Starting phenix.real_space_refine on Sat Mar 7 04:37:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9t_34581/03_2026/8h9t_34581.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9t_34581/03_2026/8h9t_34581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h9t_34581/03_2026/8h9t_34581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9t_34581/03_2026/8h9t_34581.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9t_34581/03_2026/8h9t_34581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9t_34581/03_2026/8h9t_34581.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 1.075 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 P 13 5.49 5 Mg 5 5.21 5 S 161 5.16 5 C 24416 2.51 5 N 6479 2.21 5 O 7181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 252 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38255 Number of models: 1 Model: "" Number of chains: 32 Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1573 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1259 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "3" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "R" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 422 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 8, 'TRANS': 42} Chain: "C" Number of atoms: 3745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3745 Classifications: {'peptide': 491} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 472} Chain breaks: 2 Chain: "A" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3639 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "B" Number of atoms: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3714 Classifications: {'peptide': 487} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 468} Chain breaks: 1 Chain: "E" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3522 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 441} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3562 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 444} Chain: "G" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2103 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 5, 'TRANS': 265} Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1437 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "D" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3344 Classifications: {'peptide': 442} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 416} Chain breaks: 2 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.07, per 1000 atoms: 0.24 Number of scatterers: 38255 At special positions: 0 Unit cell: (139.43, 130.67, 241.63, 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) S 161 16.00 P 13 15.00 Mg 5 11.99 O 7181 8.00 N 6479 7.00 C 24416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 2.2 seconds 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9124 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 25 sheets defined 59.7% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'K' and resid 19 through 26 Processing helix chain 'K' and resid 27 through 29 No H-bonds generated for 'chain 'K' and resid 27 through 29' Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 54 through 121 removed outlier: 3.791A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix removed outlier: 3.710A pdb=" N ALA K 99 " --> pdb=" O GLU K 95 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER K 100 " --> pdb=" O ALA K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 184 Processing helix chain 'K' and resid 194 through 207 Processing helix chain 'L' and resid 41 through 55 removed outlier: 4.172A pdb=" N ARG L 48 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU L 49 " --> pdb=" O ASP L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 83 removed outlier: 3.999A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 18 removed outlier: 3.921A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 44 removed outlier: 3.662A pdb=" N LEU M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 58 Processing helix chain 'M' and resid 64 through 75 Processing helix chain 'M' and resid 85 through 123 removed outlier: 3.529A pdb=" N VAL M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 130 Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.565A pdb=" N LYS M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing helix chain '6' and resid 2 through 17 removed outlier: 3.979A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 39 Processing helix chain '6' and resid 42 through 74 Processing helix chain '7' and resid 2 through 17 removed outlier: 3.979A pdb=" N GLY 7 17 " --> pdb=" O ALA 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 18 through 39 Processing helix chain '7' and resid 42 through 74 Processing helix chain '8' and resid 2 through 17 removed outlier: 3.979A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 39 Processing helix chain '8' and resid 42 through 74 Processing helix chain '1' and resid 2 through 17 removed outlier: 3.979A pdb=" N GLY 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 39 Processing helix chain '1' and resid 42 through 74 Processing helix chain '2' and resid 2 through 17 removed outlier: 3.980A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 39 Processing helix chain '2' and resid 42 through 74 Processing helix chain '3' and resid 2 through 17 removed outlier: 3.979A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 39 Processing helix chain '3' and resid 42 through 74 Processing helix chain '4' and resid 2 through 17 removed outlier: 3.979A pdb=" N GLY 4 17 " --> pdb=" O ALA 4 13 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 39 Processing helix chain '4' and resid 42 through 74 Processing helix chain '5' and resid 2 through 17 removed outlier: 3.979A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 39 Processing helix chain '5' and resid 42 through 74 Processing helix chain 'H' and resid 105 through 122 Processing helix chain 'H' and resid 124 through 146 removed outlier: 3.805A pdb=" N GLU H 146 " --> pdb=" O VAL H 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 40 removed outlier: 4.212A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 10 removed outlier: 4.360A pdb=" N SER N 8 " --> pdb=" O LEU N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 25 removed outlier: 3.544A pdb=" N ILE N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 31 Processing helix chain 'N' and resid 40 through 59 removed outlier: 3.664A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 68 through 87 removed outlier: 3.579A pdb=" N LEU N 87 " --> pdb=" O ASN N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 119 removed outlier: 3.598A pdb=" N ASN N 101 " --> pdb=" O GLN N 97 " (cutoff:3.500A) Proline residue: N 107 - end of helix removed outlier: 3.542A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 128 removed outlier: 3.661A pdb=" N PHE N 128 " --> pdb=" O ALA N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 136 No H-bonds generated for 'chain 'N' and resid 134 through 136' Processing helix chain 'N' and resid 137 through 182 Proline residue: N 153 - end of helix removed outlier: 4.245A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY N 167 " --> pdb=" O ASN N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 225 Processing helix chain 'P' and resid 13 through 19 removed outlier: 3.651A pdb=" N LYS P 19 " --> pdb=" O PRO P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 41 Processing helix chain 'R' and resid 26 through 32 Processing helix chain 'R' and resid 35 through 55 Processing helix chain 'R' and resid 62 through 79 removed outlier: 4.624A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 88 removed outlier: 3.636A pdb=" N ARG R 88 " --> pdb=" O LYS R 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 36 Processing helix chain 'S' and resid 44 through 62 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 68 through 95 Processing helix chain 'T' and resid 8 through 43 Proline residue: T 35 - end of helix Processing helix chain 'T' and resid 44 through 45 No H-bonds generated for 'chain 'T' and resid 44 through 45' Processing helix chain 'Q' and resid 1 through 5 removed outlier: 3.785A pdb=" N LEU Q 4 " --> pdb=" O MET Q 1 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 22 Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 30 Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.526A pdb=" N LEU C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.669A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.734A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 194 through 197 removed outlier: 3.555A pdb=" N LYS C 197 " --> pdb=" O ASP C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 239 through 260 Proline residue: C 247 - end of helix removed outlier: 4.034A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.798A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.565A pdb=" N ALA C 293 " --> pdb=" O GLY C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.550A pdb=" N GLY C 317 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.536A pdb=" N ALA C 377 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 removed outlier: 4.391A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 400 " --> pdb=" O GLN C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.709A pdb=" N LYS C 429 " --> pdb=" O THR C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 460 through 476 Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 508 Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.661A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.515A pdb=" N GLY A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.686A pdb=" N LYS A 198 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 239 through 259 Proline residue: A 247 - end of helix removed outlier: 3.910A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.689A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 295 through 296 No H-bonds generated for 'chain 'A' and resid 295 through 296' Processing helix chain 'A' and resid 297 through 307 removed outlier: 3.748A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.670A pdb=" N GLY A 317 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 380 through 401 removed outlier: 3.844A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.888A pdb=" N LYS A 455 " --> pdb=" O TYR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.627A pdb=" N LEU A 480 " --> pdb=" O HIS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 507 Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.724A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.836A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 239 through 260 Proline residue: B 247 - end of helix removed outlier: 4.008A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.691A pdb=" N GLN B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 297 through 307 removed outlier: 4.009A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.607A pdb=" N ALA B 377 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.989A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 460 through 475 Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.515A pdb=" N LEU B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 508 Processing helix chain 'E' and resid 125 through 129 Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 228 through 251 removed outlier: 4.966A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE E 246 " --> pdb=" O VAL E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 275 removed outlier: 3.829A pdb=" N PHE E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 284 Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.706A pdb=" N MET E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 322 through 329 Processing helix chain 'E' and resid 339 through 345 Processing helix chain 'E' and resid 362 through 392 removed outlier: 7.441A pdb=" N SER E 368 " --> pdb=" O ASN E 364 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N GLU E 369 " --> pdb=" O ILE E 365 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N HIS E 370 " --> pdb=" O VAL E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 417 removed outlier: 3.940A pdb=" N LYS E 404 " --> pdb=" O SER E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 426 removed outlier: 4.548A pdb=" N VAL E 426 " --> pdb=" O VAL E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 450 Processing helix chain 'E' and resid 457 through 461 removed outlier: 3.790A pdb=" N TYR E 461 " --> pdb=" O GLN E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 476 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 125 through 129 Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 164 through 180 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 228 through 249 removed outlier: 5.112A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 273 removed outlier: 4.011A pdb=" N THR F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 297 Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 322 through 330 removed outlier: 4.408A pdb=" N ALA