449 1.481 -0.031 1.45e-02 4.76e+03 4.71e+00 bond pdb=" N TYR Y 99 " pdb=" CA TYR Y 99 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.28e-02 6.10e+03 4.71e+00 ... (remaining 44919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 60144 2.51 - 5.02: 958 5.02 - 7.53: 93 7.53 - 10.04: 11 10.04 - 12.55: 4 Bond angle restraints: 61210 Sorted by residual: angle pdb=" N PRO A 529 " pdb=" CA PRO A 529 " pdb=" CB PRO A 529 " ideal model delta sigma weight residual 103.25 111.19 -7.94 1.05e+00 9.07e-01 5.72e+01 angle pdb=" N PRO A 595 " pdb=" CA PRO A 595 " pdb=" CB PRO A 595 " ideal model delta sigma weight residual 103.25 110.59 -7.34 1.05e+00 9.07e-01 4.89e+01 angle pdb=" N PRO A 521 " pdb=" CA PRO A 521 " pdb=" CB PRO A 521 " ideal model delta sigma weight residual 103.25 110.00 -6.75 1.05e+00 9.07e-01 4.14e+01 angle pdb=" N PRO Q 224 " pdb=" CA PRO Q 224 " pdb=" CB PRO Q 224 " ideal model delta sigma weight residual 103.33 110.24 -6.91 1.10e+00 8.26e-01 3.94e+01 angle pdb=" C ARG A 351 " pdb=" CA ARG A 351 " pdb=" CB ARG A 351 " ideal model delta sigma weight residual 116.63 110.50 6.13 1.16e+00 7.43e-01 2.79e+01 ... (remaining 61205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.46: 25668 28.46 - 56.93: 1120 56.93 - 85.39: 159 85.39 - 113.85: 9 113.85 - 142.31: 1 Dihedral angle restraints: 26957 sinusoidal: 11204 harmonic: 15753 Sorted by residual: dihedral pdb=" C4' U U 2 " pdb=" C3' U U 2 " pdb=" C2' U U 2 " pdb=" C1' U U 2 " ideal model delta sinusoidal sigma weight residual 36.34 -37.34 73.69 1 3.10e+00 1.04e-01 7.18e+02 dihedral pdb=" C4' G U 8 " pdb=" C3' G U 8 " pdb=" C2' G U 8 " pdb=" C1' G U 8 " ideal model delta sinusoidal sigma weight residual 36.34 -36.65 72.99 1 3.10e+00 1.04e-01 7.07e+02 dihedral pdb=" C4' G U 51 " pdb=" C3' G U 51 " pdb=" C2' G U 51 " pdb=" C1' G U 51 " ideal model delta sinusoidal sigma weight residual 36.34 -36.13 72.48 1 3.10e+00 1.04e-01 6.98e+02 ... (remaining 26954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 5855 0.062 - 0.125: 1000 0.125 - 0.187: 58 0.187 - 0.249: 71 0.249 - 0.311: 50 Chirality restraints: 7034 Sorted by residual: chirality pdb=" C2' U U 32 " pdb=" C3' U U 32 " pdb=" O2' U U 32 " pdb=" C1' U U 32 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C3' G U 51 " pdb=" C4' G U 51 " pdb=" O3' G U 51 " pdb=" C2' G U 51 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" P A U 34 " pdb=" OP1 A U 34 " pdb=" OP2 A U 34 " pdb=" O5' A U 34 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 7031 not shown) Planarity restraints: 7612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 610 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C LEU A 610 " 0.079 2.00e-02 2.50e+03 pdb=" O LEU A 610 " -0.030 2.00e-02 2.50e+03 pdb=" N GLY A 611 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 64 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO A 65 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 155 " -0.020 2.00e-02 2.50e+03 1.78e-02 5.56e+00 pdb=" CG PHE Q 155 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 155 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 155 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 155 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 155 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE Q 155 " -0.008 2.00e-02 2.50e+03 ... (remaining 7609 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 712 2.64 - 3.21: 42547 3.21 - 3.77: 70390 3.77 - 4.34: 95660 4.34 - 4.90: 151904 Nonbonded interactions: 361213 Sorted by model distance: nonbonded pdb=" O ALA J 34 " pdb=" NH2 ARG J 91 " model vdw 2.077 3.120 nonbonded pdb=" NZ LYS T 262 " pdb=" OE1 GLU T 264 " model vdw 2.112 3.120 nonbonded pdb=" NH2 ARG S 228 " pdb=" OE1 GLU Y 265 " model vdw 2.120 3.120 nonbonded pdb=" ND2 ASN V 17 " pdb=" OG1 THR V 30 " model vdw 2.123 3.120 nonbonded pdb=" NE2 HIS Q 117 " pdb="NI NI Q 302 " model vdw 2.152 2.260 ... (remaining 361208 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 'C' selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 3 through 109) selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'K' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 144 or (resid 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 through 157 or resid 190 th \ rough 335)) selection = (chain 'L' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 157 or resid 190 through 335)) selection = (chain 'M' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'N' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'O' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'P' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'R' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'T' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'V' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'W' and resid 1 through 335) } 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: 3.020 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: 0.050 Extract box with map and model: 0.640 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 44.180 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.003 0.047 44932 Z= 0.142 Angle : 0.709 12.549 61226 Z= 0.370 Chirality : 0.055 0.311 7034 Planarity : 0.004 0.082 7612 Dihedral : 15.100 142.314 16819 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.43 % Favored : 92.29 % Rotamer: Outliers : 0.04 % Allowed : 0.43 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.11), residues: 5407 helix: 0.22 (0.13), residues: 1801 sheet: -0.24 (0.18), residues: 779 loop : -1.51 (0.11), residues: 2827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 35 TYR 0.027 0.001 TYR S 20 PHE 0.041 0.001 PHE Q 155 TRP 0.031 0.001 TRP V 58 HIS 0.010 0.001 HIS Y 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (44924) covalent geometry : angle 0.70905 / 0.37 (61210) SS BOND : bond 0.00135 / 0.08 ( 8) SS BOND : angle 0.65569 / 0.37 ( 16) hydrogen bonds : bond 0.14956 / 9.93 ( 1339) hydrogen bonds : angle 6.13532 / 4.22 ( 3825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 601 time to evaluate : 1.741 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: A 31 MET cc_start: 0.4376 (mtt) cc_final: 0.4138 (mtt) REVERT: A 127 TRP cc_start: 0.6497 (m-10) cc_final: 0.6115 (m100) REVERT: A 197 ILE cc_start: 0.7799 (pt) cc_final: 0.7516 (pt) REVERT: A 198 MET cc_start: 0.6992 (mmt) cc_final: 0.6424 (ppp) REVERT: A 209 MET cc_start: 0.7624 (ptp) cc_final: 0.7363 (ptp) REVERT: C 78 GLU cc_start: 0.7132 (tp30) cc_final: 0.6829 (tp30) REVERT: F 29 ASP cc_start: 0.8514 (m-30) cc_final: 0.8142 (m-30) REVERT: H 88 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8728 (tptt) REVERT: I 46 LYS cc_start: 0.9322 (mptt) cc_final: 0.8904 (mmtm) REVERT: J 23 TYR cc_start: 0.8305 (m-80) cc_final: 0.8100 (m-10) REVERT: J 57 LYS cc_start: 0.8631 (tptp) cc_final: 0.8350 (tptp) REVERT: J 106 ASN cc_start: 0.7556 (t0) cc_final: 0.7214 (t0) REVERT: N 245 MET cc_start: 0.7982 (mmt) cc_final: 0.7638 (mmm) REVERT: Q 57 ILE cc_start: 0.9122 (mm) cc_final: 0.8808 (mm) REVERT: Q 90 TYR cc_start: 0.8680 (t80) cc_final: 0.7993 (t80) REVERT: Q 115 MET cc_start: 0.9108 (mpp) cc_final: 0.8678 (mpp) REVERT: Q 116 HIS cc_start: 0.8219 (t-90) cc_final: 0.7762 (t-90) REVERT: Q 117 HIS cc_start: 0.5960 (m-70) cc_final: 0.5260 (m-70) REVERT: Q 122 MET cc_start: 0.6787 (ppp) cc_final: 0.6309 (ppp) REVERT: Q 145 PHE cc_start: 0.8928 (t80) cc_final: 0.8411 (t80) REVERT: Q 170 VAL cc_start: 0.7581 (p) cc_final: 0.7357 (t) REVERT: R 1 MET cc_start: 0.6260 (mpp) cc_final: 0.5996 (mpp) REVERT: R 189 TYR cc_start: 0.7545 (m-10) cc_final: 0.7084 (m-10) REVERT: R 309 TYR cc_start: 0.7981 (t80) cc_final: 0.7669 (t80) REVERT: S 109 MET cc_start: 0.7555 (mmm) cc_final: 0.6780 (mmm) REVERT: T 17 ASN cc_start: 0.6841 (t160) cc_final: 0.6481 (t0) REVERT: T 51 THR cc_start: 0.8813 (t) cc_final: 0.8601 (p) REVERT: T 117 ASP cc_start: 0.8115 (p0) cc_final: 0.7842 (p0) REVERT: T 316 ASP cc_start: 0.8615 (p0) cc_final: 0.8413 (p0) REVERT: V 6 SER cc_start: 0.8443 (m) cc_final: 0.8239 (m) REVERT: V 123 PHE cc_start: 0.7696 (p90) cc_final: 0.7303 (p90) REVERT: V 124 LEU cc_start: 0.7517 (tp) cc_final: 0.7084 (tt) REVERT: V 239 LEU cc_start: 0.9131 (pp) cc_final: 0.8922 (pp) REVERT: V 307 PHE cc_start: 0.8233 (m-80) cc_final: 0.7823 (m-80) REVERT: W 140 PHE cc_start: 0.7125 (m-10) cc_final: 0.5825 (m-80) REVERT: W 229 ASN cc_start: 0.8373 (m-40) cc_final: 0.7856 (p0) REVERT: W 230 GLU cc_start: 0.8706 (mp0) cc_final: 0.8407 (pm20) REVERT: Y 65 MET cc_start: 0.9064 (ttt) cc_final: 0.8509 (mtp) outliers start: 2 outliers final: 0 residues processed: 603 average time/residue: 0.2662 time to fit residues: 269.1020 Evaluate side-chains 450 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 10.0000 chunk 497 optimal weight: 0.0030 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 