F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 344 Processing helix chain 'F' and resid 362 through 395 removed outlier: 7.812A pdb=" N SER F 368 " --> pdb=" O ASN F 364 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N GLU F 369 " --> pdb=" O ILE F 365 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N HIS F 370 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 399 Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.730A pdb=" N SER F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 423 No H-bonds generated for 'chain 'F' and resid 421 through 423' Processing helix chain 'F' and resid 424 through 429 Processing helix chain 'F' and resid 436 through 450 Processing helix chain 'F' and resid 456 through 460 Processing helix chain 'F' and resid 465 through 480 removed outlier: 3.515A pdb=" N ALA F 469 " --> pdb=" O PRO F 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 55 removed outlier: 3.853A pdb=" N ARG G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 3.732A pdb=" N LEU G 49 " --> pdb=" O GLY G 45 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 99 Processing helix chain 'G' and resid 109 through 121 removed outlier: 4.591A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N THR G 119 " --> pdb=" O ILE G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.904A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'G' and resid 197 through 222 Processing helix chain 'G' and resid 224 through 271 removed outlier: 3.582A pdb=" N ALA G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 27 Processing helix chain 'O' and resid 31 through 47 Processing helix chain 'O' and resid 48 through 57 Processing helix chain 'O' and resid 61 through 76 removed outlier: 3.733A pdb=" N GLU O 76 " --> pdb=" O ILE O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 92 Processing helix chain 'O' and resid 94 through 96 No H-bonds generated for 'chain 'O' and resid 94 through 96' Processing helix chain 'O' and resid 97 through 113 Processing helix chain 'O' and resid 127 through 140 removed outlier: 3.897A pdb=" N SER O 140 " --> pdb=" O THR O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 188 removed outlier: 3.757A pdb=" N LYS O 178 " --> pdb=" O SER O 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 164 through 179 Processing helix chain 'D' and resid 192 through 206 Processing helix chain 'D' and resid 228 through 249 removed outlier: 4.900A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 275 removed outlier: 3.858A pdb=" N PHE D 264 " --> pdb=" O ASN D 260 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 removed outlier: 3.539A pdb=" N ASP D 291 " --> pdb=" O THR D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 339 through 344 Processing helix chain 'D' and resid 367 through 384 Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 436 through 449 Processing helix chain 'D' and resid 456 through 460 removed outlier: 3.534A pdb=" N ALA D 459 " --> pdb=" O PRO D 456 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE D 460 " --> pdb=" O GLU D 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 456 through 460' Processing helix chain 'D' and resid 465 through 480 Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'H' and resid 17 through 18 removed outlier: 5.862A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 43 through 47 removed outlier: 3.908A pdb=" N VAL H 64 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU H 62 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 44 through 45 removed outlier: 6.607A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE G 108 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLY G 70 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER G 170 " --> pdb=" O ARG G 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 35 removed outlier: 5.490A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 43 current: chain 'C' and resid 60 through 66 removed outlier: 5.846A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 75 current: chain 'A' and resid 38 through 42 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 42 current: chain 'A' and resid 60 through 66 removed outlier: 5.880A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 75 current: chain 'E' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 23 through 28 current: chain 'E' and resid 49 through 57 removed outlier: 6.653A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 60 through 65 current: chain 'D' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 23 through 28 current: chain 'D' and resid 49 through 55 removed outlier: 6.687A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.999A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 108 Processing sheet with id=AA8, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.577A pdb=" N ILE C 159 " --> pdb=" O MET C 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 326 through 328 removed outlier: 6.482A pdb=" N ILE C 167 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU C 352 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 168 " --> pdb=" O LEU C 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.026A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.667A pdb=" N VAL A 108 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.626A pdb=" N ILE A 159 " --> pdb=" O MET A 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 26 through 35 removed outlier: 6.566A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 43 current: chain 'B' and resid 60 through 66 removed outlier: 5.726A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 75 current: chain 'F' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 23 through 28 current: chain 'F' and resid 49 through 57 removed outlier: 7.123A pdb=" N ALA F 53 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE F 64 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS F 55 " --> pdb=" O ARG F 62 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG F 62 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY F 57 " --> pdb=" O THR F 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 60 through 65 current: chain 'O' and resid 147 through 150 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 147 through 150 current: chain 'O' and resid 169 through 172 Processing sheet with id=AB5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.004A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 107 through 109 removed outlier: 3.614A pdb=" N TYR B 268 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 86 through 89 removed outlier: 3.994A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 97 through 98 removed outlier: 6.200A pdb=" N MET E 98 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLN E 224 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER E 184 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL E 221 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE E 186 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLY E 223 " --> pdb=" O PHE E 186 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLY E 188 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL E 254 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL E 310 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU E 256 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ALA E 312 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE E 258 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE E 155 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS E 154 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR E 336 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLY E 156 " --> pdb=" O THR E 336 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 135 through 136 removed outlier: 4.469A pdb=" N TYR E 149 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.228A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 97 through 98 removed outlier: 6.356A pdb=" N MET F 98 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER F 184 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N VAL F 221 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE F 186 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY F 223 " --> pdb=" O PHE F 186 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLY F 188 " --> pdb=" O GLY F 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 135 through 136 removed outlier: 4.139A pdb=" N TYR F 149 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 86 through 89 removed outlier: 3.943A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.280A pdb=" N MET D 98 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL D 185 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASP D 259 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA D 187 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 134 through 136 removed outlier: 4.468A pdb=" N GLU D 134 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR D 149 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 334 through 335 2256 hydrogen bonds defined for protein. 6555 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.33 Time building geometry restraints manager: 4.74 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: 11943 1.34 - 1.46: 6678 1.46 - 1.58: 19938 1.58 - 1.70: 21 1.70 - 1.82: 303 Bond restraints: 38883 Sorted by residual: bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.459 -0.122 1.10e-02 8.26e+03 1.24e+02 bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.456 -0.119 1.10e-02 8.26e+03 1.16e+02 bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.455 -0.118 1.10e-02 8.26e+03 1.15e+02 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.280 0.094 1.00e-02 1.00e+04 8.86e+01 bond pdb=" C4 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.374 1.280 0.094 1.00e-02 1.00e+04 8.77e+01 ... (remaining 38878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 52306 3.89 - 7.78: 267 7.78 - 11.67: 34 11.67 - 15.56: 2 15.56 - 19.46: 4 Bond angle restraints: 52613 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 123.51 16.36 1.00e+00 1.00e+00 2.68e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 123.51 16.36 1.00e+00 1.00e+00 2.68e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 120.93 15.90 1.00e+00 1.00e+00 2.53e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 122.53 14.30 1.00e+00 1.00e+00 2.05e+02 ... (remaining 52608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.71: 22983 32.71 - 65.42: 516 65.42 - 98.13: 77 98.13 - 130.84: 1 130.84 - 163.55: 1 Dihedral angle restraints: 23578 sinusoidal: 9323 harmonic: 14255 Sorted by residual: dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual 300.00 136.45 163.55 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 61.42 -121.42 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" CA VAL T 5 " pdb=" C VAL T 5 " pdb=" N GLN T 6 " pdb=" CA GLN T 6 " ideal model delta harmonic sigma weight residual -180.00 -152.52 -27.48 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 23575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 4434 0.052 - 0.104: 1386 0.104 - 0.156: 265 0.156 - 0.208: 49 0.208 - 0.260: 6 Chirality restraints: 6140 Sorted by residual: chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.42 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ILE P 5 " pdb=" N ILE P 5 " pdb=" C ILE P 5 " pdb=" CB ILE P 5 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.45 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 6137 not shown) Planarity restraints: 6703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 3 38 " -0.561 9.50e-02 1.11e+02 2.51e-01 3.86e+01 pdb=" NE ARG 3 38 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG 3 38 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG 3 38 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 3 38 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 6 38 " 0.359 9.50e-02 1.11e+02 1.61e-01 1.58e+01 pdb=" NE ARG 6 38 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG 6 38 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG 6 38 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 6 38 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 188 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C GLY E 188 " 0.055 2.00e-02 2.50e+03 pdb=" O GLY E 188 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL E 189 " -0.019 2.00e-02 2.50e+03 ... (remaining 6700 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 124 2.39 - 3.02: 24090 3.02 - 3.65: 57840 3.65 - 4.27: 90667 4.27 - 4.90: 150395 Nonbonded interactions: 323116 Sorted by model distance: nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 1.767 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 1.991 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 2.017 2.170 nonbonded pdb=" O3G ATP A 601 " pdb="MG MG A 602 " model vdw 2.186 2.170 nonbonded pdb=" O LEU S 77 " pdb=" OG1 THR S 80 " model vdw 2.204 3.040 ... (remaining 323111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } ncs_group { reference = (chain 'A' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'B' and resid 24 through 602) selection = (chain 'C' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) } ncs_group { reference = (chain 'D' and (resid 12 through 318 or (resid 319 and (name N or name CA or nam \ e C or name O or name CB )) or resid 320 through 403 or (resid 404 and (name N o \ r name CA or name C or name O or name CB )) or resid 405 through 477)) selection = (chain 'E' and (resid 12 through 384 or resid 403 through 420 or resid 431 throu \ gh 477)) selection = (chain 'F' and (resid 12 through 318 or (resid 319 and (name N or name CA or nam \ e C or name O or name CB )) or resid 320 through 384 or resid 403 or (resid 404 \ and (name N or name CA or name C or name O or name CB )) or resid 405 through 42 \ 0 or resid 431 through 477)) } 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: 10.