4.9990 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 0.9980 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN L 106 ASN M 12 ASN P 17 ASN P 253 ASN ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 84 ASN ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 ASN ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 253 ASN W 40 ASN ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 255 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.124390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.095389 restraints weight = 182277.211| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 4.56 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 44932 Z= 0.183 Angle : 0.884 24.998 61226 Z= 0.402 Chirality : 0.072 1.148 7034 Planarity : 0.005 0.080 7612 Dihedral : 10.181 146.721 6747 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.92 % Favored : 91.83 % Rotamer: Outliers : 0.92 % Allowed : 10.41 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.11), residues: 5407 helix: 0.24 (0.13), residues: 1873 sheet: -0.55 (0.18), residues: 817 loop : -1.57 (0.12), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG Q 80 TYR 0.037 0.001 TYR Y 20 PHE 0.031 0.002 PHE V 185 TRP 0.031 0.002 TRP V 58 HIS 0.012 0.001 HIS Q 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (44924) covalent geometry : angle 0.88422 / 0.40 (61210) SS BOND : bond 0.00810 / 0.43 ( 8) SS BOND : angle 0.70396 / 0.37 ( 16) hydrogen bonds : bond 0.04260 / 2.83 ( 1339) hydrogen bonds : angle 4.97605 / 3.41 ( 3825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 481 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.4489 (mtt) cc_final: 0.4124 (ttm) REVERT: A 69 LEU cc_start: 0.8387 (tt) cc_final: 0.7834 (mt) REVERT: A 127 TRP cc_start: 0.6622 (m-10) cc_final: 0.6210 (m100) REVERT: A 133 TRP cc_start: 0.8032 (t60) cc_final: 0.7811 (t60) REVERT: A 197 ILE cc_start: 0.7737 (pt) cc_final: 0.6888 (mp) REVERT: A 198 MET cc_start: 0.6831 (mmt) cc_final: 0.6544 (ppp) REVERT: A 209 MET cc_start: 0.7414 (ptp) cc_final: 0.6827 (ppp) REVERT: C 35 ARG cc_start: 0.7798 (tpt90) cc_final: 0.7310 (mmm160) REVERT: C 78 GLU cc_start: 0.7072 (tp30) cc_final: 0.6751 (tp30) REVERT: F 29 ASP cc_start: 0.9108 (m-30) cc_final: 0.8599 (m-30) REVERT: F 92 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8379 (mmtt) REVERT: I 23 TYR cc_start: 0.8057 (m-80) cc_final: 0.7466 (m-80) REVERT: I 46 LYS cc_start: 0.9472 (mptt) cc_final: 0.9050 (mmtm) REVERT: J 45 TYR cc_start: 0.6720 (m-80) cc_final: 0.5976 (m-80) REVERT: J 57 LYS cc_start: 0.8739 (tptp) cc_final: 0.8407 (tptp) REVERT: J 106 ASN cc_start: 0.7654 (t0) cc_final: 0.7399 (t0) REVERT: M 28 GLU cc_start: 0.7705 (mp0) cc_final: 0.7369 (mp0) REVERT: O 155 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7501 (ptm-80) REVERT: O 183 MET cc_start: 0.6713 (pmm) cc_final: 0.6513 (pmm) REVERT: Q 90 TYR cc_start: 0.8889 (t80) cc_final: 0.8426 (t80) REVERT: Q 116 HIS cc_start: 0.8184 (t-90) cc_final: 0.7823 (t70) REVERT: Q 122 MET cc_start: 0.6549 (ppp) cc_final: 0.5886 (ppp) REVERT: Q 145 PHE cc_start: 0.8905 (t80) cc_final: 0.8279 (t80) REVERT: R 1 MET cc_start: 0.6439 (mpp) cc_final: 0.6103 (mpp) REVERT: R 264 GLU cc_start: 0.8747 (tp30) cc_final: 0.8401 (tp30) REVERT: R 309 TYR cc_start: 0.8554 (t80) cc_final: 0.8129 (t80) REVERT: S 10 PHE cc_start: 0.7793 (p90) cc_final: 0.7586 (p90) REVERT: S 109 MET cc_start: 0.7178 (mmm) cc_final: 0.6317 (mmm) REVERT: T 14 HIS cc_start: 0.9142 (p90) cc_final: 0.7777 (p90) REVERT: T 17 ASN cc_start: 0.6489 (t0) cc_final: 0.5886 (t0) REVERT: T 117 ASP cc_start: 0.8461 (p0) cc_final: 0.8040 (p0) REVERT: V 6 SER cc_start: 0.8116 (m) cc_final: 0.7887 (m) REVERT: V 14 HIS cc_start: 0.7648 (p-80) cc_final: 0.7440 (p-80) REVERT: V 68 LYS cc_start: 0.8148 (pttt) cc_final: 0.7682 (pttt) REVERT: V 124 LEU cc_start: 0.7733 (tp) cc_final: 0.7493 (tt) REVERT: V 286 TYR cc_start: 0.7838 (p90) cc_final: 0.7497 (p90) REVERT: V 307 PHE cc_start: 0.8206 (m-80) cc_final: 0.7784 (m-80) REVERT: W 229 ASN cc_start: 0.8414 (m-40) cc_final: 0.7978 (p0) REVERT: W 295 LYS cc_start: 0.8746 (ptmm) cc_final: 0.8078 (mttt) REVERT: Y 65 MET cc_start: 0.9146 (ttt) cc_final: 0.8474 (mtp) outliers start: 41 outliers final: 21 residues processed: 501 average time/residue: 0.2694 time to fit residues: 224.7193 Evaluate side-chains 452 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 431 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 250 ILE Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain S residue 157 TRP Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 253 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain Y residue 54 PHE Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 271 MET Chi-restraints excluded: chain Y residue 297 THR Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 237 optimal weight: 0.7980 chunk 475 optimal weight: 0.9990 chunk 523 optimal weight: 10.0000 chunk 484 optimal weight: 10.0000 chunk 440 optimal weight: 5.9990 chunk 464 optimal weight: 20.0000 chunk 247 optimal weight: 0.5980 chunk 425 optimal weight: 0.0270 chunk 70 optimal weight: 30.0000 chunk 469 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 overall best weight: 1.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN K 17 ASN K 209 GLN ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN M 162 HIS P 53 ASN ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN S 87 ASN ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 253 ASN ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.123643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.094381 restraints weight = 180222.728| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 4.54 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 44932 Z= 0.154 Angle : 0.751 24.053 61226 Z= 0.354 Chirality : 0.060 1.268 7034 Planarity : 0.004 0.082 7612 Dihedral : 10.622 151.809 6747 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.49 % Favored : 92.27 % Rotamer: Outliers : 1.75 % Allowed : 13.16 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.12), residues: 5407 helix: 0.36 (0.13), residues: 1832 sheet: -0.60 (0.18), residues: 842 loop : -1.54 (0.12), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 49 TYR 0.017 0.001 TYR J 45 PHE 0.029 0.001 PHE T 140 TRP 0.034 0.002 TRP A 24 HIS 0.010 0.001 HIS Q 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (44924) covalent geometry : angle 0.75091 / 0.35 (61210) SS BOND : bond 0.00112 / 0.05 ( 8) SS BOND : angle 0.71030 / 0.40 ( 16) hydrogen bonds : bond 0.03672 / 2.47 ( 1339) hydrogen bonds : angle 4.74754 / 3.28 ( 3825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 470 time to evaluate : 1.615 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: A 31 MET cc_start: 0.4420 (mtt) cc_final: 0.4066 (ttm) REVERT: A 69 LEU cc_start: 0.8517 (tt) cc_final: 0.7832 (mt) REVERT: A 133 TRP cc_start: 0.8054 (t60) cc_final: 0.6656 (t-100) REVERT: A 197 ILE cc_start: 0.7926 (pt) cc_final: 0.7646 (pt) REVERT: A 198 MET cc_start: 0.6946 (mmt) cc_final: 0.6590 (ppp) REVERT: A 209 MET cc_start: 0.7405 (ptp) cc_final: 0.6834 (ppp) REVERT: C 26 ASP cc_start: 0.8390 (t0) cc_final: 0.8033 (t0) REVERT: C 75 GLU cc_start: 0.7387 (mp0) cc_final: 0.7073 (mp0) REVERT: C 78 GLU cc_start: 0.7069 (tp30) cc_final: 0.6759 (tp30) REVERT: F 29 ASP cc_start: 0.9127 (m-30) cc_final: 0.8683 (m-30) REVERT: G 81 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8865 (p) REVERT: H 89 ASP cc_start: 0.9564 (m-30) cc_final: 0.9339 (m-30) REVERT: I 23 TYR cc_start: 0.8130 (m-80) cc_final: 0.7564 (m-80) REVERT: I 46 LYS cc_start: 0.9507 (mptt) cc_final: 0.9213 (mmtm) REVERT: J 45 TYR cc_start: 0.6724 (m-80) cc_final: 0.5890 (m-80) REVERT: J 57 LYS cc_start: 0.8783 (tptp) cc_final: 0.8439 (tptp) REVERT: J 106 ASN cc_start: 0.7743 (t0) cc_final: 0.7483 (t0) REVERT: K 142 LEU cc_start: 0.8885 (mm) cc_final: 0.8652 (mm) REVERT: N 19 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: N 28 GLU cc_start: 0.8523 (pm20) cc_final: 0.7716 (pm20) REVERT: O 1 MET cc_start: 0.8281 (mmm) cc_final: 0.7463 (tpp) REVERT: O 155 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7526 (ptm-80) REVERT: O 183 MET cc_start: 0.6940 (pmm) cc_final: 0.6659 (pmm) REVERT: P 28 GLU cc_start: 0.8532 (pm20) cc_final: 0.8190 (pm20) REVERT: Q 84 HIS cc_start: 0.4492 (p-80) cc_final: 0.3678 (p-80) REVERT: Q 90 TYR cc_start: 0.8951 (t80) cc_final: 0.8563 (t80) REVERT: Q 116 HIS cc_start: 0.8220 (t-90) cc_final: 0.7818 (t70) REVERT: Q 122 MET cc_start: 0.6443 (ppp) cc_final: 0.5759 (ppp) REVERT: Q 145 PHE cc_start: 0.8807 (t80) cc_final: 0.8077 (t80) REVERT: R 1 MET cc_start: 0.6330 (mpp) cc_final: 0.6004 (mpp) REVERT: R 264 GLU cc_start: 0.8773 (tp30) cc_final: 0.8443 (tp30) REVERT: R 309 TYR cc_start: 0.8569 (t80) cc_final: 0.8190 (t80) REVERT: S 10 PHE cc_start: 0.7905 (p90) cc_final: 0.7668 (p90) REVERT: S 87 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7431 (p0) REVERT: S 89 PHE cc_start: 0.8656 (m-80) cc_final: 0.8369 (m-80) REVERT: S 109 MET cc_start: 0.7214 (mmm) cc_final: 0.6432 (mmm) REVERT: S 224 ARG cc_start: 0.8820 (tmm-80) cc_final: 0.8410 (tmm-80) REVERT: T 1 MET cc_start: 0.8376 (mpp) cc_final: 0.7896 (mpp) REVERT: T 17 ASN cc_start: 0.6420 (t0) cc_final: 0.5809 (t0) REVERT: T 54 MET cc_start: 0.7622 (mmp) cc_final: 0.7060 (mmp) REVERT: T 117 ASP cc_start: 0.8482 (p0) cc_final: 0.7996 (p0) REVERT: V 5 ILE cc_start: 0.9551 (OUTLIER) cc_final: 0.9047 (tp) REVERT: V 6 SER cc_start: 0.8255 (m) cc_final: 0.8016 (t) REVERT: V 14 HIS cc_start: 0.7452 (p-80) cc_final: 0.7121 (p-80) REVERT: V 54 MET cc_start: 0.2318 (mtt) cc_final: 0.1783 (mtt) REVERT: V 124 LEU cc_start: 0.7843 (tp) cc_final: 0.7632 (tt) REVERT: V 231 ARG cc_start: 0.7409 (mmm-85) cc_final: 0.6975 (mmt90) REVERT: V 236 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8784 (mm-30) REVERT: V 245 MET cc_start: 0.8665 (mmm) cc_final: 0.8449 (mmm) REVERT: V 253 ASN cc_start: 0.5799 (OUTLIER) cc_final: 0.4909 (t0) REVERT: V 286 TYR cc_start: 0.7901 (p90) cc_final: 0.7480 (p90) REVERT: V 307 PHE cc_start: 0.8196 (m-80) cc_final: 0.7764 (m-80) REVERT: W 229 ASN cc_start: 0.8591 (m-40) cc_final: 0.8186 (p0) REVERT: Y 65 MET cc_start: 0.9174 (ttt) cc_final: 0.8317 (mtp) REVERT: Y 68 LEU cc_start: 0.8480 (tt) cc_final: 0.7884 (mt) REVERT: Y 111 MET cc_start: 0.7937 (mmp) cc_final: 0.7094 (mmp) REVERT: Y 222 ARG cc_start: 0.7974 (tpp-160) cc_final: 0.7386 (tpp80) outliers start: 78 outliers final: 40 residues processed: 516 average time/residue: 0.2653 time to fit residues: 229.2203 Evaluate side-chains 471 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 425 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain Q residue 29 TYR Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 249 TYR Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 87 ASN Chi-restraints excluded: chain S residue 157 TRP Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 269 ILE Chi-restraints excluded: chain T residue 312 ASP Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 253 ASN Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain Y residue 54 PHE Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 271 MET Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 85 optimal weight: 8.9990 chunk 408 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 388 optimal weight: 2.9990 chunk 277 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 530 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 ASN M 17 ASN M 162 HIS N 162 HIS ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN T 19 GLN ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 253 ASN ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.124832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.095595 restraints weight = 185927.651| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 4.64 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 44932 Z= 0.127 Angle : 0.700 15.078 61226 Z= 0.333 Chirality : 0.055 0.891 7034 Planarity : 0.004 0.072 7612 Dihedral : 10.599 146.702 6747 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.62 % Favored : 92.16 % Rotamer: Outliers : 1.77 % Allowed : 14.95 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.12), residues: 5407 helix: 0.37 (0.13), residues: 1841 sheet: -0.56 (0.18), residues: 842 loop : -1.53 (0.12), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG Q 80 TYR 0.030 0.001 TYR Y 20 PHE 0.025 0.001 PHE Q 155 TRP 0.043 0.001 TRP A 24 HIS 0.008 0.001 HIS V 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (44924) covalent geometry : angle 0.69958 / 0.33 (61210) SS BOND : bond 0.00113 / 0.06 ( 8) SS BOND : angle 0.61149 / 0.35 ( 16) hydrogen bonds : bond 0.03397 / 2.28 ( 1339) hydrogen bonds : angle 4.64514 / 3.21 ( 3825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 466 time to evaluate : 1.779 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: A 31 MET cc_start: 0.4432 (mtt) cc_final: 0.4071 (ttm) REVERT: A 69 LEU cc_start: 0.8663 (tt) cc_final: 0.7911 (mt) REVERT: A 133 TRP cc_start: 0.8021 (t60) cc_final: 0.6680 (t-100) REVERT: A 163 ILE cc_start: 0.8546 (pt) cc_final: 0.8329 (mm) REVERT: A 197 ILE cc_start: 0.7925 (pt) cc_final: 0.7241 (mp) REVERT: A 198 MET cc_start: 0.7017 (mmt) cc_final: 0.6566 (ppp) REVERT: C 10 ARG cc_start: 0.6514 (mmp-170) cc_final: 0.6207 (mmm160) REVERT: C 26 ASP cc_start: 0.8474 (t0) cc_final: 0.8123 (t0) REVERT: C 35 ARG cc_start: 0.7684 (tpt90) cc_final: 0.7325 (mmm160) REVERT: C 78 GLU cc_start: 0.6987 (tp30) cc_final: 0.6674 (tp30) REVERT: F 29 ASP cc_start: 0.9129 (m-30) cc_final: 0.8700 (m-30) REVERT: F 53 LYS cc_start: 0.9355 (tttp) cc_final: 0.9144 (tmtt) REVERT: G 46 LYS cc_start: 0.9403 (mppt) cc_final: 0.8974 (mppt) REVERT: I 23 TYR cc_start: 0.8161 (m-80) cc_final: 0.7638 (m-80) REVERT: I 46 LYS cc_start: 0.9502 (mptt) cc_final: 0.9016 (mmtm) REVERT: J 36 THR cc_start: 0.6574 (OUTLIER) cc_final: 0.6360 (m) REVERT: J 45 TYR cc_start: 0.6855 (m-80) cc_final: 0.5954 (m-80) REVERT: J 57 LYS cc_start: 0.8795 (tptp) cc_final: 0.8420 (tptp) REVERT: J 106 ASN cc_start: 0.7566 (t0) cc_final: 0.7331 (t0) REVERT: K 154 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8232 (tp30) REVERT: L 165 VAL cc_start: 0.7492 (OUTLIER) cc_final: 0.7153 (p) REVERT: O 1 MET cc_start: 0.8292 (mmm) cc_final: 0.7702 (tpp) REVERT: O 183 MET cc_start: 0.6923 (pmm) cc_final: 0.6631 (pmm) REVERT: O 334 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8940 (mtmm) REVERT: P 28 GLU cc_start: 0.8664 (pm20) cc_final: 0.8272 (pm20) REVERT: Q 90 TYR cc_start: 0.8946 (t80) cc_final: 0.8541 (t80) REVERT: Q 116 HIS cc_start: 0.8321 (t-90) cc_final: 0.8112 (t-90) REVERT: Q 122 MET cc_start: 0.6494 (ppp) cc_final: 0.5887 (ppp) REVERT: Q 145 PHE cc_start: 0.8784 (t80) cc_final: 0.8041 (t80) REVERT: R 1 MET cc_start: 0.6285 (mpp) cc_final: 0.6001 (mpp) REVERT: R 245 MET cc_start: 0.8902 (tpp) cc_final: 0.8695 (mmt) REVERT: R 264 GLU cc_start: 0.8809 (tp30) cc_final: 0.8410 (tp30) REVERT: S 10 PHE cc_start: 0.7923 (p90) cc_final: 0.7654 (p90) REVERT: S 87 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8397 (p0) REVERT: S 109 MET cc_start: 0.7325 (mmm) cc_final: 0.6559 (mmm) REVERT: S 224 ARG cc_start: 0.8944 (tmm-80) cc_final: 0.8546 (tmm-80) REVERT: T 1 MET cc_start: 0.8343 (mpp) cc_final: 0.7901 (mpp) REVERT: T 17 ASN cc_start: 0.6460 (t0) cc_final: 0.5901 (t0) REVERT: T 54 MET cc_start: 0.7614 (mmp) cc_final: 0.6777 (mmp) REVERT: T 58 TRP cc_start: 0.6625 (m-90) cc_final: 0.5909 (m100) REVERT: T 117 ASP cc_start: 0.8442 (p0) cc_final: 0.8068 (p0) REVERT: T 119 ASP cc_start: 0.8053 (t0) cc_final: 0.7803 (t70) REVERT: V 5 ILE cc_start: 0.9590 (OUTLIER) cc_final: 0.9058 (tp) REVERT: V 14 HIS cc_start: 0.7692 (p-80) cc_final: 0.7456 (p-80) REVERT: V 19 GLN cc_start: 0.7358 (tp-100) cc_final: 0.7123 (tp-100) REVERT: V 68 LYS cc_start: 0.8092 (pttt) cc_final: 0.7712 (pttt) REVERT: V 231 ARG cc_start: 0.7395 (mmm-85) cc_final: 0.6981 (mmt90) REVERT: V 236 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8797 (mm-30) REVERT: V 245 MET cc_start: 0.8528 (mmm) cc_final: 0.8179 (mmm) REVERT: V 253 ASN cc_start: 0.5466 (OUTLIER) cc_final: 0.4637 (t0) REVERT: V 286 TYR cc_start: 0.7982 (p90) cc_final: 0.7654 (p90) REVERT: V 307 PHE cc_start: 0.8134 (m-80) cc_final: 0.7688 (m-80) REVERT: W 229 ASN cc_start: 0.8609 (m-40) cc_final: 0.8231 (p0) REVERT: W 236 GLU cc_start: 0.8431 (mp0) cc_final: 0.8181 (mp0) REVERT: W 295 LYS cc_start: 0.8485 (ptmm) cc_final: 0.7931 (pttt) REVERT: Y 65 MET cc_start: 0.9150 (ttt) cc_final: 0.8279 (mtp) REVERT: Y 68 LEU cc_start: 0.8414 (tt) cc_final: 0.7882 (mt) REVERT: Y 222 ARG cc_start: 0.8036 (tpp-160) cc_final: 0.7468 (tpp80) REVERT: Y 307 ILE cc_start: 0.7341 (mm) cc_final: 0.6799 (tt) outliers start: 79 outliers final: 45 residues processed: 515 average time/residue: 0.2569 time to fit residues: 222.0028 Evaluate side-chains 492 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 440 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain Q residue 29 TYR Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 249 TYR Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 87 ASN Chi-restraints excluded: chain S residue 157 TRP Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 269 ILE Chi-restraints excluded: chain T residue 312 ASP Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 253 ASN Chi-restraints excluded: chain V residue 266 LEU Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 333 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain Y residue 17 TYR Chi-restraints excluded: chain Y residue 54 PHE Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 297 THR Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 461 optimal weight: 30.0000 chunk 61 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 360 optimal weight: 8.9990 chunk 310 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 281 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 260 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 456 optimal weight: 20.