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.990 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 40.360 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:7.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.144 38883 Z= 0.406 Angle : 0.832 19.456 52613 Z= 0.518 Chirality : 0.051 0.260 6140 Planarity : 0.006 0.251 6703 Dihedral : 14.481 163.552 14454 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.09 % Rotamer: Outliers : 0.05 % Allowed : 4.86 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % 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: -2.81 (0.10), residues: 4931 helix: -1.36 (0.09), residues: 2614 sheet: -1.93 (0.19), residues: 571 loop : -2.39 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 77 TYR 0.022 0.002 TYR O 170 PHE 0.021 0.002 PHE D 262 TRP 0.012 0.002 TRP M 53 HIS 0.009 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00784 (38883) covalent geometry : angle 0.83230 (52613) hydrogen bonds : bond 0.13933 ( 2256) hydrogen bonds : angle 6.95815 ( 6555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 898 time to evaluate : 1.432 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: K 29 THR cc_start: 0.6220 (OUTLIER) cc_final: 0.5776 (t) REVERT: L 87 MET cc_start: 0.8145 (mpp) cc_final: 0.7680 (mpp) REVERT: L 104 GLU cc_start: 0.7699 (pt0) cc_final: 0.7461 (pp20) REVERT: M 33 TRP cc_start: 0.8523 (m100) cc_final: 0.8257 (m-10) REVERT: 6 75 MET cc_start: 0.5799 (mmt) cc_final: 0.5461 (tpp) REVERT: 2 75 MET cc_start: 0.4741 (mmt) cc_final: 0.4156 (tpp) REVERT: 3 65 LEU cc_start: 0.8868 (tt) cc_final: 0.8627 (tm) REVERT: 3 73 PHE cc_start: 0.8475 (m-80) cc_final: 0.8180 (m-80) REVERT: 4 73 PHE cc_start: 0.5194 (m-80) cc_final: 0.4259 (t80) REVERT: H 15 GLN cc_start: 0.5456 (tp40) cc_final: 0.5001 (tt0) REVERT: H 34 ARG cc_start: 0.7743 (ptm-80) cc_final: 0.7523 (mtm110) REVERT: H 111 ASN cc_start: 0.7613 (m110) cc_final: 0.7330 (m110) REVERT: I 44 LYS cc_start: 0.8855 (mttt) cc_final: 0.8584 (mttm) REVERT: N 140 MET cc_start: 0.6712 (pmm) cc_final: 0.6461 (pmm) REVERT: R 87 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7929 (tm-30) REVERT: S 54 LYS cc_start: 0.8822 (tppt) cc_final: 0.8572 (tppt) REVERT: S 86 PHE cc_start: 0.9026 (t80) cc_final: 0.8796 (t80) REVERT: T 5 VAL cc_start: 0.4955 (m) cc_final: 0.4286 (m) REVERT: T 36 ARG cc_start: 0.7644 (mpp80) cc_final: 0.7236 (mpp80) REVERT: C 26 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7479 (mp0) REVERT: C 67 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7889 (mt-10) REVERT: C 140 ILE cc_start: 0.8924 (tt) cc_final: 0.8722 (tp) REVERT: C 195 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7399 (tm-30) REVERT: C 453 LEU cc_start: 0.7893 (mm) cc_final: 0.7601 (mm) REVERT: C 463 LYS cc_start: 0.8641 (ttpt) cc_final: 0.8340 (ttmt) REVERT: C 475 GLN cc_start: 0.7550 (mm110) cc_final: 0.7326 (mm-40) REVERT: C 484 ARG cc_start: 0.6336 (ttp80) cc_final: 0.5792 (ttm-80) REVERT: C 499 GLU cc_start: 0.8123 (tp30) cc_final: 0.7801 (tp30) REVERT: C 503 ASN cc_start: 0.5809 (m-40) cc_final: 0.5572 (m-40) REVERT: A 96 ASP cc_start: 0.8366 (p0) cc_final: 0.7977 (p0) REVERT: A 362 ARG cc_start: 0.7519 (mtt180) cc_final: 0.6518 (mtt90) REVERT: A 391 LYS cc_start: 0.7213 (ttpt) cc_final: 0.6986 (tttp) REVERT: A 415 GLN cc_start: 0.6244 (pt0) cc_final: 0.6015 (pm20) REVERT: B 328 GLU cc_start: 0.7950 (tt0) cc_final: 0.7686 (tt0) REVERT: B 355 GLU cc_start: 0.7477 (mp0) cc_final: 0.7076 (mp0) REVERT: E 205 GLU cc_start: 0.8249 (tt0) cc_final: 0.7773 (pt0) REVERT: F 217 LYS cc_start: 0.8053 (ptpp) cc_final: 0.7460 (mttp) REVERT: F 408 SER cc_start: 0.7586 (m) cc_final: 0.7259 (p) REVERT: F 422 GLN cc_start: 0.7777 (tp40) cc_final: 0.7570 (tm-30) REVERT: G 130 GLU cc_start: 0.7740 (tp30) cc_final: 0.6888 (tm-30) REVERT: G 260 LYS cc_start: 0.8604 (tttt) cc_final: 0.8264 (tttp) REVERT: O 33 GLU cc_start: 0.7149 (pt0) cc_final: 0.6560 (pm20) REVERT: O 37 LYS cc_start: 0.7202 (tttt) cc_final: 0.6444 (tppt) REVERT: D 64 ILE cc_start: 0.8428 (mt) cc_final: 0.8119 (pt) REVERT: D 180 HIS cc_start: 0.7621 (t-90) cc_final: 0.7223 (t-90) REVERT: D 259 ASP cc_start: 0.8597 (t0) cc_final: 0.8210 (t0) REVERT: D 462 MET cc_start: 0.5221 (mmt) cc_final: 0.4858 (mmt) outliers start: 2 outliers final: 6 residues processed: 899 average time/residue: 0.7402 time to fit residues: 797.5111 Evaluate side-chains 636 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 629 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain 3 residue 39 ASN Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 393 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0370 chunk 470 optimal weight: 2.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 88 GLN K 103 HIS K 114 GLN K 158 HIS ** K 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS M 123 ASN 6 45 GLN 8 45 GLN 2 39 ASN 2 45 GLN 4 39 ASN 4 45 GLN H 32 ASN H 85 ASN H 111 ASN N 4 ASN N 46 GLN N 47 GLN N 61 HIS N 101 ASN N 163 ASN N 225 ASN P 8 ASN T 6 GLN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN A 163 GLN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN B 476 HIS E 419 GLN F 133 GLN F 180 HIS F 266 GLN O 84 ASN O 92 ASN D 54 GLN D 210 ASN D 364 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.156595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120505 restraints weight = 57979.723| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.39 r_work: 0.3425 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 38883 Z= 0.146 Angle : 0.634 9.481 52613 Z= 0.328 Chirality : 0.044 0.285 6140 Planarity : 0.005 0.049 6703 Dihedral : 7.222 144.317 5498 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.14 % Favored : 96.84 % Rotamer: Outliers : 3.20 % Allowed : 14.22 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.11), residues: 4931 helix: 0.21 (0.10), residues: 2660 sheet: -1.30 (0.20), residues: 563 loop : -1.69 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 128 TYR 0.023 0.001 TYR Q 47 PHE 0.026 0.002 PHE C 464 TRP 0.016 0.002 TRP I 5 HIS 0.009 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00305 (38883) covalent geometry : angle 0.63368 (52613) hydrogen bonds : bond 0.05277 ( 2256) hydrogen bonds : angle 5.10150 ( 6555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 741 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 134 MET cc_start: 0.8880 (mtp) cc_final: 0.8580 (ttt) REVERT: L 49 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: L 50 TYR cc_start: 0.6900 (t80) cc_final: 0.6688 (t80) REVERT: L 104 GLU cc_start: 0.7866 (pt0) cc_final: 0.7360 (pp20) REVERT: M 23 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: M 33 TRP cc_start: 0.8705 (m100) cc_final: 0.8364 (m-10) REVERT: M 67 ASP cc_start: 0.8583 (t0) cc_final: 0.8259 (p0) REVERT: M 112 VAL cc_start: 0.8897 (t) cc_final: 0.8623 (p) REVERT: M 115 GLU cc_start: 0.8704 (tt0) cc_final: 0.8494 (pp20) REVERT: M 130 MET cc_start: 0.8425 (ttm) cc_final: 0.8202 (ttm) REVERT: M 145 ASP cc_start: 0.8676 (t0) cc_final: 0.8420 (t0) REVERT: 6 66 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8557 (mmm) REVERT: 8 66 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7652 (pp-130) REVERT: 8 75 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6330 (mpt) REVERT: 1 60 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7419 (mmm) REVERT: 2 75 MET cc_start: 0.4825 (mmt) cc_final: 0.4042 (mpp) REVERT: 3 25 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8561 (mt) REVERT: 3 38 ARG cc_start: 0.7715 (tpp80) cc_final: 0.7443 (tpp80) REVERT: 3 71 ILE cc_start: 0.7116 (pt) cc_final: 0.6909 (pt) REVERT: 3 75 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6493 (mmp) REVERT: 4 73 PHE cc_start: 0.5357 (m-80) cc_final: 0.4326 (t80) REVERT: 5 51 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7164 (mp) REVERT: 5 75 MET cc_start: 0.5551 (mpm) cc_final: 0.5213 (mpm) REVERT: H 15 GLN cc_start: 0.4771 (tp40) cc_final: 0.4570 (tt0) REVERT: H 34 ARG cc_start: 0.8130 (ptm-80) cc_final: 0.7729 (mtm110) REVERT: H 128 ARG cc_start: 0.8887 (mtp85) cc_final: 0.8679 (ttm-80) REVERT: I 44 LYS cc_start: 0.8732 (mttt) cc_final: 0.8439 (mttm) REVERT: N 30 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9209 (mp) REVERT: N 140 MET cc_start: 0.6752 (pmm) cc_final: 0.6483 (pmm) REVERT: R 30 LEU cc_start: 0.9171 (mm) cc_final: 0.8915 (mm) REVERT: R 87 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8279 (tm-30) REVERT: S 54 LYS cc_start: 0.8887 (tppt) cc_final: 0.8638 (tppt) REVERT: S 90 GLU cc_start: 0.8768 (pp20) cc_final: 0.8527 (pp20) REVERT: T 36 ARG cc_start: 0.7769 (mpp80) cc_final: 0.7439 (mpp80) REVERT: T 40 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8179 (mm-30) REVERT: Q 49 LYS cc_start: 0.8030 (mppt) cc_final: 0.7757 (mppt) REVERT: C 26 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7234 (mp0) REVERT: C 67 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8017 (mt-10) REVERT: C 140 ILE cc_start: 0.8617 (tt) cc_final: 0.8381 (tp) REVERT: C 195 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7151 (tp30) REVERT: C 390 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.6803 (tpp) REVERT: C 465 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7196 (tt0) REVERT: C 484 ARG cc_start: 0.6270 (ttp80) cc_final: 0.5617 (ttm-80) REVERT: A 36 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7401 (p0) REVERT: A 96 ASP cc_start: 0.8309 (p0) cc_final: 0.7908 (p0) REVERT: A 218 LYS cc_start: 0.7488 (tttp) cc_final: 0.7175 (tttt) REVERT: A 362 ARG cc_start: 0.7549 (mtt180) cc_final: 0.6410 (mtt90) REVERT: A 391 LYS cc_start: 0.7036 (ttpt) cc_final: 0.6831 (tttp) REVERT: B 195 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: E 195 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7622 (mm-30) REVERT: E 205 GLU cc_start: 0.8790 (tt0) cc_final: 0.8140 (pt0) REVERT: E 227 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8023 (mt-10) REVERT: E 234 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.6425 (mmt90) REVERT: E 344 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7388 (pt0) REVERT: E 361 MET cc_start: 0.7708 (mmm) cc_final: 0.7355 (tpt) REVERT: E 390 ILE cc_start: 0.5771 (OUTLIER) cc_final: 0.5520 (mp) REVERT: E 442 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6737 (ttpt) REVERT: F 30 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7763 (pt0) REVERT: F 217 LYS cc_start: 0.7677 (ptpp) cc_final: 0.6813 (mttp) REVERT: F 380 ILE cc_start: 0.7945 (mp) cc_final: 0.7660 (mm) REVERT: F 389 ASP cc_start: 0.7985 (m-30) cc_final: 0.7730 (t0) REVERT: F 402 GLU cc_start: 0.7519 (tp30) cc_final: 0.7253 (tp30) REVERT: F 408 SER cc_start: 0.7165 (m) cc_final: 0.6878 (p) REVERT: F 422 GLN cc_start: 0.7678 (tp40) cc_final: 0.7367 (tm-30) REVERT: G 52 TYR cc_start: 0.7935 (m-80) cc_final: 0.7562 (m-80) REVERT: G 123 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6530 (pm20) REVERT: G 130 GLU cc_start: 0.8131 (tp30) cc_final: 0.6780 (tm-30) REVERT: G 172 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6778 (tptp) REVERT: G 260 LYS cc_start: 0.8220 (tttt) cc_final: 0.7817 (tttp) REVERT: O 33 GLU cc_start: 0.7015 (pt0) cc_final: 0.6365 (pm20) REVERT: O 37 LYS cc_start: 0.7041 (tttt) cc_final: 0.6290 (tppt) REVERT: O 142 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.6216 (pp) REVERT: D 64 ILE cc_start: 0.8377 (mt) cc_final: 0.7999 (pt) REVERT: D 149 TYR cc_start: 0.6564 (m-10) cc_final: 0.6270 (m-10) REVERT: D 180 HIS cc_start: 0.7380 (t-90) cc_final: 0.6839 (t-90) REVERT: D 248 ASP cc_start: 0.7506 (m-30) cc_final: 0.7140 (m-30) REVERT: D 342 ILE cc_start: 0.7857 (mt) cc_final: 0.7571 (tt) REVERT: D 458 GLN cc_start: 0.5065 (OUTLIER) cc_final: 0.4643 (tp40) REVERT: D 462 MET cc_start: 0.5468 (mmt) cc_final: 0.5266 (mmt) outliers start: 129 outliers final: 30 residues processed: 794 average time/residue: 0.6693 time to fit residues: 647.9484 Evaluate side-chains 674 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 622 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 65 LEU Chi-restraints excluded: chain 8 residue 66 MET Chi-restraints excluded: chain 8 residue 75 MET Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 60 MET Chi-restraints excluded: chain 2 residue 15 THR Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 67 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain T residue 7 VAL Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 458 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 277 optimal weight: 0.9980 chunk 477 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 355 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 426 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 45 GLN 2 39 ASN 2 45 GLN 4 45 GLN 5 39 ASN H 85 ASN H 111 ASN ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 210 GLN P 8 ASN A 396 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN F 224 GLN G 120 HIS G 123 GLN O 112 HIS D 54 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN D 364 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.154087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.117625 restraints weight = 58051.388| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.39 r_work: 0.3383 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 38883 Z= 0.197 Angle : 0.636 9.717 52613 Z= 0.327 Chirality : 0.045 0.259 6140 Planarity : 0.004 0.052 6703 Dihedral : 6.933 125.258 5491 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 3.87 % Allowed : 17.32 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.12), residues: 4931 helix: 0.68 (0.10), residues: 2671 sheet: -1.21 (0.20), residues: 585 loop : -1.42 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 154 TYR 0.019 0.002 TYR K 26 PHE 0.028 0.002 PHE M 69 TRP 0.015 0.002 TRP K 176 HIS 0.009 0.001 HIS K 180 Details of bonding type rmsd covalent geometry : bond 0.00458 (38883) covalent geometry : angle 0.63562 (52613) hydrogen bonds : bond 0.05290 ( 2256) hydrogen bonds : angle 4.91234 ( 6555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 671 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 146 ARG cc_start: 0.8398 (ttm170) cc_final: 0.7746 (ttt-90) REVERT: L 49 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7837 (pm20) REVERT: L 50 TYR cc_start: 0.7161 (t80) cc_final: 0.6722 (t80) REVERT: L 68 GLN cc_start: 0.8596 (tp40) cc_final: 0.8240 (mm-40) REVERT: L 104 GLU cc_start: 0.7970 (pt0) cc_final: 0.7389 (pp20) REVERT: M 33 TRP cc_start: 0.8728 (m100) cc_final: 0.8357 (m-10) REVERT: M 69 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.5885 (t80) REVERT: M 130 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8101 (ttm) REVERT: M 145 ASP cc_start: 0.8792 (t0) cc_final: 0.8502 (t0) REVERT: 7 63 PHE cc_start: 0.8086 (t80) cc_final: 0.7723 (t80) REVERT: 8 75 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6529 (mpt) REVERT: 1 54 PHE cc_start: 0.6969 (t80) cc_final: 0.6656 (t80) REVERT: 1 60 MET cc_start: 0.7976 (mpp) cc_final: 0.7693 (tpp) REVERT: 2 51 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7221 (mp) REVERT: 2 69 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6837 (m-80) REVERT: 2 75 MET cc_start: 0.4771 (mmt) cc_final: 0.3953 (mpp) REVERT: 3 38 ARG cc_start: 0.7883 (tpp80) cc_final: 0.7647 (tpp-160) REVERT: 3 60 MET cc_start: 0.8059 (mmp) cc_final: 0.7842 (mmm) REVERT: 4 73 PHE cc_start: 0.5412 (m-80) cc_final: 0.4406 (t80) REVERT: 5 7 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.7007 (mmtm) REVERT: 5 51 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7155 (mp) REVERT: 5 75 MET cc_start: 0.5827 (mpm) cc_final: 0.4169 (mtm) REVERT: H 15 GLN cc_start: 0.4803 (tp40) cc_final: 0.4543 (tt0) REVERT: H 34 ARG cc_start: 0.8151 (ptm-80) cc_final: 0.7702 (mtm110) REVERT: H 59 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7677 (ptt180) REVERT: I 38 THR cc_start: 0.8823 (m) cc_final: 0.8598 (t) REVERT: I 44 LYS cc_start: 0.8718 (mttt) cc_final: 0.8443 (mttm) REVERT: N 30 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9230 (mp) REVERT: N 140 MET cc_start: 0.6691 (pmm) cc_final: 0.6316 (pmt) REVERT: P 7 LYS cc_start: 0.8739 (tptm) cc_final: 0.8383 (tptp) REVERT: R 30 LEU cc_start: 0.9149 (mm) cc_final: 0.8873 (mm) REVERT: R 32 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.4846 (mmm-85) REVERT: R 87 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8237 (tm-30) REVERT: S 54 LYS cc_start: 0.8904 (tppt) cc_final: 0.8635 (tppt) REVERT: T 30 TYR cc_start: 0.6985 (t80) cc_final: 0.6599 (t80) REVERT: T 31 ASN cc_start: 0.8976 (m-40) cc_final: 0.8367 (p0) REVERT: T 40 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8262 (mm-30) REVERT: C 26 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7264 (mp0) REVERT: C 140 ILE cc_start: 0.8629 (tt) cc_final: 0.8390 (tp) REVERT: C 195 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7102 (tp30) REVERT: C 390 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.6611 (tpp) REVERT: C 484 ARG cc_start: 0.6312 (ttp80) cc_final: 0.5602 (ttm-80) REVERT: C 499 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7481 (tp30) REVERT: A 89 LYS cc_start: 0.7831 (mmtm) cc_final: 0.7576 (mmmt) REVERT: A 96 ASP cc_start: 0.8372 (p0) cc_final: 0.7970 (p0) REVERT: A 218 LYS cc_start: 0.7494 (tttp) cc_final: 0.7129 (tttt) REVERT: A 226 MET cc_start: 0.8943 (tpt) cc_final: 0.8275 (tpt) REVERT: A 351 PHE cc_start: 0.7129 (m-80) cc_final: 0.6503 (t80) REVERT: A 362 ARG cc_start: 0.7559 (mtt180) cc_final: 0.6489 (mtt90) REVERT: A 482 THR cc_start: 0.6668 (OUTLIER) cc_final: 0.6327 (t) REVERT: B 477 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7622 (mm110) REVERT: E 195 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7644 (mm-30) REVERT: E 205 GLU cc_start: 0.8815 (tt0) cc_final: 0.8181 (pt0) REVERT: E 227 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8018 (mt-10) REVERT: E 234 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.5650 (mmp80) REVERT: E 344 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7352 (pt0) REVERT: E 361 MET cc_start: 0.7760 (mmm) cc_final: 0.7429 (tpt) REVERT: E 369 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7174 (tp30) REVERT: E 390 ILE cc_start: 0.5835 (OUTLIER) cc_final: 0.5599 (mt) REVERT: E 442 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6745 (ttpt) REVERT: F 30 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7732 (pt0) REVERT: F 171 GLU cc_start: 0.7881 (tp30) cc_final: 0.7556 (tp30) REVERT: F 217 LYS cc_start: 0.7786 (ptpp) cc_final: 0.6902 (mttp) REVERT: F 389 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7739 (t0) REVERT: F 402 GLU cc_start: 0.7596 (tp30) cc_final: 0.7303 (tp30) REVERT: F 422 GLN cc_start: 0.7726 (tp40) cc_final: 0.7427 (tm-30) REVERT: G 123 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6767 (pm20) REVERT: G 130 GLU cc_start: 0.8148 (tp30) cc_final: 0.6769 (tm-30) REVERT: G 172 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6745 (tptp) REVERT: G 260 LYS cc_start: 0.8278 (tttt) cc_final: 0.7910 (tttp) REVERT: O 33 GLU cc_start: 0.7021 (pt0) cc_final: 0.6419 (pm20) REVERT: O 37 LYS cc_start: 0.7154 (tttt) cc_final: 0.6429 (tppt) REVERT: O 148 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6868 (mp) REVERT: O 162 MET cc_start: 0.6948 (ptt) cc_final: 0.6651 (pmt) REVERT: D 64 ILE cc_start: 0.8321 (mt) cc_final: 0.7935 (pt) REVERT: D 149 TYR cc_start: 0.6602 (m-10) cc_final: 0.6229 (m-10) REVERT: D 180 HIS cc_start: 0.7410 (t-90) cc_final: 0.6837 (t-90) REVERT: D 248 ASP cc_start: 0.7518 (m-30) cc_final: 0.7162 (m-30) REVERT: D 259 ASP cc_start: 0.8420 (t0) cc_final: 0.8167 (t0) REVERT: D 458 GLN cc_start: 0.5248 (OUTLIER) cc_final: 0.4851 (tp40) REVERT: D 462 MET cc_start: 0.5564 (mmt) cc_final: 0.5336 (mmt) outliers start: 156 outliers final: 52 residues processed: 755 average time/residue: 0.6820 time to fit residues: 626.8302 Evaluate side-chains 695 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 618 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain 8 residue 75 MET Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 2 residue 71 ILE Chi-restraints excluded: chain 3 residue 15 THR Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 5 residue 7 LYS Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 32 ARG Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain T residue 7 VAL Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 458 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 97 optimal weight: 4.9990 chunk 423 optimal weight: 8.9990 chunk 393 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 295 optimal weight: 0.7980 chunk 353 optimal weight: 0.8980 chunk 282 optimal weight: 3.9990 chunk 342 optimal weight: 7.9990 chunk 394 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 328 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN M 123 ASN M 155 GLN 8 45 GLN 2 39 ASN 4 45 GLN H 85 ASN H 111 ASN ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN R 44 GLN A 366 ASN A 396 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN D 54 GLN D 210 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.156478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120422 restraints weight = 57579.388| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.39 r_work: 0.3422 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 38883 Z= 0.135 Angle : 0.595 9.442 52613 Z= 0.303 Chirality : 0.043 0.237 6140 Planarity : 0.004 0.053 6703 Dihedral : 6.620 114.497 5491 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.00 % Favored : 96.98 % Rotamer: Outliers : 3.52 % Allowed : 19.48 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.12), residues: 4931 helix: 1.02 (0.10), residues: 2694 sheet: -1.02 (0.20), residues: 577 loop : -1.23 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 40 TYR 0.024 0.001 TYR F 461 PHE 0.032 0.001 PHE L 82 TRP 0.017 0.001 TRP K 176 HIS 0.006 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00289 (38883) covalent geometry : angle 0.59455 (52613) hydrogen bonds : bond 0.04774 ( 2256) hydrogen bonds : angle 4.72081 ( 6555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 678 time to evaluate : 1.485 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: K 87 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7898 (mm-30) REVERT: K 134 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8547 (ttm) REVERT: K 136 LEU cc_start: 0.9076 (pp) cc_final: 0.8870 (mt) REVERT: K 146 ARG cc_start: 0.8386 (ttm170) cc_final: 0.7727 (ttt-90) REVERT: K 178 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8586 (mm-30) REVERT: L 49 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7978 (pm20) REVERT: L 50 TYR cc_start: 0.7243 (t80) cc_final: 0.6857 (t80) REVERT: L 96 GLU cc_start: 0.4622 (pp20) cc_final: 0.4389 (pp20) REVERT: L 104 GLU cc_start: 0.7936 (pt0) cc_final: 0.7384 (pp20) REVERT: M 33 TRP cc_start: 0.8735 (m100) cc_final: 0.8361 (m-10) REVERT: M 40 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7912 (mmm-85) REVERT: M 130 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8098 (ttm) REVERT: M 145 ASP cc_start: 0.8765 (t0) cc_final: 0.8484 (t0) REVERT: 8 1 ASP cc_start: 0.8025 (t0) cc_final: 0.7271 (p0) REVERT: 8 75 MET cc_start: 0.6848 (tpt) cc_final: 0.6549 (mpt) REVERT: 2 51 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7193 (mp) REVERT: 2 69 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: 2 75 MET cc_start: 0.4751 (mmt) cc_final: 0.3943 (mpp) REVERT: 3 38 ARG cc_start: 0.7851 (tpp80) cc_final: 0.7572 (tpp-160) REVERT: 4 73 PHE cc_start: 0.5224 (m-80) cc_final: 0.4305 (t80) REVERT: 5 7 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6886 (mmtm) REVERT: 5 39 ASN cc_start: 0.8465 (t0) cc_final: 0.8143 (t0) REVERT: 5 51 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.7084 (mp) REVERT: 5 75 MET cc_start: 0.5950 (mpm) cc_final: 0.4360 (mtm) REVERT: H 15 GLN cc_start: 0.4632 (tp40) cc_final: 0.4420 (tt0) REVERT: H 128 ARG cc_start: 0.8890 (ttm-80) cc_final: 0.8150 (ttm-80) REVERT: I 44 LYS cc_start: 0.8702 (mttt) cc_final: 0.8451 (mttm) REVERT: N 30 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9233 (mp) REVERT: N 181 MET cc_start: 0.7030 (mmt) cc_final: 0.6805 (mpp) REVERT: P 6 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7786 (tt) REVERT: P 7 LYS cc_start: 0.8763 (tptm) cc_final: 0.8412 (tptp) REVERT: R 30 LEU cc_start: 0.9143 (mm) cc_final: 0.8892 (mm) REVERT: R 69 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.6857 (mp) REVERT: R 87 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8172 (tm-30) REVERT: S 54 LYS cc_start: 0.8905 (tppt) cc_final: 0.8653 (tppt) REVERT: T 30 TYR cc_start: 0.7019 (t80) cc_final: 0.6622 (t80) REVERT: T 31 ASN cc_start: 0.8842 (m-40) cc_final: 0.8273 (p0) REVERT: T 40 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8311 (mm-30) REVERT: C 140 ILE cc_start: 0.8547 (tt) cc_final: 0.8303 (tp) REVERT: C 195 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7032 (tp30) REVERT: C 390 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.6569 (tpp) REVERT: C 484 ARG cc_start: 0.6237 (ttp80) cc_final: 0.5557 (ttm170) REVERT: A 89 LYS cc_start: 0.7770 (mmtm) cc_final: 0.7491 (mmmt) REVERT: A 96 ASP cc_start: 0.8377 (p0) cc_final: 0.8005 (p0) REVERT: A 218 LYS cc_start: 0.7543 (tttp) cc_final: 0.7195 (tttt) REVERT: A 226 MET cc_start: 0.8941 (tpt) cc_final: 0.8293 (tpt) REVERT: A 351 PHE cc_start: 0.7131 (m-80) cc_final: 