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN K 17 ASN K 223 ASN L 162 HIS ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 162 HIS ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN T 19 GLN ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 ASN ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.123560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.094114 restraints weight = 185783.405| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.61 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 44932 Z= 0.159 Angle : 0.700 13.133 61226 Z= 0.336 Chirality : 0.053 0.637 7034 Planarity : 0.004 0.070 7612 Dihedral : 10.720 157.468 6747 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.82 % Favored : 91.97 % Rotamer: Outliers : 2.24 % Allowed : 16.12 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.12), residues: 5407 helix: 0.44 (0.13), residues: 1829 sheet: -0.54 (0.18), residues: 837 loop : -1.54 (0.12), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 164 TYR 0.033 0.001 TYR Y 20 PHE 0.023 0.001 PHE Q 155 TRP 0.043 0.002 TRP A 24 HIS 0.007 0.001 HIS V 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (44924) covalent geometry : angle 0.69995 / 0.34 (61210) SS BOND : bond 0.00137 / 0.07 ( 8) SS BOND : angle 0.66646 / 0.38 ( 16) hydrogen bonds : bond 0.03333 / 2.23 ( 1339) hydrogen bonds : angle 4.59191 / 3.18 ( 3825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 457 time to evaluate : 1.265 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: A 31 MET cc_start: 0.4383 (mtt) cc_final: 0.4007 (ttm) REVERT: A 127 TRP cc_start: 0.6522 (m-10) cc_final: 0.5993 (m100) REVERT: A 133 TRP cc_start: 0.8076 (t60) cc_final: 0.6697 (t-100) REVERT: A 197 ILE cc_start: 0.7970 (pt) cc_final: 0.7311 (mp) REVERT: A 198 MET cc_start: 0.7159 (mmt) cc_final: 0.6624 (ppp) REVERT: C 26 ASP cc_start: 0.8485 (t0) cc_final: 0.8238 (t70) REVERT: C 35 ARG cc_start: 0.7717 (tpt90) cc_final: 0.7272 (mmm160) REVERT: C 78 GLU cc_start: 0.6968 (tp30) cc_final: 0.6663 (tp30) REVERT: E 15 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.6030 (tt) REVERT: F 29 ASP cc_start: 0.9110 (m-30) cc_final: 0.8706 (m-30) REVERT: F 53 LYS cc_start: 0.9392 (tttp) cc_final: 0.9177 (tmtt) REVERT: G 46 LYS cc_start: 0.9407 (mppt) cc_final: 0.8988 (mppt) REVERT: G 82 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: H 83 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: I 23 TYR cc_start: 0.8237 (m-80) cc_final: 0.7706 (m-80) REVERT: I 46 LYS cc_start: 0.9525 (mptt) cc_final: 0.9027 (mmtm) REVERT: J 57 LYS cc_start: 0.8759 (tptp) cc_final: 0.8390 (tptp) REVERT: J 106 ASN cc_start: 0.7649 (t0) cc_final: 0.7416 (t0) REVERT: K 154 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8263 (tp30) REVERT: K 236 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8213 (pp20) REVERT: L 165 VAL cc_start: 0.7407 (OUTLIER) cc_final: 0.7066 (p) REVERT: M 1 MET cc_start: 0.6776 (tpp) cc_final: 0.6534 (tpp) REVERT: M 335 MET cc_start: 0.8785 (ppp) cc_final: 0.7732 (ppp) REVERT: N 19 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7105 (mp10) REVERT: N 25 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7989 (p0) REVERT: O 1 MET cc_start: 0.8446 (mmm) cc_final: 0.7603 (tpp) REVERT: O 183 MET cc_start: 0.7166 (pmm) cc_final: 0.6849 (pmm) REVERT: P 28 GLU cc_start: 0.8726 (pm20) cc_final: 0.8343 (pm20) REVERT: P 164 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6847 (ptm-80) REVERT: Q 90 TYR cc_start: 0.8945 (t80) cc_final: 0.8522 (t80) REVERT: Q 116 HIS cc_start: 0.8426 (t-90) cc_final: 0.8129 (t-90) REVERT: Q 122 MET cc_start: 0.6343 (ppp) cc_final: 0.5810 (ppp) REVERT: Q 145 PHE cc_start: 0.8760 (t80) cc_final: 0.8121 (t80) REVERT: R 1 MET cc_start: 0.6574 (mpp) cc_final: 0.6288 (mpp) REVERT: R 54 MET cc_start: 0.9130 (tpp) cc_final: 0.8852 (tpp) REVERT: R 264 GLU cc_start: 0.8803 (tp30) cc_final: 0.8474 (tp30) REVERT: S 10 PHE cc_start: 0.8041 (p90) cc_final: 0.7759 (p90) REVERT: S 84 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9061 (mt) REVERT: S 109 MET cc_start: 0.7365 (mmm) cc_final: 0.6615 (mmm) REVERT: S 224 ARG cc_start: 0.8911 (tmm-80) cc_final: 0.8457 (tmm-80) REVERT: T 17 ASN cc_start: 0.6700 (t0) cc_final: 0.6065 (t0) REVERT: T 54 MET cc_start: 0.7697 (mmp) cc_final: 0.6860 (mmp) REVERT: T 58 TRP cc_start: 0.6762 (m-90) cc_final: 0.5566 (m100) REVERT: T 117 ASP cc_start: 0.8483 (p0) cc_final: 0.8147 (p0) REVERT: T 119 ASP cc_start: 0.8165 (t0) cc_final: 0.7876 (t0) REVERT: T 249 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.6941 (m-80) REVERT: V 5 ILE cc_start: 0.9557 (OUTLIER) cc_final: 0.9089 (tp) REVERT: V 14 HIS cc_start: 0.7652 (p-80) cc_final: 0.7362 (p-80) REVERT: V 68 LYS cc_start: 0.8169 (pttt) cc_final: 0.7790 (pttt) REVERT: V 231 ARG cc_start: 0.7377 (mmm-85) cc_final: 0.7013 (mmt90) REVERT: V 235 ILE cc_start: 0.9345 (mm) cc_final: 0.8878 (pt) REVERT: V 236 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8552 (mm-30) REVERT: V 245 MET cc_start: 0.8578 (mmm) cc_final: 0.8310 (mmm) REVERT: V 253 ASN cc_start: 0.5373 (OUTLIER) cc_final: 0.4673 (t0) REVERT: V 286 TYR cc_start: 0.8212 (p90) cc_final: 0.7646 (p90) REVERT: V 307 PHE cc_start: 0.8346 (m-80) cc_final: 0.7894 (m-80) REVERT: W 229 ASN cc_start: 0.8604 (m-40) cc_final: 0.8327 (p0) REVERT: W 236 GLU cc_start: 0.8528 (mp0) cc_final: 0.7981 (mm-30) REVERT: W 246 LEU cc_start: 0.8562 (mt) cc_final: 0.8304 (mm) REVERT: W 295 LYS cc_start: 0.8514 (ptmm) cc_final: 0.7951 (pttt) REVERT: Y 7 THR cc_start: 0.7045 (OUTLIER) cc_final: 0.6634 (p) REVERT: Y 68 LEU cc_start: 0.8616 (tt) cc_final: 0.8004 (mt) REVERT: Y 307 ILE cc_start: 0.7330 (mm) cc_final: 0.6769 (tt) outliers start: 100 outliers final: 51 residues processed: 521 average time/residue: 0.2588 time to fit residues: 226.9152 Evaluate side-chains 495 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 430 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 164 ARG Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 29 TYR Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 249 TYR Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 157 TRP Chi-restraints excluded: chain T residue 19 GLN Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 249 TYR Chi-restraints excluded: chain T residue 269 ILE Chi-restraints excluded: chain T residue 279 VAL Chi-restraints excluded: chain T residue 312 ASP Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 253 ASN Chi-restraints excluded: chain V residue 266 LEU Chi-restraints excluded: chain V residue 335 MET Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 54 PHE Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 297 THR Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 309 optimal weight: 4.9990 chunk 341 optimal weight: 40.0000 chunk 57 optimal weight: 9.9990 chunk 364 optimal weight: 8.9990 chunk 397 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 370 optimal weight: 7.9990 chunk 391 optimal weight: 0.2980 chunk 448 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN K 17 ASN ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.120113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.089968 restraints weight = 187463.444| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 4.52 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.143 44932 Z= 0.320 Angle : 0.839 16.619 61226 Z= 0.412 Chirality : 0.057 0.740 7034 Planarity : 0.005 0.078 7612 Dihedral : 11.124 158.641 6747 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.82 % Favored : 90.97 % Rotamer: Outliers : 2.87 % Allowed : 17.08 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.11), residues: 5407 helix: 0.16 (0.12), residues: 1846 sheet: -0.83 (0.17), residues: 841 loop : -1.68 (0.12), residues: 2720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG Q 80 TYR 0.031 0.002 TYR Y 20 PHE 0.033 0.003 PHE K 258 TRP 0.024 0.002 TRP T 58 HIS 0.016 0.002 HIS L 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.32 (44924) covalent geometry : angle 0.83909 / 0.41 (61210) SS BOND : bond 0.00225 / 0.12 ( 8) SS BOND : angle 0.94191 / 0.53 ( 16) hydrogen bonds : bond 0.03966 / 2.63 ( 1339) hydrogen bonds : angle 4.86265 / 3.38 ( 3825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 431 time to evaluate : 1.668 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: A 31 MET cc_start: 0.4372 (mtt) cc_final: 0.4015 (ttm) REVERT: A 133 TRP cc_start: 0.8260 (t60) cc_final: 0.6643 (t-100) REVERT: A 197 ILE cc_start: 0.7746 (pt) cc_final: 0.7220 (mp) REVERT: A 198 MET cc_start: 0.7518 (mmt) cc_final: 0.6931 (ppp) REVERT: F 29 ASP cc_start: 0.9060 (m-30) cc_final: 0.8662 (m-30) REVERT: G 46 LYS cc_start: 0.9457 (mppt) cc_final: 0.9058 (mppt) REVERT: H 83 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8042 (pm20) REVERT: I 23 TYR cc_start: 0.8332 (m-80) cc_final: 0.7831 (m-80) REVERT: I 46 LYS cc_start: 0.9552 (mptt) cc_final: 0.9045 (mmtm) REVERT: J 57 LYS cc_start: 0.8852 (tptp) cc_final: 0.8559 (tptp) REVERT: J 106 ASN cc_start: 0.7616 (t0) cc_final: 0.7381 (t0) REVERT: K 154 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8261 (tp30) REVERT: L 165 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7417 (p) REVERT: M 1 MET cc_start: 0.6756 (tpp) cc_final: 0.6323 (tpp) REVERT: M 335 MET cc_start: 0.8882 (ppp) cc_final: 0.7942 (ppp) REVERT: N 19 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7054 (mp10) REVERT: N 28 GLU cc_start: 0.8740 (pm20) cc_final: 0.8132 (pm20) REVERT: N 156 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8178 (pp) REVERT: N 245 MET cc_start: 0.9081 (mmp) cc_final: 0.8595 (mmm) REVERT: O 1 MET cc_start: 0.8219 (mmm) cc_final: 0.7355 (tpp) REVERT: O 183 MET cc_start: 0.7870 (pmm) cc_final: 0.7460 (pmm) REVERT: Q 69 TYR cc_start: 0.6456 (t80) cc_final: 0.6242 (t80) REVERT: Q 83 ARG cc_start: 0.7879 (mmm160) cc_final: 0.7484 (mmm160) REVERT: Q 90 TYR cc_start: 0.8764 (t80) cc_final: 0.8310 (t80) REVERT: Q 116 HIS cc_start: 0.8533 (t-90) cc_final: 0.8112 (t-90) REVERT: Q 122 MET cc_start: 0.6545 (ppp) cc_final: 0.5825 (ppp) REVERT: Q 145 PHE cc_start: 0.8788 (t80) cc_final: 0.8085 (t80) REVERT: R 1 MET cc_start: 0.6943 (mpp) cc_final: 0.6203 (mpp) REVERT: R 264 GLU cc_start: 0.8742 (tp30) cc_final: 0.8434 (tp30) REVERT: S 84 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9040 (mt) REVERT: S 109 MET cc_start: 0.7469 (mmm) cc_final: 0.6671 (mmm) REVERT: S 224 ARG cc_start: 0.8953 (tmm-80) cc_final: 0.8431 (tmm-80) REVERT: T 54 MET cc_start: 0.7679 (mmp) cc_final: 0.7047 (mmp) REVERT: T 58 TRP cc_start: 0.7048 (m-90) cc_final: 0.6046 (m100) REVERT: T 117 ASP cc_start: 0.8564 (p0) cc_final: 0.8319 (p0) REVERT: T 249 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: V 14 HIS cc_start: 0.7570 (p-80) cc_final: 0.7017 (p-80) REVERT: V 16 LEU cc_start: 0.6168 (mp) cc_final: 0.5871 (mt) REVERT: V 231 ARG cc_start: 0.7520 (mmm-85) cc_final: 0.7182 (mmt90) REVERT: V 235 ILE cc_start: 0.9392 (mm) cc_final: 0.9169 (mm) REVERT: V 236 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8772 (mm-30) REVERT: V 245 MET cc_start: 0.8779 (mmm) cc_final: 0.8460 (mmm) REVERT: V 286 TYR cc_start: 0.8406 (p90) cc_final: 0.7805 (p90) REVERT: W 229 ASN cc_start: 0.8644 (m-40) cc_final: 0.8230 (p0) REVERT: W 236 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8030 (mm-30) REVERT: W 246 LEU cc_start: 0.8650 (mt) cc_final: 0.8421 (mm) REVERT: W 290 ASN cc_start: 0.7646 (m-40) cc_final: 0.7351 (m110) REVERT: W 295 LYS cc_start: 0.8648 (ptmm) cc_final: 0.8104 (pttt) REVERT: Y 7 THR cc_start: 0.7224 (OUTLIER) cc_final: 0.6581 (p) REVERT: Y 65 MET cc_start: 0.9252 (ttt) cc_final: 0.8796 (tpt) REVERT: Y 222 ARG cc_start: 0.8164 (tpp-160) cc_final: 0.7573 (tpp80) REVERT: Y 307 ILE cc_start: 0.7599 (mm) cc_final: 0.6938 (tt) REVERT: Y 308 MET cc_start: 0.8766 (mmp) cc_final: 0.8494 (mmp) outliers start: 128 outliers final: 73 residues processed: 519 average time/residue: 0.2693 time to fit residues: 233.1647 Evaluate side-chains 492 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 411 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain N residue 235 ILE Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 185 PHE Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 185 PHE Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain P residue 336 VAL Chi-restraints excluded: chain Q residue 29 TYR Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 249 TYR Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 144 ASP Chi-restraints excluded: chain S residue 157 TRP Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 249 TYR Chi-restraints excluded: chain T residue 279 VAL Chi-restraints excluded: chain T residue 312 ASP Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 332 LEU Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 335 MET Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 186 ILE Chi-restraints excluded: chain Y residue 297 THR Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 453 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 523 optimal weight: 10.0000 chunk 312 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 522 optimal weight: 8.9990 chunk 252 optimal weight: 0.9990 chunk 247 optimal weight: 0.1980 chunk 135 optimal weight: 3.9990 chunk 51 optimal weight: 50.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN M 162 HIS ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 9 GLN Q 14 HIS ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN T 19 GLN ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.119509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.089488 restraints weight = 182876.086| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 4.55 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 44932 Z= 0.137 Angle : 0.725 11.995 61226 Z= 0.349 Chirality : 0.053 0.583 7034 Planarity : 0.004 0.065 7612 Dihedral : 11.010 168.906 6747 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.51 % Favored : 92.29 % Rotamer: Outliers : 2.04 % Allowed : 18.56 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.11), residues: 5407 helix: 0.40 (0.13), residues: 1838 sheet: -0.50 (0.18), residues: 744 loop : -1.60 (0.11), residues: 2825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 91 TYR 0.033 0.001 TYR Y 20 PHE 0.024 0.001 PHE P 185 TRP 0.021 0.002 TRP P 58 HIS 0.006 0.001 HIS V 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (44924) covalent geometry : angle 0.72505 / 0.35 (61210) SS BOND : bond 0.01177 / 0.47 ( 8) SS BOND : angle 0.70922 / 0.40 ( 16) hydrogen bonds : bond 0.03386 / 2.24 ( 1339) hydrogen bonds : angle 4.61449 / 3.21 ( 3825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 451 time to evaluate : 1.835 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: A 31 MET cc_start: 0.4317 (mtt) cc_final: 0.3957 (ttm) REVERT: A 69 LEU cc_start: 0.8613 (tt) cc_final: 0.7854 (mt) REVERT: A 133 TRP cc_start: 0.8192 (t60) cc_final: 0.7809 (t60) REVERT: A 197 ILE cc_start: 0.7707 (pt) cc_final: 0.7183 (mp) REVERT: A 198 MET cc_start: 0.7398 (mmt) cc_final: 0.6881 (ppp) REVERT: C 67 ARG cc_start: 0.6663 (tpt90) cc_final: 0.6346 (tpt90) REVERT: C 78 GLU cc_start: 0.7118 (tp30) cc_final: 0.6875 (tp30) REVERT: F 29 ASP cc_start: 0.9080 (m-30) cc_final: 0.8696 (m-30) REVERT: F 53 LYS cc_start: 0.9194 (ttmm) cc_final: 0.8555 (ttmm) REVERT: G 46 LYS cc_start: 0.9397 (mppt) cc_final: 0.9064 (mppt) REVERT: H 29 ASP cc_start: 0.8587 (m-30) cc_final: 0.8305 (m-30) REVERT: H 83 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: I 23 TYR cc_start: 0.8339 (m-80) cc_final: 0.7954 (m-80) REVERT: I 46 LYS cc_start: 0.9492 (mptt) cc_final: 0.9032 (mmtm) REVERT: J 42 GLU cc_start: 0.9204 (pt0) cc_final: 0.8957 (pt0) REVERT: J 45 TYR cc_start: 0.6774 (m-80) cc_final: 0.5826 (m-80) REVERT: J 57 LYS cc_start: 0.8854 (tptp) cc_final: 0.8551 (tptp) REVERT: J 106 ASN cc_start: 0.7624 (t0) cc_final: 0.7306 (t0) REVERT: J 107 ASN cc_start: 0.7699 (p0) cc_final: 0.7449 (p0) REVERT: L 165 VAL cc_start: 0.7513 (OUTLIER) cc_final: 0.7280 (p) REVERT: M 1 MET cc_start: 0.6694 (tpp) cc_final: 0.6250 (tpp) REVERT: M 335 MET cc_start: 0.8879 (ppp) cc_final: 0.7795 (ppp) REVERT: N 19 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7275 (mp10) REVERT: N 25 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8369 (p0) REVERT: N 28 GLU cc_start: 0.8537 (pm20) cc_final: 0.7941 (pm20) REVERT: N 245 MET cc_start: 0.9035 (mmp) cc_final: 0.8303 (mmm) REVERT: O 1 MET cc_start: 0.8130 (mmm) cc_final: 0.7682 (tpp) REVERT: O 183 MET cc_start: 0.7601 (pmm) cc_final: 0.7192 (pmm) REVERT: Q 90 TYR cc_start: 0.8914 (t80) cc_final: 0.8517 (t80) REVERT: Q 116 HIS cc_start: 0.8463 (t-90) cc_final: 0.8230 (t-90) REVERT: Q 122 MET cc_start: 0.6291 (ppp) cc_final: 0.5769 (ppp) REVERT: Q 145 PHE cc_start: 0.8740 (t80) cc_final: 0.8080 (t80) REVERT: Q 149 MET cc_start: 0.6778 (mmm) cc_final: 0.6437 (mmm) REVERT: R 1 MET cc_start: 0.6683 (mpp) cc_final: 0.5898 (mpp) REVERT: R 264 GLU cc_start: 0.8842 (tp30) cc_final: 0.8413 (mm-30) REVERT: S 10 PHE cc_start: 0.7935 (p90) cc_final: 0.7655 (p90) REVERT: S 84 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8985 (mt) REVERT: S 109 MET cc_start: 0.7273 (mmm) cc_final: 0.6654 (mmm) REVERT: S 224 ARG cc_start: 0.8895 (tmm-80) cc_final: 0.8612 (ptt90) REVERT: T 54 MET cc_start: 0.7840 (mmp) cc_final: 0.6991 (mmp) REVERT: T 58 TRP cc_start: 0.7060 (m-90) cc_final: 0.5488 (m100) REVERT: T 117 ASP cc_start: 0.8414 (p0) cc_final: 0.8181 (p0) REVERT: T 265 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7014 (pm20) REVERT: V 14 HIS cc_start: 0.7744 (p-80) cc_final: 0.7273 (p-80) REVERT: V 54 MET cc_start: 0.2356 (mtt) cc_final: 0.2141 (mtt) REVERT: V 68 LYS cc_start: 0.8164 (pttt) cc_final: 0.7836 (pttt) REVERT: V 231 ARG cc_start: 0.7487 (mmm-85) cc_final: 0.6908 (mmt90) REVERT: V 235 ILE cc_start: 0.9404 (mm) cc_final: 0.9180 (mm) REVERT: V 236 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8772 (mm-30) REVERT: V 245 MET cc_start: 0.8643 (mmm) cc_final: 0.8261 (mmm) REVERT: V 286 TYR cc_start: 0.8347 (p90) cc_final: 0.7803 (p90) REVERT: V 307 PHE cc_start: 0.8124 (m-80) cc_final: 0.7639 (m-80) REVERT: W 229 ASN cc_start: 0.8467 (m-40) cc_final: 0.8040 (p0) REVERT: W 236 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8267 (mm-30) REVERT: W 290 ASN cc_start: 0.7473 (m-40) cc_final: 0.7169 (m110) REVERT: W 295 LYS cc_start: 0.8596 (ptmm) cc_final: 0.8036 (pttt) REVERT: Y 7 THR cc_start: 0.7054 (OUTLIER) cc_final: 0.6566 (p) REVERT: Y 65 MET cc_start: 0.9158 (ttt) cc_final: 0.8374 (mtp) REVERT: Y 222 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7600 (tpp80) REVERT: Y 307 ILE cc_start: 0.7581 (mm) cc_final: 0.6932 (tt) REVERT: Y 308 MET cc_start: 0.8696 (mmp) cc_final: 0.8445 (mmp) outliers start: 91 outliers final: 62 residues processed: 512 average time/residue: 0.2713 time to fit residues: 233.0263 Evaluate side-chains 484 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 414 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 185 PHE Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain P residue 336 VAL Chi-restraints excluded: chain Q residue 7 GLN Chi-restraints excluded: chain Q residue 29 TYR Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 110 ARG Chi-restraints excluded: chain S residue 157 TRP Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain T residue 19 GLN Chi-restraints excluded: chain T residue 265 GLU Chi-restraints excluded: chain T residue 279 VAL Chi-restraints excluded: chain T residue 312 ASP Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 266 LEU Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain W residue 246 LEU Chi-restraints excluded: chain W residue 287 ILE Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 463 optimal weight: 0.0870 chunk 20 optimal weight: 30.0000 chunk 16 optimal weight: 6.9990 chunk 467 optimal weight: 0.0370 chunk 333 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 490 optimal weight: 0.5980 chunk 27 optimal weight: 20.0000 chunk 270 optimal weight: 0.9990 chunk 308 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN K 17 ASN M 162 HIS ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN ** T 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.119818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.089876 restraints weight = 183750.987| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 4.58 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 44932 Z= 0.137 Angle : 0.718 11.396 61226 Z= 0.345 Chirality : 0.052 0.574 7034 Planarity : 0.004 0.062 7612 Dihedral : 10.967 168.735 6747 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.03 % Favored : 91.77 % Rotamer: Outliers : 2.08 % Allowed : 19.05 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.11), residues: 5407 helix: 0.43 (0.13), residues: 1838 sheet: -0.52 (0.18), residues: 756 loop : -1.56 (0.11), residues: 2813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 91 TYR 0.032 0.001 TYR Y 20 PHE 0.027 0.001 PHE Q 155 TRP 0.032 0.002 TRP V 58 HIS 0.005 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (44924) covalent geometry : angle 0.71793 / 0.34 (61210) SS BOND : bond 0.00169 / 0.08 ( 8) SS BOND : angle 0.75918 / 0.43 ( 16) hydrogen bonds : bond 0.03304 / 2.20 ( 1339) hydrogen bonds : angle 4.58820 / 3.19 ( 3825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 433 time to evaluate : 1.655 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: A 31 MET cc_start: 0.4327 (mtt) cc_final: 0.3965 (ttm) REVERT: A 69 LEU cc_start: 0.8626 (tt) cc_final: 0.7880 (mt) REVERT: A 133 TRP cc_start: 0.8201 (t60) cc_final: 0.7826 (t60) REVERT: A 197 ILE cc_start: 0.7687 (pt) cc_final: 0.7173 (mp) REVERT: A 198 MET cc_start: 0.7483 (mmt) cc_final: 0.6967 (ppp) REVERT: A 209 MET cc_start: 0.7546 (ptt) cc_final: 0.7054 (ppp) REVERT: C 67 ARG cc_start: 0.6531 (tpt90) cc_final: 0.6279 (tpt90) REVERT: C 78 GLU cc_start: 0.7108 (tp30) cc_final: 0.6866 (tp30) REVERT: F 29 ASP cc_start: 0.9081 (m-30) cc_final: 0.8703 (m-30) REVERT: F 53 LYS cc_start: 0.9217 (ttmm) cc_final: 0.8615 (ttmm) REVERT: G 46 LYS cc_start: 0.9390 (mppt) cc_final: 0.9060 (mppt) REVERT: H 29 ASP cc_start: 0.8614 (m-30) cc_final: 0.8270 (m-30) REVERT: H 83 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: I 23 TYR cc_start: 0.8327 (m-80) cc_final: 0.7942 (m-80) REVERT: I 46 LYS cc_start: 0.9510 (mptt) cc_final: 0.9268 (mptt) REVERT: I 57 LYS cc_start: 0.9402 (tptp) cc_final: 0.9123 (tptp) REVERT: J 42 GLU cc_start: 0.9162 (pt0) cc_final: 0.8894 (pt0) REVERT: J 45 TYR cc_start: 0.6734 (m-80) cc_final: 0.5797 (m-80) REVERT: J 57 LYS cc_start: 0.8875 (tptp) cc_final: 0.8564 (tptp) REVERT: J 106 ASN cc_start: 0.7603 (t0) cc_final: 0.7296 (t0) REVERT: J 107 ASN cc_start: 0.7709 (p0) cc_final: 0.7413 (p0) REVERT: K 33 LYS cc_start: 0.9064 (mmtp) cc_final: 0.8268 (tttp) REVERT: L 165 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7256 (p) REVERT: M 1 MET cc_start: 0.6633 (tpp) cc_final: 0.6166 (tpp) REVERT: M 335 MET cc_start: 0.8925 (ppp) cc_final: 0.7871 (ppp) REVERT: N 19 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7367 (mp10) REVERT: N 25 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8319 (p0) REVERT: N 28 GLU cc_start: 0.8536 (pm20) cc_final: 0.7967 (pm20) REVERT: N 245 MET cc_start: 0.9091 (mmp) cc_final: 0.8510 (mmm) REVERT: O 1 MET cc_start: 0.8460 (mmm) cc_final: 0.7905 (tpp) REVERT: O 155 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7837 (mtm-85) REVERT: O 183 MET cc_start: 0.7521 (pmm) cc_final: 0.7124 (pmm) REVERT: P 335 MET cc_start: 0.9507 (ptm) cc_final: 0.9124 (ppp) REVERT: Q 53 MET cc_start: 0.5418 (mmm) cc_final: 0.5197 (mmm) REVERT: Q 90 TYR cc_start: 0.8891 (t80) cc_final: 0.8505 (t80) REVERT: Q 116 HIS cc_start: 0.8450 (t-90) cc_final: 0.8045 (t70) REVERT: Q 122 MET cc_start: 0.6120 (ppp) cc_final: 0.5657 (ppp) REVERT: Q 145 PHE cc_start: 0.8692 (t80) cc_final: 0.8084 (t80) REVERT: R 1 MET cc_start: 0.6670 (mpp) cc_final: 0.5892 (mpp) REVERT: R 46 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7333 (tm-30) REVERT: R 264 GLU cc_start: 0.8863 (tp30) cc_final: 0.8443 (mm-30) REVERT: S 10 PHE cc_start: 0.8027 (p90) cc_final: 0.7746 (p90) REVERT: S 84 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8994 (mt) REVERT: S 109 MET cc_start: 0.7226 (mmm) cc_final: 0.6621 (mmm) REVERT: S 224 ARG cc_start: 0.8943 (tmm-80) cc_final: 0.8642 (ptt90) REVERT: T 54 MET cc_start: 0.7918 (mmp) cc_final: 0.7047 (mmp) REVERT: T 58 TRP cc_start: 0.7004 (m-90) cc_final: 0.5471 (m100) REVERT: T 117 ASP cc_start: 0.8421 (p0) cc_final: 0.8133 (p0) REVERT: T 265 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: V 14 HIS cc_start: 0.7718 (p-80) cc_final: 0.7364 (p-80) REVERT: V 68 LYS cc_start: 0.8095 (pttt) cc_final: 0.7733 (pmtt) REVERT: V 231 ARG cc_start: 0.7505 (mmm-85) cc_final: 0.7158 (mmt90) REVERT: V 235 ILE cc_start: 0.9389 (mm) cc_final: 0.9166 (mm) REVERT: V 236 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8743 (mm-30) REVERT: V 245 MET cc_start: 0.8712 (mmm) cc_final: 0.8236 (mmm) REVERT: V 286 TYR cc_start: 0.8422 (p90) cc_final: 0.8068 (p90) REVERT: V 307 PHE cc_start: 0.8056 (m-80) cc_final: 0.7581 (m-80) REVERT: W 229 ASN cc_start: 0.8476 (m-40) cc_final: 0.8070 (p0) REVERT: W 236 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8303 (mm-30) REVERT: W 290 ASN cc_start: 0.7580 (m-40) cc_final: 0.7285 (m110) REVERT: W 295 LYS cc_start: 0.8591 (ptmm) cc_final: 0.8023 (pttt) REVERT: Y 7 THR cc_start: 0.6993 (OUTLIER) cc_final: 0.6520 (p) REVERT: Y 65 MET cc_start: 0.9178 (ttt) cc_final: 0.8382 (mtp) REVERT: Y 199 SER cc_start: 0.9398 (t) cc_final: 0.9180 (p) REVERT: Y 222 ARG cc_start: 0.8219 (tpp-160) cc_final: 0.7652 (tpp80) REVERT: Y 307 ILE cc_start: 0.7598 (mm) cc_final: 0.7137 (tp) REVERT: Y 308 MET cc_start: 0.8692 (mmp) cc_final: 0.8479 (mmp) outliers start: 93 outliers final: 70 residues processed: 498 average time/residue: 0.2609 time to fit residues: 218.3078 Evaluate side-chains 494 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 416 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 75 GLU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain P residue 336 VAL Chi-restraints excluded: chain Q residue 7 GLN Chi-restraints excluded: chain Q residue 29 TYR Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 115 MET Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 157 TRP Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain T residue 19 GLN Chi-restraints excluded: chain T residue 265 GLU Chi-restraints excluded: chain T residue 279 VAL Chi-restraints excluded: chain T residue 312 ASP Chi-restraints excluded: chain T residue 313 LEU Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 215 PHE Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 250 ILE Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 266 LEU Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 333 VAL Chi-restraints excluded: chain W residue 287 ILE Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 58 optimal weight: 7.9990 chunk 147 optimal weight: 0.0010 chunk 361 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 225 optimal weight: 0.5980 chunk 467 optimal weight: 1.9990 chunk 335 optimal weight: 8.9990 chunk 431 optimal weight: 3.9990 chunk 484 optimal weight: 2.9990 chunk 379 optimal weight: 1.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN K 17 ASN M 162 HIS ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN T 19 GLN ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 331 ASN ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.119671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.089567 restraints weight = 183161.312| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 4.59 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 0.041 44932 Z= 0.144 Angle : 0.712 12.296 61226 Z= 0.344 Chirality : 0.051 0.511 7034 Planarity : 0.004 0.064 7612 Dihedral : 10.971 169.284 6747 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.86 % Favored : 91.92 % Rotamer: Outliers : 1.95 % Allowed : 19.43 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.12), residues: 5407 helix: 0.46 (0.13), residues: 1839 sheet: -0.68 (0.18), residues: 799 loop : -1.56 (0.12), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 91 TYR 0.031 0.001 TYR Y 20 PHE 0.024 0.001 PHE Q 155 TRP 0.025 0.002 TRP V 58 HIS 0.005 0.001 HIS L 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (44924) covalent geometry : angle 0.71152 / 0.34 (61210) SS BOND : bond 0.00149 / 0.08 ( 8) SS BOND : angle 0.78535 / 0.45 ( 16) hydrogen bonds : bond 0.03237 / 2.16 ( 1339) hydrogen bonds : angle 4.58824 / 3.19 ( 3825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 430 time to evaluate : 1.696 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: A 31 MET cc_start: 0.4307 (mtt) cc_final: 0.3931 (ttm) REVERT: A 133 TRP cc_start: 0.8240 (t60) cc_final: 0.7790 (t60) REVERT: A 197 ILE cc_start: 0.7671 (pt) cc_final: 0.7163 (mp) REVERT: A 198 MET cc_start: 0.7451 (mmt) cc_final: 0.6948 (ppp) REVERT: A 209 MET cc_start: 0.7541 (ptt) cc_final: 0.7056 (ppp) REVERT: C 67 ARG cc_start: 0.6696 (tpt90) cc_final: 0.6447 (tpt90) REVERT: C 78 GLU cc_start: 0.7100 (tp30) cc_final: 0.6859 (tp30) REVERT: F 29 ASP cc_start: 0.9075 (m-30) cc_final: 0.8753 (m-30) REVERT: F 53 LYS cc_start: 0.9281 (ttmm) cc_final: 0.8716 (ttmm) REVERT: G 46 LYS cc_start: 0.9391 (mppt) cc_final: 0.9061 (mppt) REVERT: H 29 ASP cc_start: 0.8579 (m-30) cc_final: 0.8227 (m-30) REVERT: H 83 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: I 23 TYR cc_start: 0.8356 (m-80) cc_final: 0.7980 (m-80) REVERT: I 46 LYS cc_start: 0.9514 (mptt) cc_final: 0.9283 (mptt) REVERT: I 57 LYS cc_start: 0.9409 (tptp) cc_final: 0.9116 (tptp) REVERT: J 39 GLU cc_start: 0.7241 (pm20) cc_final: 0.7000 (pm20) REVERT: J 42 GLU cc_start: 0.9197 (pt0) cc_final: 0.8949 (pt0) REVERT: J 45 TYR cc_start: 0.6774 (m-80) cc_final: 0.5818 (m-80) REVERT: J 57 LYS cc_start: 0.8919 (tptp) cc_final: 0.8568 (tptp) REVERT: J 106 ASN cc_start: 0.7625 (t0) cc_final: 0.7332 (t0) REVERT: J 107 ASN cc_start: 0.7749 (p0) cc_final: 0.7473 (p0) REVERT: L 165 VAL cc_start: 0.7475 (OUTLIER) cc_final: 0.7212 (p) REVERT: L 335 MET cc_start: 0.9042 (ptm) cc_final: 0.8743 (ppp) REVERT: M 1 MET cc_start: 0.6712 (tpp) cc_final: 0.6209 (tpp) REVERT: M 335 MET cc_start: 0.8931 (ppp) cc_final: 0.7891 (ppp) REVERT: N 25 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8328 (p0) REVERT: N 245 MET cc_start: 0.9082 (mmp) cc_final: 0.8560 (mmm) REVERT: O 1 MET cc_start: 0.8475 (mmm) cc_final: 0.7929 (tpp) REVERT: O 183 MET cc_start: 0.7540 (pmm) cc_final: 0.7133 (pmm) REVERT: Q 90 TYR cc_start: 0.8821 (t80) cc_final: 0.8454 (t80) REVERT: Q 116 HIS cc_start: 0.8406 (t-90) cc_final: 0.8010 (t70) REVERT: Q 122 MET cc_start: 0.6117 (ppp) cc_final: 0.5679 (ppp) REVERT: Q 145 PHE cc_start: 0.8586 (t80) cc_final: 0.8006 (t80) REVERT: R 264 GLU cc_start: 0.8835 (tp30) cc_final: 0.8422 (mm-30) REVERT: S 10 PHE cc_start: 0.8101 (p90) cc_final: 0.7808 (p90) REVERT: S 84 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9017 (mt) REVERT: S 89 PHE cc_start: 0.9126 (m-80) cc_final: 0.8669 (m-80) REVERT: S 109 MET cc_start: 0.7272 (mmm) cc_final: 0.6608 (mmm) REVERT: S 224 ARG cc_start: 0.8995 (tmm-80) cc_final: 0.8666 (tmm-80) REVERT: T 54 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7147 (mmp) REVERT: T 58 TRP cc_start: 0.7000 (m-90) cc_final: 0.5499 (m100) REVERT: T 117 ASP cc_start: 0.8426 (p0) cc_final: 0.8184 (p0) REVERT: T 265 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: V 14 HIS cc_start: 0.7703 (p-80) cc_final: 0.7361 (p-80) REVERT: V 68 LYS cc_start: 0.8107 (pttt) cc_final: 0.7732 (pttt) REVERT: V 231 ARG cc_start: 0.7523 (mmm-85) cc_final: 0.7165 (mmt90) REVERT: V 235 ILE cc_start: 0.9390 (mm) cc_final: 0.9170 (mm) REVERT: V 236 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8743 (mm-30) REVERT: V 245 MET cc_start: 0.8731 (mmm) cc_final: 0.8234 (mmm) REVERT: V 286 TYR cc_start: 0.8431 (p90) cc_final: 0.8075 (p90) REVERT: V 307 PHE cc_start: 0.8091 (m-80) cc_final: 0.7614 (m-80) REVERT: W 60 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.5843 (m-10) REVERT: W 229 ASN cc_start: 0.8468 (m-40) cc_final: 0.8076 (p0) REVERT: W 236 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8315 (mm-30) REVERT: W 246 LEU cc_start: 0.8572 (mt) cc_final: 0.8342 (mm) REVERT: W 290 ASN cc_start: 0.7617 (m-40) cc_final: 0.7313 (m110) REVERT: W 295 LYS cc_start: 0.8593 (ptmm) cc_final: 0.8020 (pttt) REVERT: Y 7 THR cc_start: 0.6969 (OUTLIER) cc_final: 0.6492 (p) REVERT: Y 65 MET cc_start: 0.9179 (ttt) cc_final: 0.8388 (mtp) REVERT: Y 111 MET cc_start: 0.7874 (mmp) cc_final: 0.7649 (mmp) REVERT: Y 199 SER cc_start: 0.9391 (t) cc_final: 0.9187 (p) REVERT: Y 222 ARG cc_start: 0.8226 (tpp-160) cc_final: 0.7659 (tpp80) REVERT: Y 307 ILE cc_start: 0.7632 (mm) cc_final: 0.7157 (tp) REVERT: Y 308 MET cc_start: 0.8690 (mmp) cc_final: 0.8478 (mmp) outliers start: 87 outliers final: 69 residues processed: 490 average time/residue: 0.2665 time to fit residues: 219.3174 Evaluate side-chains 496 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 418 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 75 GLU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 245 MET Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain P residue 336 VAL Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 60 HIS Chi-restraints excluded: chain Q residue 115 MET Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 110 ARG Chi-restraints excluded: chain S residue 157 TRP Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain T residue 19 GLN Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 265 GLU Chi-restraints excluded: chain T residue 279 VAL Chi-restraints excluded: chain T residue 312 ASP Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 266 LEU Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 333 VAL Chi-restraints excluded: chain W residue 60 PHE Chi-restraints excluded: chain W residue 287 ILE Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 239 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 359 optimal weight: 2.9990 chunk 521 optimal weight: 5.9990 chunk 448 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 304 optimal weight: 2.9990 chunk 212 optimal weight: 0.0470 chunk 275 optimal weight: 0.4980 chunk 433 optimal weight: 3.9990 chunk 411 optimal weight: 4.9990 overall best weight: 1.