0.6485 (t80) REVERT: A 362 ARG cc_start: 0.7488 (mtt180) cc_final: 0.6516 (mtt90) REVERT: A 476 HIS cc_start: 0.6169 (m-70) cc_final: 0.5501 (m-70) REVERT: A 482 THR cc_start: 0.6596 (OUTLIER) cc_final: 0.6386 (t) REVERT: B 195 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: B 477 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7603 (mm110) REVERT: E 195 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7661 (mm-30) REVERT: E 205 GLU cc_start: 0.8784 (tt0) cc_final: 0.8147 (pt0) REVERT: E 227 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7484 (mp0) REVERT: E 234 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.5645 (mmp80) REVERT: E 344 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7361 (pt0) REVERT: E 361 MET cc_start: 0.7806 (mmm) cc_final: 0.7458 (tpt) REVERT: E 369 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7076 (tp30) REVERT: F 30 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7684 (pt0) REVERT: F 202 GLU cc_start: 0.7503 (pt0) cc_final: 0.7241 (pt0) REVERT: F 217 LYS cc_start: 0.7757 (ptpp) cc_final: 0.6858 (mttp) REVERT: F 380 ILE cc_start: 0.7954 (mp) cc_final: 0.7690 (mm) REVERT: F 402 GLU cc_start: 0.7615 (tp30) cc_final: 0.7266 (tp30) REVERT: F 422 GLN cc_start: 0.7740 (tp40) cc_final: 0.7434 (tm-30) REVERT: G 89 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6471 (ttm) REVERT: G 130 GLU cc_start: 0.8168 (tp30) cc_final: 0.6670 (tm-30) REVERT: G 260 LYS cc_start: 0.8206 (tttt) cc_final: 0.7840 (tttp) REVERT: O 33 GLU cc_start: 0.7039 (pt0) cc_final: 0.6382 (pm20) REVERT: O 37 LYS cc_start: 0.7112 (tttt) cc_final: 0.6341 (tppt) REVERT: O 148 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6692 (mp) REVERT: O 162 MET cc_start: 0.7037 (ptt) cc_final: 0.6725 (pmt) REVERT: D 59 SER cc_start: 0.8661 (m) cc_final: 0.8229 (p) REVERT: D 64 ILE cc_start: 0.8286 (mt) cc_final: 0.7880 (pt) REVERT: D 180 HIS cc_start: 0.7304 (t-90) cc_final: 0.6750 (t-90) REVERT: D 202 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7478 (tp30) REVERT: D 248 ASP cc_start: 0.7423 (m-30) cc_final: 0.7057 (m-30) REVERT: D 259 ASP cc_start: 0.8314 (t0) cc_final: 0.8044 (t70) REVERT: D 290 THR cc_start: 0.5698 (t) cc_final: 0.5263 (p) REVERT: D 342 ILE cc_start: 0.7680 (mt) cc_final: 0.7454 (tt) REVERT: D 372 ASP cc_start: 0.7703 (m-30) cc_final: 0.7477 (m-30) REVERT: D 458 GLN cc_start: 0.5175 (OUTLIER) cc_final: 0.4826 (tp40) REVERT: D 462 MET cc_start: 0.5694 (mmt) cc_final: 0.5482 (mmt) outliers start: 142 outliers final: 45 residues processed: 756 average time/residue: 0.6683 time to fit residues: 617.6434 Evaluate side-chains 690 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 625 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 65 LEU Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 65 LEU Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 45 GLN Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 5 residue 7 LYS Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 7 VAL Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain G residue 89 MET Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 458 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 436 optimal weight: 5.9990 chunk 469 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 290 optimal weight: 4.9990 chunk 371 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 463 optimal weight: 5.9990 chunk 407 optimal weight: 10.0000 chunk 450 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN M 155 GLN 8 45 GLN 2 45 GLN 3 45 GLN 4 45 GLN H 66 HIS H 111 ASN H 116 GLN H 138 ASN I 42 ASN ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 163 ASN P 8 ASN ** A 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 ASN A 396 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN G 66 HIS ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN D 54 GLN D 210 ASN D 364 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.151277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115534 restraints weight = 58243.287| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.42 r_work: 0.3345 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 38883 Z= 0.286 Angle : 0.697 10.996 52613 Z= 0.357 Chirality : 0.048 0.287 6140 Planarity : 0.005 0.062 6703 Dihedral : 6.935 114.722 5489 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 4.34 % Allowed : 20.45 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.12), residues: 4931 helix: 0.87 (0.10), residues: 2673 sheet: -1.12 (0.20), residues: 570 loop : -1.20 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 373 TYR 0.022 0.002 TYR A 397 PHE 0.035 0.002 PHE L 82 TRP 0.013 0.002 TRP M 53 HIS 0.007 0.001 HIS E 370 Details of bonding type rmsd covalent geometry : bond 0.00688 (38883) covalent geometry : angle 0.69717 (52613) hydrogen bonds : bond 0.05524 ( 2256) hydrogen bonds : angle 4.91117 ( 6555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 633 time to evaluate : 1.368 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: K 134 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8657 (ttt) REVERT: K 146 ARG cc_start: 0.8415 (ttm170) cc_final: 0.7755 (ttt-90) REVERT: L 49 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: L 54 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7459 (tmm160) REVERT: L 104 GLU cc_start: 0.8029 (pt0) cc_final: 0.7489 (pp20) REVERT: M 33 TRP cc_start: 0.8743 (m100) cc_final: 0.8324 (m-10) REVERT: M 130 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8211 (ttm) REVERT: M 145 ASP cc_start: 0.8880 (t0) cc_final: 0.8581 (t0) REVERT: 6 58 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8003 (mm-30) REVERT: 8 66 MET cc_start: 0.7911 (pp-130) cc_final: 0.7690 (pp-130) REVERT: 8 75 MET cc_start: 0.6971 (tpt) cc_final: 0.6645 (mpt) REVERT: 2 51 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7346 (mp) REVERT: 2 69 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6812 (m-80) REVERT: 2 75 MET cc_start: 0.4710 (mmt) cc_final: 0.4014 (mpp) REVERT: 3 38 ARG cc_start: 0.7926 (tpp80) cc_final: 0.7696 (tpp-160) REVERT: 3 60 MET cc_start: 0.8101 (mmp) cc_final: 0.7825 (mmm) REVERT: 5 39 ASN cc_start: 0.8779 (t0) cc_final: 0.8484 (t0) REVERT: 5 51 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.7107 (mp) REVERT: 5 75 MET cc_start: 0.5896 (mpm) cc_final: 0.4310 (mtm) REVERT: H 15 GLN cc_start: 0.4610 (tp40) cc_final: 0.4351 (tt0) REVERT: H 16 MET cc_start: 0.6110 (mmm) cc_final: 0.5774 (mmp) REVERT: H 34 ARG cc_start: 0.8098 (ptm-80) cc_final: 0.7688 (mtm110) REVERT: I 44 LYS cc_start: 0.8647 (mttt) cc_final: 0.8388 (mttm) REVERT: N 30 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9204 (mp) REVERT: N 163 ASN cc_start: 0.9145 (OUTLIER) cc_final: 0.8707 (m110) REVERT: P 6 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7846 (tt) REVERT: P 7 LYS cc_start: 0.8791 (tptm) cc_final: 0.8378 (tptp) REVERT: R 19 GLU cc_start: 0.3167 (OUTLIER) cc_final: 0.2920 (tm-30) REVERT: R 30 LEU cc_start: 0.9164 (mm) cc_final: 0.8866 (mm) REVERT: R 32 ARG cc_start: 0.6356 (OUTLIER) cc_final: 0.4881 (mmm-85) REVERT: R 69 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7045 (mp) REVERT: R 87 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8095 (tm-30) REVERT: R 91 LYS cc_start: 0.8003 (pptt) cc_final: 0.7789 (pptt) REVERT: S 54 LYS cc_start: 0.8914 (tppt) cc_final: 0.8638 (tppt) REVERT: T 30 TYR cc_start: 0.7157 (t80) cc_final: 0.6770 (t80) REVERT: T 31 ASN cc_start: 0.8817 (m-40) cc_final: 0.8257 (p0) REVERT: T 40 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8359 (mm-30) REVERT: C 140 ILE cc_start: 0.8623 (tt) cc_final: 0.8409 (tp) REVERT: C 195 GLU cc_start: 0.7603 (tm-30) cc_final: 0.6950 (tp30) REVERT: C 390 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.6730 (tpp) REVERT: C 399 GLU cc_start: 0.6936 (pt0) cc_final: 0.6471 (pp20) REVERT: C 484 ARG cc_start: 0.6348 (ttp80) cc_final: 0.5629 (ttm170) REVERT: C 499 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: A 89 LYS cc_start: 0.7831 (mmtm) cc_final: 0.7509 (mmmt) REVERT: A 96 ASP cc_start: 0.8388 (p0) cc_final: 0.8021 (p0) REVERT: A 351 PHE cc_start: 0.7197 (m-80) cc_final: 0.6533 (t80) REVERT: A 362 ARG cc_start: 0.7591 (mtt180) cc_final: 0.6490 (mtt90) REVERT: A 476 HIS cc_start: 0.6226 (m-70) cc_final: 0.5715 (m-70) REVERT: A 482 THR cc_start: 0.6698 (OUTLIER) cc_final: 0.6379 (t) REVERT: B 36 ASP cc_start: 0.6505 (m-30) cc_final: 0.5902 (p0) REVERT: B 195 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: B 328 GLU cc_start: 0.8782 (tt0) cc_final: 0.8369 (tt0) REVERT: B 445 ILE cc_start: 0.7930 (mt) cc_final: 0.7699 (mm) REVERT: B 477 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7598 (mm110) REVERT: E 205 GLU cc_start: 0.8804 (tt0) cc_final: 0.8169 (pt0) REVERT: E 227 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8018 (mt-10) REVERT: E 234 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.5534 (mmp80) REVERT: E 344 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7389 (pt0) REVERT: E 361 MET cc_start: 0.7867 (mmm) cc_final: 0.7276 (tpt) REVERT: F 30 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7660 (pt0) REVERT: F 128 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: F 171 GLU cc_start: 0.7795 (tp30) cc_final: 0.7425 (tp30) REVERT: F 202 GLU cc_start: 0.7656 (pt0) cc_final: 0.7354 (pt0) REVERT: F 217 LYS cc_start: 0.7825 (ptpp) cc_final: 0.6917 (mttp) REVERT: F 402 GLU cc_start: 0.7693 (tp30) cc_final: 0.7366 (tp30) REVERT: F 422 GLN cc_start: 0.7736 (tp40) cc_final: 0.7396 (tm-30) REVERT: G 130 GLU cc_start: 0.8260 (tp30) cc_final: 0.6795 (tm-30) REVERT: G 201 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7622 (mp) REVERT: G 260 LYS cc_start: 0.8259 (tttt) cc_final: 0.7871 (tttp) REVERT: O 33 GLU cc_start: 0.7092 (pt0) cc_final: 0.6442 (pm20) REVERT: O 37 LYS cc_start: 0.7165 (tttt) cc_final: 0.6423 (tppt) REVERT: O 173 MET cc_start: 0.7399 (mtm) cc_final: 0.6924 (mtm) REVERT: D 64 ILE cc_start: 0.8289 (mt) cc_final: 0.8039 (mm) REVERT: D 180 HIS cc_start: 0.7446 (t-90) cc_final: 0.6821 (t-90) REVERT: D 248 ASP cc_start: 0.7438 (m-30) cc_final: 0.7072 (m-30) REVERT: D 259 ASP cc_start: 0.8513 (t0) cc_final: 0.8237 (t70) REVERT: D 342 ILE cc_start: 0.7665 (mt) cc_final: 0.7343 (tt) REVERT: D 458 GLN cc_start: 0.5385 (OUTLIER) cc_final: 0.5129 (tp40) REVERT: D 462 MET cc_start: 0.5594 (mmt) cc_final: 0.5348 (mmt) outliers start: 175 outliers final: 75 residues processed: 745 average time/residue: 0.6677 time to fit residues: 605.5521 Evaluate side-chains 691 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 593 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 65 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 9 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 57 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 2 residue 71 ILE Chi-restraints excluded: chain 3 residue 15 THR Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 71 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 32 ARG Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 7 VAL Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 468 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 175 VAL Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 458 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 178 optimal weight: 1.9990 chunk 440 optimal weight: 7.9990 chunk 334 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 416 optimal weight: 5.9990 chunk 282 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 254 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN M 123 ASN M 155 GLN 8 45 GLN 2 45 GLN 4 45 GLN H 111 ASN ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 163 ASN P 8 ASN R 44 GLN A 366 ASN A 396 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN D 210 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.154419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118214 restraints weight = 57960.731| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.48 r_work: 0.3389 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38883 Z= 0.151 Angle : 0.616 10.564 52613 Z= 0.313 Chirality : 0.044 0.237 6140 Planarity : 0.004 0.055 6703 Dihedral : 6.675 111.035 5489 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.96 % Favored : 97.02 % Rotamer: Outliers : 3.57 % Allowed : 22.26 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.12), residues: 4931 helix: 1.10 (0.10), residues: 2682 sheet: -1.02 (0.21), residues: 560 loop : -1.08 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 128 TYR 0.028 0.001 TYR F 461 PHE 0.028 0.001 PHE L 82 TRP 0.015 0.002 TRP I 5 HIS 0.006 0.001 HIS E 370 Details of bonding type rmsd covalent geometry : bond 0.00339 (38883) covalent geometry : angle 0.61642 (52613) hydrogen bonds : bond 0.04868 ( 2256) hydrogen bonds : angle 4.74379 ( 6555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 640 time to evaluate : 1.541 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: K 134 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8620 (ttt) REVERT: K 146 ARG cc_start: 0.8415 (ttm170) cc_final: 0.7750 (ttt-90) REVERT: L 49 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: L 54 ARG cc_start: 0.7662 (tpm170) cc_final: 0.7387 (tmm160) REVERT: L 96 GLU cc_start: 0.4381 (pp20) cc_final: 0.4059 (pp20) REVERT: L 104 GLU cc_start: 0.8020 (pt0) cc_final: 0.7501 (pp20) REVERT: M 33 TRP cc_start: 0.8738 (m100) cc_final: 0.8309 (m-10) REVERT: M 40 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7940 (mmm-85) REVERT: M 69 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6449 (t80) REVERT: M 130 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8171 (ttm) REVERT: M 145 ASP cc_start: 0.8853 (t0) cc_final: 0.8551 (t0) REVERT: 8 75 MET cc_start: 0.7018 (tpt) cc_final: 0.6670 (mpt) REVERT: 2 51 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7320 (mp) REVERT: 2 69 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: 2 75 MET cc_start: 0.4594 (mmt) cc_final: 0.3852 (mpp) REVERT: 5 39 ASN cc_start: 0.8655 (t0) cc_final: 0.8408 (t0) REVERT: 5 75 MET cc_start: 0.5972 (mpm) cc_final: 0.4372 (mtm) REVERT: H 15 GLN cc_start: 0.4566 (tp40) cc_final: 0.4260 (tt0) REVERT: H 16 MET cc_start: 0.6086 (mmm) cc_final: 0.5763 (mmp) REVERT: H 34 ARG cc_start: 0.8120 (ptm-80) cc_final: 0.7902 (ptm-80) REVERT: H 122 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8366 (p) REVERT: I 44 LYS cc_start: 0.8666 (mttt) cc_final: 0.8439 (mttm) REVERT: N 30 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9204 (mp) REVERT: P 6 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7749 (tt) REVERT: P 7 LYS cc_start: 0.8782 (tptm) cc_final: 0.8415 (tptp) REVERT: R 30 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8856 (mm) REVERT: R 69 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.6912 (mp) REVERT: R 87 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8140 (tm-30) REVERT: R 91 LYS cc_start: 0.7986 (pptt) cc_final: 0.7759 (pptt) REVERT: S 54 LYS cc_start: 0.8927 (tppt) cc_final: 0.8644 (tppt) REVERT: S 85 TRP cc_start: 0.8305 (m100) cc_final: 0.7789 (t60) REVERT: T 12 LYS cc_start: 0.6473 (mmtt) cc_final: 0.6206 (mmtt) REVERT: T 30 TYR cc_start: 0.7217 (t80) cc_final: 0.6795 (t80) REVERT: T 31 ASN cc_start: 0.8714 (m-40) cc_final: 0.8265 (p0) REVERT: T 40 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8371 (mm-30) REVERT: C 26 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7287 (mp0) REVERT: C 140 ILE cc_start: 0.8591 (tt) cc_final: 0.8353 (tp) REVERT: C 195 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6902 (tp30) REVERT: C 390 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.6722 (tpp) REVERT: C 484 ARG cc_start: 0.6309 (ttp80) cc_final: 0.5618 (ttm170) REVERT: A 96 ASP cc_start: 0.8406 (p0) cc_final: 0.8074 (p0) REVERT: A 218 LYS cc_start: 0.7558 (tttp) cc_final: 0.7262 (tttt) REVERT: A 226 MET cc_start: 0.8925 (tpt) cc_final: 0.8268 (tpt) REVERT: A 351 PHE cc_start: 0.7197 (m-80) cc_final: 0.6588 (t80) REVERT: A 362 ARG cc_start: 0.7579 (mtt180) cc_final: 0.6443 (mtt90) REVERT: A 476 HIS cc_start: 0.6121 (m-70) cc_final: 0.5639 (m-70) REVERT: A 482 THR cc_start: 0.6566 (OUTLIER) cc_final: 0.6317 (t) REVERT: B 195 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: E 134 GLU cc_start: 0.8180 (tt0) cc_final: 0.7742 (tt0) REVERT: E 205 GLU cc_start: 0.8798 (tt0) cc_final: 0.8137 (pt0) REVERT: E 227 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7501 (mp0) REVERT: E 234 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.5516 (mmp80) REVERT: E 361 MET cc_start: 0.7787 (mmm) cc_final: 0.7404 (tpt) REVERT: E 369 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7092 (tp30) REVERT: F 30 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7664 (pt0) REVERT: F 45 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7916 (mm-30) REVERT: F 128 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: F 202 GLU cc_start: 0.7482 (pt0) cc_final: 0.7205 (pt0) REVERT: F 217 LYS cc_start: 0.7782 (ptpp) cc_final: 0.6870 (mttp) REVERT: F 380 ILE cc_start: 0.7986 (mp) cc_final: 0.7731 (mm) REVERT: F 390 ILE cc_start: 0.7757 (tp) cc_final: 0.7460 (tp) REVERT: F 402 GLU cc_start: 0.7668 (tp30) cc_final: 0.7322 (tp30) REVERT: F 422 GLN cc_start: 0.7730 (tp40) cc_final: 0.7399 (tm-30) REVERT: G 130 GLU cc_start: 0.8217 (tp30) cc_final: 0.6700 (tm-30) REVERT: G 260 LYS cc_start: 0.8192 (tttt) cc_final: 0.7816 (tttp) REVERT: O 33 GLU cc_start: 0.7036 (pt0) cc_final: 0.6359 (pm20) REVERT: O 37 LYS cc_start: 0.7188 (tttt) cc_final: 0.6436 (tppt) REVERT: O 173 MET cc_start: 0.7458 (mtm) cc_final: 0.6997 (mtm) REVERT: D 59 SER cc_start: 0.8715 (m) cc_final: 0.8335 (p) REVERT: D 64 ILE cc_start: 0.8280 (mt) cc_final: 0.8024 (mm) REVERT: D 180 HIS cc_start: 0.7297 (t-90) cc_final: 0.6654 (t-90) REVERT: D 203 MET cc_start: 0.8325 (mtt) cc_final: 0.8111 (mtt) REVERT: D 248 ASP cc_start: 0.7378 (m-30) cc_final: 0.6964 (m-30) REVERT: D 259 ASP cc_start: 0.8374 (t0) cc_final: 0.8086 (t70) REVERT: D 342 ILE cc_start: 0.7748 (mt) cc_final: 0.7402 (tt) REVERT: D 458 GLN cc_start: 0.5383 (OUTLIER) cc_final: 0.5134 (tp40) REVERT: D 462 MET cc_start: 0.5761 (mmt) cc_final: 0.5511 (mmt) outliers start: 144 outliers final: 66 residues processed: 725 average time/residue: 0.6927 time to fit residues: 616.9879 Evaluate side-chains 682 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 596 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 88 ASN Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain 6 residue 9 ILE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 3 residue 15 THR Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 45 GLN Chi-restraints excluded: chain 4 residue 71 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 7 VAL Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 458 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 133 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 231 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 415 optimal weight: 7.9990 chunk 308 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 317 optimal weight: 4.9990 chunk 390 optimal weight: 6.9990 chunk 328 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 GLN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 172 HIS L 80 GLN 8 45 GLN 2 45 GLN 4 45 GLN H 111 ASN H 116 GLN ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN A 366 ASN A 396 GLN B 70 ASN B 466 ASN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.156276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120233 restraints weight = 57786.984| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.56 r_work: 0.3413 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 38883 Z= 0.130 Angle : 0.598 13.190 52613 Z= 0.303 Chirality : 0.043 0.315 6140 Planarity : 0.004 0.055 6703 Dihedral : 6.460 107.605 5489 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.16 % Favored : 96.82 % Rotamer: Outliers : 3.30 % Allowed : 23.13 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.12), residues: 4931 helix: 1.28 (0.10), residues: 2673 sheet: -0.87 (0.21), residues: 574 loop : -0.93 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 373 TYR 0.029 0.001 TYR A 397 PHE 0.024 0.001 PHE L 82 TRP 0.015 0.002 TRP I 5 HIS 0.006 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00283 (38883) covalent geometry : angle 0.59788 (52613) hydrogen bonds : bond 0.04556 ( 2256) hydrogen bonds : angle 4.62494 ( 6555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 647 time to evaluate : 1.235 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: K 87 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7942 (mm-30) REVERT: K 134 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8631 (ttm) REVERT: K 146 ARG cc_start: 0.8398 (ttm170) cc_final: 0.7743 (ttt-90) REVERT: K 165 MET cc_start: 0.8273 (mtp) cc_final: 0.7905 (mmp) REVERT: K 174 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7874 (tt) REVERT: L 49 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8037 (pm20) REVERT: L 54 ARG cc_start: 0.7556 (tpm170) cc_final: 0.7277 (tmm160) REVERT: L 87 MET cc_start: 0.8172 (mpt) cc_final: 0.7736 (mpt) REVERT: L 104 GLU cc_start: 0.8000 (pt0) cc_final: 0.7484 (pp20) REVERT: M 33 TRP cc_start: 0.8754 (m100) cc_final: 0.8308 (m-10) REVERT: M 35 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8746 (mm-30) REVERT: M 40 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.7910 (mmm-85) REVERT: M 110 ARG cc_start: 0.7897 (ttm110) cc_final: 0.7523 (mtm-85) REVERT: M 130 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8090 (ttm) REVERT: M 145 ASP cc_start: 0.8820 (t0) cc_final: 0.8519 (t0) REVERT: 8 75 MET cc_start: 0.7023 (tpt) cc_final: 0.6769 (mpt) REVERT: 1 54 PHE cc_start: 0.6670 (t80) cc_final: 0.6311 (t80) REVERT: 2 51 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7294 (mp) REVERT: 2 69 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: 2 75 MET cc_start: 0.4614 (mmt) cc_final: 0.3875 (mpp) REVERT: 3 60 MET cc_start: 0.8030 (mmp) cc_final: 0.7749 (mmm) REVERT: 3 75 MET cc_start: 0.6530 (mmp) cc_final: 0.5267 (tpp) REVERT: 5 39 ASN cc_start: 0.8603 (t0) cc_final: 0.8390 (t0) REVERT: 5 75 MET cc_start: 0.6057 (mpm) cc_final: 0.4604 (mtm) REVERT: H 15 GLN cc_start: 0.4589 (tp40) cc_final: 0.4363 (tt0) REVERT: H 16 MET cc_start: 0.6071 (mmm) cc_final: 0.5751 (mmp) REVERT: H 34 ARG cc_start: 0.8135 (ptm-80) cc_final: 0.7725 (mtm110) REVERT: I 44 LYS cc_start: 0.8679 (mttt) cc_final: 0.8465 (mttm) REVERT: N 30 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9197 (mp) REVERT: N 163 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8483 (m110) REVERT: P 6 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7733 (tt) REVERT: P 7 LYS cc_start: 0.8754 (tptm) cc_final: 0.8399 (tptp) REVERT: R 69 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.6896 (mp) REVERT: R 87 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8210 (tm-30) REVERT: S 36 GLU cc_start: 0.7773 (tp30) cc_final: 0.7374 (tp30) REVERT: S 54 LYS cc_start: 0.8942 (tppt) cc_final: 0.8652 (tppt) REVERT: S 85 TRP cc_start: 0.8316 (m100) cc_final: 0.7967 (t60) REVERT: S 90 GLU cc_start: 0.8345 (pp20) cc_final: 0.7878 (pp20) REVERT: T 36 ARG cc_start: 0.7698 (mpp80) cc_final: 0.7337 (mpp80) REVERT: T 40 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8371 (mm-30) REVERT: Q 33 TYR cc_start: 0.8417 (m-80) cc_final: 0.8167 (m-80) REVERT: C 140 ILE cc_start: 0.8540 (tt) cc_final: 0.8286 (tp) REVERT: C 195 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6882 (tp30) REVERT: C 390 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6612 (tpp) REVERT: C 484 ARG cc_start: 0.6265 (ttp80) cc_final: 0.5576 (ttm170) REVERT: A 62 MET cc_start: 0.8638 (ttm) cc_final: 0.8203 (ttt) REVERT: A 96 ASP cc_start: 0.8409 (p0) cc_final: 0.8079 (p0) REVERT: A 218 LYS cc_start: 0.7577 (tttp) cc_final: 0.7239 (tttt) REVERT: A 226 MET cc_start: 0.8947 (tpt) cc_final: 0.8347 (tpt) REVERT: A 351 PHE cc_start: 0.7158 (m-80) cc_final: 0.6469 (t80) REVERT: A 362 ARG cc_start: 0.7427 (mtt180) cc_final: 0.6436 (mtt90) REVERT: A 397 TYR cc_start: 0.7031 (t80) cc_final: 0.6812 (t80) REVERT: A 422 VAL cc_start: 0.6102 (p) cc_final: 0.5869 (m) REVERT: A 475 GLN cc_start: 0.7710 (mp-120) cc_final: 0.7507 (mp-120) REVERT: A 476 HIS cc_start: 0.6108 (m-70) cc_final: 0.5745 (m-70) REVERT: A 482 THR cc_start: 0.6514 (OUTLIER) cc_final: 0.6268 (t) REVERT: B 224 ASP cc_start: 0.8454 (t70) cc_final: 0.8254 (t0) REVERT: B 477 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7630 (mm110) REVERT: E 205 GLU cc_start: 0.8787 (tt0) cc_final: 0.8177 (pt0) REVERT: E 227 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7463 (mp0) REVERT: E 234 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.5522 (mmp80) REVERT: E 361 MET cc_start: 0.7816 (mmm) cc_final: 0.7336 (tpt) REVERT: E 369 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7066 (tp30) REVERT: F 58 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8140 (mm-30) REVERT: F 202 GLU cc_start: 0.7482 (pt0) cc_final: 0.7189 (pt0) REVERT: F 217 LYS cc_start: 0.7770 (ptpp) cc_final: 0.6839 (mttp) REVERT: F 248 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8165 (m-30) REVERT: F 380 ILE cc_start: 0.7980 (mp) cc_final: 0.7729 (mm) REVERT: F 402 GLU cc_start: 0.7651 (tp30) cc_final: 0.7283 (tp30) REVERT: F 422 GLN cc_start: 0.7708 (tp40) cc_final: 0.7383 (tm-30) REVERT: G 64 LYS cc_start: 0.8400 (mppt) cc_final: 0.7057 (ttpt) REVERT: G 130 GLU cc_start: 0.8110 (tp30) cc_final: 0.6668 (tm-30) REVERT: G 260 LYS cc_start: 0.8205 (tttt) cc_final: 0.7828 (tttp) REVERT: O 33 GLU cc_start: 0.7065 (pt0) cc_final: 0.6357 (pm20) REVERT: O 37 LYS cc_start: 0.7145 (tttt) cc_final: 0.6356 (tppt) REVERT: O 162 MET cc_start: 0.6846 (ptt) cc_final: 0.6555 (pmt) REVERT: O 173 MET cc_start: 0.7449 (mtm) cc_final: 0.6790 (mtm) REVERT: D 59 SER cc_start: 0.8673 (m) cc_final: 0.8303 (p) REVERT: D 64 ILE cc_start: 0.8280 (mt) cc_final: 0.7862 (pt) REVERT: D 180 HIS cc_start: 0.7217 (t-90) cc_final: 0.6634 (t-90) REVERT: D 248 ASP cc_start: 0.7300 (m-30) cc_final: 0.6865 (m-30) REVERT: D 259 ASP cc_start: 0.8296 (t0) cc_final: 0.8018 (t70) REVERT: D 290 THR cc_start: 