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN M 162 HIS ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN ** T 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 296 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 = 0.4100 r_free = 0.4100 target = 0.118622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.089144 restraints weight = 187221.606| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 4.57 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 44932 Z= 0.150 Angle : 0.720 12.668 61226 Z= 0.347 Chirality : 0.051 0.507 7034 Planarity : 0.004 0.072 7612 Dihedral : 10.984 169.758 6747 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.97 % Favored : 91.81 % Rotamer: Outliers : 1.93 % Allowed : 19.70 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.11), residues: 5407 helix: 0.46 (0.13), residues: 1839 sheet: -0.56 (0.18), residues: 763 loop : -1.57 (0.12), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 91 TYR 0.031 0.001 TYR Y 20 PHE 0.025 0.001 PHE Q 155 TRP 0.023 0.002 TRP V 58 HIS 0.007 0.001 HIS T 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (44924) covalent geometry : angle 0.71983 / 0.35 (61210) SS BOND : bond 0.00136 / 0.07 ( 8) SS BOND : angle 0.79046 / 0.46 ( 16) hydrogen bonds : bond 0.03258 / 2.18 ( 1339) hydrogen bonds : angle 4.58982 / 3.19 ( 3825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 424 time to evaluate : 1.761 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: A 31 MET cc_start: 0.4321 (mtt) cc_final: 0.3942 (ttm) REVERT: A 133 TRP cc_start: 0.8174 (t60) cc_final: 0.6661 (t-100) REVERT: A 197 ILE cc_start: 0.7645 (pt) cc_final: 0.7128 (mp) REVERT: A 198 MET cc_start: 0.7412 (mmt) cc_final: 0.6974 (ppp) REVERT: A 209 MET cc_start: 0.7567 (ptt) cc_final: 0.7089 (ppp) REVERT: C 67 ARG cc_start: 0.6653 (tpt90) cc_final: 0.6358 (tpt90) REVERT: C 78 GLU cc_start: 0.7128 (tp30) cc_final: 0.6868 (tp30) REVERT: F 29 ASP cc_start: 0.9114 (m-30) cc_final: 0.8752 (m-30) REVERT: F 53 LYS cc_start: 0.9302 (ttmm) cc_final: 0.8755 (ttmm) REVERT: G 46 LYS cc_start: 0.9380 (mppt) cc_final: 0.9079 (mppt) REVERT: H 29 ASP cc_start: 0.8595 (m-30) cc_final: 0.8258 (m-30) REVERT: H 83 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7728 (pm20) REVERT: I 23 TYR cc_start: 0.8381 (m-80) cc_final: 0.8016 (m-80) REVERT: I 46 LYS cc_start: 0.9520 (mptt) cc_final: 0.9289 (mptt) REVERT: J 39 GLU cc_start: 0.7352 (pm20) cc_final: 0.7136 (pm20) REVERT: J 42 GLU cc_start: 0.9194 (pt0) cc_final: 0.8951 (pt0) REVERT: J 45 TYR cc_start: 0.6835 (m-80) cc_final: 0.5865 (m-80) REVERT: J 57 LYS cc_start: 0.8880 (tptp) cc_final: 0.8524 (tptp) REVERT: J 106 ASN cc_start: 0.7682 (t0) cc_final: 0.7401 (t0) REVERT: J 107 ASN cc_start: 0.7790 (p0) cc_final: 0.7481 (p0) REVERT: K 295 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8835 (mmtt) REVERT: L 165 VAL cc_start: 0.7463 (OUTLIER) cc_final: 0.7205 (p) REVERT: L 335 MET cc_start: 0.9043 (ptm) cc_final: 0.8787 (ppp) REVERT: M 1 MET cc_start: 0.6694 (tpp) cc_final: 0.6175 (tpp) REVERT: M 335 MET cc_start: 0.8953 (ppp) cc_final: 0.7914 (ppp) REVERT: N 245 MET cc_start: 0.8995 (mmp) cc_final: 0.8379 (mmm) REVERT: O 1 MET cc_start: 0.8503 (mmm) cc_final: 0.7968 (tpp) REVERT: O 183 MET cc_start: 0.7700 (pmm) cc_final: 0.7225 (pmm) REVERT: P 335 MET cc_start: 0.9514 (ptm) cc_final: 0.9291 (ppp) REVERT: Q 90 TYR cc_start: 0.8859 (t80) cc_final: 0.8464 (t80) REVERT: Q 116 HIS cc_start: 0.8349 (t-90) cc_final: 0.7906 (t70) REVERT: Q 122 MET cc_start: 0.6285 (ppp) cc_final: 0.5880 (ppp) REVERT: Q 145 PHE cc_start: 0.8615 (t80) cc_final: 0.8049 (t80) REVERT: R 264 GLU cc_start: 0.8840 (tp30) cc_final: 0.8423 (mm-30) REVERT: S 10 PHE cc_start: 0.8132 (p90) cc_final: 0.7833 (p90) REVERT: S 84 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9030 (mt) REVERT: S 89 PHE cc_start: 0.9133 (m-80) cc_final: 0.8634 (m-10) REVERT: S 90 LEU cc_start: 0.8692 (mt) cc_final: 0.8473 (mp) REVERT: S 109 MET cc_start: 0.7261 (mmm) cc_final: 0.6658 (mmm) REVERT: S 127 ASN cc_start: 0.8758 (m-40) cc_final: 0.8167 (p0) REVERT: S 224 ARG cc_start: 0.8988 (tmm-80) cc_final: 0.8658 (tmm-80) REVERT: T 17 ASN cc_start: 0.6799 (t0) cc_final: 0.6242 (t0) REVERT: T 54 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7171 (mmp) REVERT: T 58 TRP cc_start: 0.6962 (m-90) cc_final: 0.5512 (m100) REVERT: T 117 ASP cc_start: 0.8456 (p0) cc_final: 0.8167 (p0) REVERT: T 265 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7200 (pm20) REVERT: V 68 LYS cc_start: 0.8133 (pttt) cc_final: 0.7740 (pttt) REVERT: V 231 ARG cc_start: 0.7506 (mmm-85) cc_final: 0.7141 (mmt90) REVERT: V 235 ILE cc_start: 0.9422 (mm) cc_final: 0.9194 (mm) REVERT: V 236 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8730 (mm-30) REVERT: V 245 MET cc_start: 0.8656 (mmm) cc_final: 0.8169 (mmm) REVERT: V 286 TYR cc_start: 0.8373 (p90) cc_final: 0.8085 (p90) REVERT: V 307 PHE cc_start: 0.8123 (m-80) cc_final: 0.7637 (m-80) REVERT: W 60 PHE cc_start: 0.6387 (OUTLIER) cc_final: 0.5520 (m-10) REVERT: W 229 ASN cc_start: 0.8449 (m-40) cc_final: 0.8035 (p0) REVERT: W 236 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8430 (mm-30) REVERT: W 246 LEU cc_start: 0.8535 (mt) cc_final: 0.8246 (mm) REVERT: W 290 ASN cc_start: 0.7615 (m-40) cc_final: 0.7295 (m110) REVERT: W 295 LYS cc_start: 0.8726 (ptmm) cc_final: 0.8128 (pttt) REVERT: Y 7 THR cc_start: 0.6946 (OUTLIER) cc_final: 0.6447 (p) REVERT: Y 65 MET cc_start: 0.9164 (ttt) cc_final: 0.8372 (mtp) REVERT: Y 111 MET cc_start: 0.7899 (mmp) cc_final: 0.7559 (mmp) REVERT: Y 199 SER cc_start: 0.9359 (t) cc_final: 0.9153 (p) REVERT: Y 222 ARG cc_start: 0.8330 (tpp-160) cc_final: 0.7739 (tpp80) REVERT: Y 307 ILE cc_start: 0.7636 (mm) cc_final: 0.7168 (tp) REVERT: Y 308 MET cc_start: 0.8679 (mmp) cc_final: 0.8478 (mmp) outliers start: 86 outliers final: 71 residues processed: 484 average time/residue: 0.2677 time to fit residues: 217.2503 Evaluate side-chains 496 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 416 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 75 GLU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 295 LYS Chi-restraints excluded: chain K residue 311 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain N residue 19 GLN Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 PHE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 198 ILE Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 325 VAL Chi-restraints excluded: chain P residue 336 VAL Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 60 HIS Chi-restraints excluded: chain Q residue 115 MET Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain T residue 19 GLN Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 140 PHE Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 265 GLU Chi-restraints excluded: chain T residue 279 VAL Chi-restraints excluded: chain T residue 312 ASP Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain V residue 61 VAL Chi-restraints excluded: chain V residue 63 PHE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 94 THR Chi-restraints excluded: chain V residue 183 MET Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 260 VAL Chi-restraints excluded: chain V residue 266 LEU Chi-restraints excluded: chain V residue 325 VAL Chi-restraints excluded: chain V residue 333 VAL Chi-restraints excluded: chain V residue 335 MET Chi-restraints excluded: chain W residue 60 PHE Chi-restraints excluded: chain W residue 287 ILE Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 56 HIS Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 305 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 419 optimal weight: 4.9990 chunk 453 optimal weight: 6.9990 chunk 263 optimal weight: 2.9990 chunk 395 optimal weight: 0.5980 chunk 534 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 418 optimal weight: 9.9990 chunk 495 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 ASN ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 ASN M 162 HIS ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN ** T 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.116655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.086674 restraints weight = 188736.365| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 4.56 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 44932 Z= 0.248 Angle : 0.781 13.706 61226 Z= 0.383 Chirality : 0.053 0.423 7034 Planarity : 0.005 0.066 7612 Dihedral : 11.217 166.237 6747 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.99 % Favored : 90.79 % Rotamer: Outliers : 2.15 % Allowed : 19.72 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.11), residues: 5407 helix: 0.35 (0.13), residues: 1842 sheet: -0.72 (0.18), residues: 758 loop : -1.63 (0.11), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 91 TYR 0.043 0.002 TYR V 309 PHE 0.036 0.002 PHE Q 155 TRP 0.027 0.002 TRP T 58 HIS 0.009 0.002 HIS L 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.25 (44924) covalent geometry : angle 0.78138 / 0.38 (61210) SS BOND : bond 0.00229 / 0.11 ( 8) SS BOND : angle 1.01219 / 0.59 ( 16) hydrogen bonds : bond 0.03643 / 2.43 ( 1339) hydrogen bonds : angle 4.73851 / 3.30 ( 3825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10544.42 seconds wall clock time: 182 minutes 27.71 seconds (10947.71 seconds total)