0.5759 (t) cc_final: 0.5313 (p) REVERT: D 342 ILE cc_start: 0.7744 (mt) cc_final: 0.7415 (tt) REVERT: D 458 GLN cc_start: 0.5305 (OUTLIER) cc_final: 0.5055 (tp40) REVERT: D 462 MET cc_start: 0.5843 (mmt) cc_final: 0.5616 (mmt) outliers start: 133 outliers final: 57 residues processed: 727 average time/residue: 0.6716 time to fit residues: 596.9115 Evaluate side-chains 681 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 607 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 1 residue 9 ILE Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 57 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 3 residue 15 THR Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 7 VAL Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 458 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 236 optimal weight: 0.1980 chunk 342 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 180 optimal weight: 0.0060 chunk 229 optimal weight: 3.9990 chunk 267 optimal weight: 0.4980 chunk 402 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 380 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN M 88 GLN M 123 ASN 8 45 GLN 2 45 GLN H 111 ASN H 116 GLN ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN A 366 ASN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN D 364 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.156223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.119959 restraints weight = 57572.659| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.38 r_work: 0.3423 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38883 Z= 0.133 Angle : 0.613 12.657 52613 Z= 0.306 Chirality : 0.043 0.266 6140 Planarity : 0.004 0.056 6703 Dihedral : 6.383 107.607 5489 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.96 % Favored : 97.02 % Rotamer: Outliers : 2.80 % Allowed : 24.07 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.12), residues: 4931 helix: 1.35 (0.10), residues: 2671 sheet: -0.82 (0.21), residues: 574 loop : -0.84 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 373 TYR 0.029 0.001 TYR F 461 PHE 0.037 0.001 PHE L 82 TRP 0.022 0.002 TRP Q 51 HIS 0.006 0.001 HIS E 370 Details of bonding type rmsd covalent geometry : bond 0.00292 (38883) covalent geometry : angle 0.61347 (52613) hydrogen bonds : bond 0.04500 ( 2256) hydrogen bonds : angle 4.58643 ( 6555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 638 time to evaluate : 1.565 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: K 87 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7966 (mm-30) REVERT: K 134 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8623 (ttm) REVERT: K 146 ARG cc_start: 0.8429 (ttm170) cc_final: 0.7765 (ttt-90) REVERT: K 150 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: K 164 MET cc_start: 0.8929 (tpp) cc_final: 0.8496 (tmm) REVERT: K 174 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7867 (tt) REVERT: K 180 HIS cc_start: 0.8492 (t-90) cc_final: 0.8228 (t70) REVERT: L 49 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: L 54 ARG cc_start: 0.7514 (tpm170) cc_final: 0.7250 (tmm160) REVERT: L 77 LYS cc_start: 0.8313 (ttmm) cc_final: 0.8068 (mttm) REVERT: L 87 MET cc_start: 0.8151 (mpt) cc_final: 0.7753 (mpt) REVERT: L 96 GLU cc_start: 0.4027 (pp20) cc_final: 0.3733 (pp20) REVERT: L 104 GLU cc_start: 0.8018 (pt0) cc_final: 0.7495 (pp20) REVERT: M 33 TRP cc_start: 0.8741 (m100) cc_final: 0.8048 (t60) REVERT: M 35 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8729 (mm-30) REVERT: M 110 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7513 (mtm-85) REVERT: M 130 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8080 (ttm) REVERT: M 145 ASP cc_start: 0.8848 (t0) cc_final: 0.8559 (t0) REVERT: 8 75 MET cc_start: 0.6941 (tpt) cc_final: 0.6739 (mpt) REVERT: 1 54 PHE cc_start: 0.6713 (t80) cc_final: 0.6387 (t80) REVERT: 2 51 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7368 (mp) REVERT: 2 69 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6814 (m-80) REVERT: 2 75 MET cc_start: 0.4616 (mmt) cc_final: 0.3888 (mpp) REVERT: 3 75 MET cc_start: 0.6492 (mmp) cc_final: 0.5377 (tpp) REVERT: 5 75 MET cc_start: 0.6013 (mpm) cc_final: 0.4613 (mtm) REVERT: H 15 GLN cc_start: 0.4623 (tp40) cc_final: 0.3562 (mt0) REVERT: H 16 MET cc_start: 0.6015 (mmm) cc_final: 0.5750 (mmp) REVERT: H 34 ARG cc_start: 0.8145 (ptm-80) cc_final: 0.7735 (mtm110) REVERT: I 44 LYS cc_start: 0.8664 (mttt) cc_final: 0.8458 (mttm) REVERT: N 30 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9172 (mp) REVERT: P 6 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7724 (tt) REVERT: P 7 LYS cc_start: 0.8743 (tptm) cc_final: 0.8368 (tptp) REVERT: R 19 GLU cc_start: 0.2377 (OUTLIER) cc_final: 0.1951 (tm-30) REVERT: R 69 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.6915 (mp) REVERT: R 87 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8092 (tm-30) REVERT: S 54 LYS cc_start: 0.8920 (tppt) cc_final: 0.8621 (tppt) REVERT: S 85 TRP cc_start: 0.8310 (m100) cc_final: 0.8004 (t60) REVERT: S 90 GLU cc_start: 0.8741 (pp20) cc_final: 0.8536 (pp20) REVERT: T 36 ARG cc_start: 0.7660 (mpp80) cc_final: 0.7294 (mpp80) REVERT: T 40 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8328 (mm-30) REVERT: Q 33 TYR cc_start: 0.8391 (m-80) cc_final: 0.8125 (m-80) REVERT: C 140 ILE cc_start: 0.8499 (tt) cc_final: 0.8255 (tp) REVERT: C 195 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6886 (tp30) REVERT: C 373 ARG cc_start: 0.7960 (mtt90) cc_final: 0.7688 (mtt90) REVERT: C 390 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6615 (tpp) REVERT: C 484 ARG cc_start: 0.6271 (ttp80) cc_final: 0.5571 (ttm170) REVERT: A 62 MET cc_start: 0.8646 (ttm) cc_final: 0.8186 (ttt) REVERT: A 96 ASP cc_start: 0.8396 (p0) cc_final: 0.8054 (p0) REVERT: A 218 LYS cc_start: 0.7618 (tttp) cc_final: 0.7354 (tttt) REVERT: A 226 MET cc_start: 0.8942 (tpt) cc_final: 0.8378 (tpt) REVERT: A 351 PHE cc_start: 0.7146 (m-80) cc_final: 0.6533 (t80) REVERT: A 362 ARG cc_start: 0.7392 (mtt180) cc_final: 0.6444 (mtt90) REVERT: A 397 TYR cc_start: 0.6967 (t80) cc_final: 0.6736 (t80) REVERT: A 422 VAL cc_start: 0.6223 (p) cc_final: 0.5980 (m) REVERT: A 453 LEU cc_start: 0.8334 (mp) cc_final: 0.8102 (tp) REVERT: A 476 HIS cc_start: 0.6053 (m-70) cc_final: 0.5728 (m-70) REVERT: A 482 THR cc_start: 0.6548 (OUTLIER) cc_final: 0.6297 (t) REVERT: B 195 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: B 224 ASP cc_start: 0.8441 (t70) cc_final: 0.8225 (t0) REVERT: B 390 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8284 (tpt) REVERT: B 477 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7572 (mm110) REVERT: E 134 GLU cc_start: 0.8165 (tt0) cc_final: 0.7724 (tt0) REVERT: E 205 GLU cc_start: 0.8767 (tt0) cc_final: 0.8167 (pt0) REVERT: E 227 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7433 (mp0) REVERT: E 361 MET cc_start: 0.7762 (mmm) cc_final: 0.7304 (tpt) REVERT: E 369 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6992 (tp30) REVERT: F 58 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8068 (mm-30) REVERT: F 171 GLU cc_start: 0.7740 (tp30) cc_final: 0.7314 (tp30) REVERT: F 202 GLU cc_start: 0.7462 (pt0) cc_final: 0.7159 (pt0) REVERT: F 217 LYS cc_start: 0.7788 (ptpp) cc_final: 0.6874 (mttp) REVERT: F 248 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: F 402 GLU cc_start: 0.7630 (tp30) cc_final: 0.7248 (tp30) REVERT: F 422 GLN cc_start: 0.7718 (tp40) cc_final: 0.7370 (tm-30) REVERT: G 64 LYS cc_start: 0.8413 (mppt) cc_final: 0.7108 (tttt) REVERT: G 123 GLN cc_start: 0.6453 (pt0) cc_final: 0.6154 (pm20) REVERT: G 130 GLU cc_start: 0.8076 (tp30) cc_final: 0.6706 (tp30) REVERT: G 260 LYS cc_start: 0.8151 (tttt) cc_final: 0.7775 (tttp) REVERT: O 33 GLU cc_start: 0.7007 (pt0) cc_final: 0.6361 (pm20) REVERT: O 37 LYS cc_start: 0.7165 (tttt) cc_final: 0.6434 (tppt) REVERT: O 162 MET cc_start: 0.6859 (ptt) cc_final: 0.6564 (pmt) REVERT: O 173 MET cc_start: 0.7457 (mtm) cc_final: 0.6821 (mtm) REVERT: D 59 SER cc_start: 0.8616 (m) cc_final: 0.8244 (p) REVERT: D 64 ILE cc_start: 0.8229 (mt) cc_final: 0.7853 (pt) REVERT: D 180 HIS cc_start: 0.7201 (t-90) cc_final: 0.6621 (t-90) REVERT: D 259 ASP cc_start: 0.8289 (t0) cc_final: 0.7988 (t70) REVERT: D 342 ILE cc_start: 0.7743 (mt) cc_final: 0.7366 (tt) REVERT: D 458 GLN cc_start: 0.5350 (OUTLIER) cc_final: 0.5096 (tp40) outliers start: 113 outliers final: 60 residues processed: 711 average time/residue: 0.6812 time to fit residues: 588.8025 Evaluate side-chains 686 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 607 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 1 residue 9 ILE Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 57 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 65 LEU Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain S residue 91 ILE Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 7 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 458 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 4 optimal weight: 8.9990 chunk 190 optimal weight: 0.8980 chunk 442 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 471 optimal weight: 0.0870 chunk 485 optimal weight: 6.9990 chunk 484 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN 8 45 GLN 2 45 GLN H 116 GLN ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN A 349 GLN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN G 205 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.156104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120585 restraints weight = 58027.098| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.48 r_work: 0.3416 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 38883 Z= 0.142 Angle : 0.628 14.977 52613 Z= 0.314 Chirality : 0.044 0.297 6140 Planarity : 0.004 0.057 6703 Dihedral : 6.310 110.431 5489 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 2.51 % Allowed : 24.94 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.12), residues: 4931 helix: 1.38 (0.10), residues: 2676 sheet: -0.76 (0.21), residues: 562 loop : -0.79 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG O 113 TYR 0.037 0.001 TYR T 30 PHE 0.029 0.001 PHE L 82 TRP 0.022 0.002 TRP Q 51 HIS 0.008 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00321 (38883) covalent geometry : angle 0.62755 (52613) hydrogen bonds : bond 0.04508 ( 2256) hydrogen bonds : angle 4.58922 ( 6555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 626 time to evaluate : 1.376 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: K 87 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7982 (mm-30) REVERT: K 134 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8474 (ttm) REVERT: K 146 ARG cc_start: 0.8433 (ttm170) cc_final: 0.7781 (ttt-90) REVERT: K 150 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: K 164 MET cc_start: 0.8964 (tpp) cc_final: 0.8506 (tmm) REVERT: K 174 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7879 (tt) REVERT: L 49 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7971 (pm20) REVERT: L 87 MET cc_start: 0.8141 (mpt) cc_final: 0.7747 (mpt) REVERT: L 96 GLU cc_start: 0.4092 (pp20) cc_final: 0.3769 (pp20) REVERT: L 104 GLU cc_start: 0.8018 (pt0) cc_final: 0.7530 (pp20) REVERT: M 33 TRP cc_start: 0.8742 (m100) cc_final: 0.8075 (t60) REVERT: M 35 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8738 (mm-30) REVERT: M 130 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8088 (ttm) REVERT: M 145 ASP cc_start: 0.8861 (t0) cc_final: 0.8564 (t0) REVERT: 8 75 MET cc_start: 0.7009 (tpt) cc_final: 0.6753 (mpt) REVERT: 1 54 PHE cc_start: 0.6764 (t80) cc_final: 0.6453 (t80) REVERT: 2 69 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6824 (m-80) REVERT: 2 75 MET cc_start: 0.4641 (mmt) cc_final: 0.3915 (mpp) REVERT: 3 60 MET cc_start: 0.7729 (mmm) cc_final: 0.7518 (mmp) REVERT: 3 75 MET cc_start: 0.6471 (mmp) cc_final: 0.5395 (tpp) REVERT: 5 75 MET cc_start: 0.6015 (mpm) cc_final: 0.4596 (mtm) REVERT: H 15 GLN cc_start: 0.4644 (tp40) cc_final: 0.3575 (mt0) REVERT: H 16 MET cc_start: 0.6028 (mmm) cc_final: 0.5757 (mmp) REVERT: H 34 ARG cc_start: 0.8146 (ptm-80) cc_final: 0.7750 (mtm110) REVERT: I 32 LYS cc_start: 0.7788 (tptm) cc_final: 0.7321 (tptp) REVERT: N 30 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9198 (mp) REVERT: N 181 MET cc_start: 0.6959 (mmt) cc_final: 0.6620 (mpp) REVERT: N 209 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8574 (mp) REVERT: P 6 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7724 (tt) REVERT: P 7 LYS cc_start: 0.8717 (tptm) cc_final: 0.8322 (tptp) REVERT: R 19 GLU cc_start: 0.2384 (OUTLIER) cc_final: 0.1909 (tm-30) REVERT: R 31 MET cc_start: 0.7225 (ptt) cc_final: 0.6996 (ptt) REVERT: R 69 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.6926 (mp) REVERT: R 87 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7977 (tm-30) REVERT: S 54 LYS cc_start: 0.8907 (tppt) cc_final: 0.8616 (tppt) REVERT: S 85 TRP cc_start: 0.8306 (m100) cc_final: 0.7995 (t60) REVERT: T 36 ARG cc_start: 0.7601 (mpp80) cc_final: 0.7227 (mpp80) REVERT: T 40 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8346 (mm-30) REVERT: Q 33 TYR cc_start: 0.8408 (m-80) cc_final: 0.8141 (m-80) REVERT: C 140 ILE cc_start: 0.8487 (tt) cc_final: 0.8246 (tp) REVERT: C 195 GLU cc_start: 0.7496 (tm-30) cc_final: 0.6877 (tp30) REVERT: C 390 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.6609 (tpp) REVERT: C 477 GLN cc_start: 0.7562 (tp40) cc_final: 0.6819 (mm110) REVERT: C 484 ARG cc_start: 0.6262 (ttp80) cc_final: 0.5560 (ttm170) REVERT: A 62 MET cc_start: 0.8666 (ttm) cc_final: 0.8185 (ttt) REVERT: A 96 ASP cc_start: 0.8400 (p0) cc_final: 0.8054 (p0) REVERT: A 218 LYS cc_start: 0.7611 (tttp) cc_final: 0.7355 (tttt) REVERT: A 226 MET cc_start: 0.8953 (tpt) cc_final: 0.8393 (tpt) REVERT: A 349 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8524 (pt0) REVERT: A 351 PHE cc_start: 0.7115 (m-80) cc_final: 0.6449 (t80) REVERT: A 362 ARG cc_start: 0.7395 (mtt180) cc_final: 0.6303 (mtt180) REVERT: A 397 TYR cc_start: 0.6945 (t80) cc_final: 0.6708 (t80) REVERT: A 422 VAL cc_start: 0.6231 (p) cc_final: 0.5991 (m) REVERT: A 453 LEU cc_start: 0.8261 (mp) cc_final: 0.8040 (tp) REVERT: A 476 HIS cc_start: 0.5855 (m-70) cc_final: 0.5636 (m-70) REVERT: A 482 THR cc_start: 0.6551 (OUTLIER) cc_final: 0.6304 (t) REVERT: B 195 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: B 390 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8260 (tpt) REVERT: B 476 HIS cc_start: 0.7220 (m-70) cc_final: 0.6841 (m90) REVERT: B 477 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7567 (mm110) REVERT: E 134 GLU cc_start: 0.8186 (tt0) cc_final: 0.7766 (tt0) REVERT: E 205 GLU cc_start: 0.8764 (tt0) cc_final: 0.8165 (pt0) REVERT: E 227 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7423 (mp0) REVERT: E 361 MET cc_start: 0.7792 (mmm) cc_final: 0.7311 (tpt) REVERT: E 369 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7003 (tp30) REVERT: F 58 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8121 (mm-30) REVERT: F 202 GLU cc_start: 0.7455 (pt0) cc_final: 0.7152 (pt0) REVERT: F 217 LYS cc_start: 0.7771 (ptpp) cc_final: 0.6839 (mttp) REVERT: F 402 GLU cc_start: 0.7664 (tp30) cc_final: 0.7201 (tp30) REVERT: F 422 GLN cc_start: 0.7726 (tp40) cc_final: 0.7374 (tm-30) REVERT: G 64 LYS cc_start: 0.8428 (mppt) cc_final: 0.7126 (tttt) REVERT: G 123 GLN cc_start: 0.6499 (pt0) cc_final: 0.6228 (pm20) REVERT: G 130 GLU cc_start: 0.8066 (tp30) cc_final: 0.6430 (tm-30) REVERT: G 260 LYS cc_start: 0.8157 (tttt) cc_final: 0.7776 (tttp) REVERT: O 33 GLU cc_start: 0.7019 (pt0) cc_final: 0.6572 (mp0) REVERT: O 37 LYS cc_start: 0.7194 (tttt) cc_final: 0.6433 (tppt) REVERT: O 162 MET cc_start: 0.6962 (ptt) cc_final: 0.6591 (pmt) REVERT: O 173 MET cc_start: 0.7495 (mtm) cc_final: 0.6765 (mtm) REVERT: D 59 SER cc_start: 0.8589 (m) cc_final: 0.8209 (p) REVERT: D 64 ILE cc_start: 0.8229 (mt) cc_final: 0.7985 (mm) REVERT: D 180 HIS cc_start: 0.7203 (t-90) cc_final: 0.6617 (t-90) REVERT: D 202 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7295 (tm-30) REVERT: D 248 ASP cc_start: 0.7329 (m-30) cc_final: 0.6982 (m-30) REVERT: D 458 GLN cc_start: 0.5160 (mt0) cc_final: 0.4955 (tp40) outliers start: 101 outliers final: 57 residues processed: 690 average time/residue: 0.6830 time to fit residues: 575.3658 Evaluate side-chains 680 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 605 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 1 residue 57 SER Chi-restraints excluded: chain 1 residue 65 LEU Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 65 LEU Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 209 ILE Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain S residue 91 ILE Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 435 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 465 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 426 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 410 optimal weight: 10.0000 chunk 434 optimal weight: 5.9990 chunk 345 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 390 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN M 123 ASN 8 45 GLN 2 45 GLN H 116 GLN ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 163 ASN R 44 GLN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN G 205 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.155051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119501 restraints weight = 57621.747| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.47 r_work: 0.3402 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 38883 Z= 0.167 Angle : 0.667 15.134 52613 Z= 0.331 Chirality : 0.045 0.272 6140 Planarity : 0.004 0.064 6703 Dihedral : 6.332 109.555 5489 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.02 % Favored : 96.94 % Rotamer: Outliers : 2.33 % Allowed : 25.51 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.12), residues: 4931 helix: 1.33 (0.10), residues: 2674 sheet: -0.81 (0.21), residues: 565 loop : -0.80 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG O 113 TYR 0.039 0.002 TYR Q 47 PHE 0.031 0.001 PHE S 29 TRP 0.027 0.002 TRP Q 51 HIS 0.006 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00387 (38883) covalent geometry : angle 0.66742 (52613) hydrogen bonds : bond 0.04675 ( 2256) hydrogen bonds : angle 4.64516 ( 6555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 614 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 87 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8008 (mm-30) REVERT: K 134 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8481 (ttm) REVERT: K 146 ARG cc_start: 0.8423 (ttm170) cc_final: 0.7784 (ttt-90) REVERT: K 150 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: K 164 MET cc_start: 0.8935 (tpp) cc_final: 0.8494 (tmm) REVERT: K 174 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7867 (tt) REVERT: K 180 HIS cc_start: 0.8519 (t70) cc_final: 0.8196 (t-90) REVERT: L 49 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: L 87 MET cc_start: 0.8149 (mpt) cc_final: 0.7770 (mpt) REVERT: L 96 GLU cc_start: 0.4124 (pp20) cc_final: 0.3786 (pp20) REVERT: L 104 GLU cc_start: 0.8031 (pt0) cc_final: 0.7568 (pp20) REVERT: M 33 TRP cc_start: 0.8753 (m100) cc_final: 0.8097 (t60) REVERT: M 35 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8729 (mm-30) REVERT: M 40 ARG cc_start: 0.8177 (mmm-85) cc_final: 0.7896 (mmm-85) REVERT: M 130 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8176 (ttm) REVERT: M 145 ASP cc_start: 0.8881 (t0) cc_final: 0.8592 (t0) REVERT: 8 75 MET cc_start: 0.7047 (tpt) cc_final: 0.6817 (mpt) REVERT: 2 60 MET cc_start: 0.6413 (mmm) cc_final: 0.6038 (mtm) REVERT: 2 69 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6817 (m-80) REVERT: 2 75 MET cc_start: 0.4678 (mmt) cc_final: 0.3959 (mpp) REVERT: 3 75 MET cc_start: 0.6519 (mmp) cc_final: 0.5276 (tpp) REVERT: 5 75 MET cc_start: 0.6064 (mpm) cc_final: 0.4679 (mtm) REVERT: H 15 GLN cc_start: 0.4638 (tp40) cc_final: 0.3570 (mt0) REVERT: H 16 MET cc_start: 0.6123 (mmm) cc_final: 0.5814 (mmp) REVERT: H 34 ARG cc_start: 0.8109 (ptm-80) cc_final: 0.7733 (mtm110) REVERT: I 32 LYS cc_start: 0.7807 (tptm) cc_final: 0.7342 (tptp) REVERT: N 30 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9192 (mp) REVERT: N 181 MET cc_start: 0.7001 (mmt) cc_final: 0.6748 (mpp) REVERT: P 6 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7723 (tt) REVERT: P 7 LYS cc_start: 0.8668 (tptm) cc_final: 0.8308 (tptp) REVERT: R 19 GLU cc_start: 0.2232 (OUTLIER) cc_final: 0.1886 (tm-30) REVERT: R 69 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.6954 (mp) REVERT: R 87 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7961 (tm-30) REVERT: S 54 LYS cc_start: 0.8931 (tppt) cc_final: 0.8635 (tppt) REVERT: S 85 TRP cc_start: 0.8337 (m100) cc_final: 0.8032 (t60) REVERT: S 90 GLU cc_start: 0.8632 (pp20) cc_final: 0.8402 (pp20) REVERT: T 36 ARG cc_start: 0.7573 (mpp80) cc_final: 0.7205 (mpp80) REVERT: T 40 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8360 (mm-30) REVERT: Q 51 TRP cc_start: 0.7592 (p-90) cc_final: 0.6470 (p-90) REVERT: C 140 ILE cc_start: 0.8487 (tt) cc_final: 0.8252 (tp) REVERT: C 195 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6880 (tp30) REVERT: C 390 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.6593 (tpp) REVERT: C 484 ARG cc_start: 0.6263 (ttp80) cc_final: 0.5561 (ttm170) REVERT: A 96 ASP cc_start: 0.8421 (p0) cc_final: 0.8100 (p0) REVERT: A 218 LYS cc_start: 0.7586 (tttp) cc_final: 0.7293 (tttt) REVERT: A 226 MET cc_start: 0.8959 (tpt) cc_final: 0.8365 (tpt) REVERT: A 351 PHE cc_start: 0.7244 (m-80) cc_final: 0.6670 (t80) REVERT: A 362 ARG cc_start: 0.7485 (mtt180) cc_final: 0.6462 (mtt90) REVERT: A 397 TYR cc_start: 0.6976 (t80) cc_final: 0.6775 (t80) REVERT: A 422 VAL cc_start: 0.6297 (p) cc_final: 0.6046 (m) REVERT: A 482 THR cc_start: 0.6543 (OUTLIER) cc_final: 0.6293 (t) REVERT: B 195 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: B 390 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8208 (tpt) REVERT: B 476 HIS cc_start: 0.7375 (m-70) cc_final: 0.7013 (m90) REVERT: B 477 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7628 (mm110) REVERT: B 491 GLU cc_start: 0.7108 (pm20) cc_final: 0.6764 (tm-30) REVERT: E 134 GLU cc_start: 0.8193 (tt0) cc_final: 0.7776 (tt0) REVERT: E 205 GLU cc_start: 0.8765 (tt0) cc_final: 0.8168 (pt0) REVERT: E 227 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7460 (mp0) REVERT: E 361 MET cc_start: 0.7829 (mmm) cc_final: 0.7417 (tpt) REVERT: E 369 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6990 (tp30) REVERT: E 375 ARG cc_start: 0.7913 (mmp-170) cc_final: 0.7615 (mmm160) REVERT: F 45 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7929 (mm-30) REVERT: F 202 GLU cc_start: 0.7508 (pt0) cc_final: 0.7209 (pt0) REVERT: F 217 LYS cc_start: 0.7824 (ptpp) cc_final: 0.6909 (mttp) REVERT: F 402 GLU cc_start: 0.7557 (tp30) cc_final: 0.7178 (tp30) REVERT: F 422 GLN cc_start: 0.7749 (tp40) cc_final: 0.7388 (tm-30) REVERT: F 476 LEU cc_start: 0.7229 (mp) cc_final: 0.6931 (pp) REVERT: G 64 LYS cc_start: 0.8392 (mppt) cc_final: 0.7112 (tttt) REVERT: G 123 GLN cc_start: 0.6588 (pt0) cc_final: 0.6281 (pm20) REVERT: G 130 GLU cc_start: 0.8074 (tp30) cc_final: 0.6504 (tm-30) REVERT: G 260 LYS cc_start: 0.8177 (tttt) cc_final: 0.7796 (tttp) REVERT: O 33 GLU cc_start: 0.6981 (pt0) cc_final: 0.6569 (mp0) REVERT: O 37 LYS cc_start: 0.7176 (tttt) cc_final: 0.6464 (tppt) REVERT: O 162 MET cc_start: 0.6959 (ptt) cc_final: 0.6575 (pmt) REVERT: O 173 MET cc_start: 0.7503 (mtm) cc_final: 0.6777 (mtm) REVERT: D 59 SER cc_start: 0.8594 (m) cc_final: 0.8215 (p) REVERT: D 64 ILE cc_start: 0.8258 (mt) cc_final: 0.8012 (mm) REVERT: D 180 HIS cc_start: 0.7242 (t-90) cc_final: 0.6625 (t-90) REVERT: D 259 ASP cc_start: 0.8347 (t0) cc_final: 0.8045 (t70) REVERT: D 342 ILE cc_start: 0.7701 (mt) cc_final: 0.7354 (tt) outliers start: 94 outliers final: 63 residues processed: 671 average time/residue: 0.6723 time to fit residues: 547.8040 Evaluate side-chains 675 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 595 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 88 GLN Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 1 residue 57 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 69 PHE Chi-restraints excluded: chain 2 residue 71 ILE Chi-restraints excluded: chain 3 residue 15 THR Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 65 LEU Chi-restraints excluded: chain 4 residue 71 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain S residue 91 ILE Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 435 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 80 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 371 optimal weight: 1.9990 chunk 386 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN 8 45 GLN H 111 ASN H 116 GLN ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 163 ASN R 44 GLN A 349 GLN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN E 378 GLN G 205 GLN D 458 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.155149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.119506 restraints weight = 57864.716| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.50 r_work: 0.3399 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.386 38883 Z= 0.259 Angle : 0.788 65.853 52613 Z= 0.429 Chirality : 0.045 0.577 6140 Planarity : 0.006 0.290 6703 Dihedral : 6.325 109.539 5489 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer: Outliers : 2.21 % Allowed : 25.88 % Favored : 71.91 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.12), residues: 4931 helix: 1.33 (0.10), residues: 2674 sheet: -0.81 (0.21), residues: 565 loop : -0.80 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 113 TYR 0.034 0.001 TYR T 30 PHE 0.022 0.001 PHE S 29 TRP 0.024 0.002 TRP Q 51 HIS 0.006 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00544 (38883) covalent geometry : angle 0.78758 (52613) hydrogen bonds : bond 0.04701 ( 2256) hydrogen bonds : angle 4.64673 ( 6555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20531.17 seconds wall clock time: 348 minutes 6.94 seconds (20886.94 seconds total)