Starting phenix.real_space_refine on Wed Oct 28 11:42:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ybs_10772/10_2026/6ybs_10772.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ybs_10772/10_2026/6ybs_10772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ybs_10772/10_2026/6ybs_10772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ybs_10772/10_2026/6ybs_10772.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ybs_10772/10_2026/6ybs_10772.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ybs_10772/10_2026/6ybs_10772.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ybs_10772/10_2026/6ybs_10772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ybs_10772/10_2026/6ybs_10772.map" } resolution = 3.1 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 501 5.49 5 Mg 29 5.21 5 S 85 5.16 5 C 16104 2.51 5 N 5248 2.21 5 O 6764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28732 Number of models: 1 Model: "" Number of chains: 21 Chain: "x" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2317 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PTRANS': 13, 'TRANS': 346} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 633 Unresolved non-hydrogen angles: 806 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 13, 'ASP:plan': 17, 'PHE:plan': 9, 'GLN:plan1': 5, 'ARG:plan': 14, 'TYR:plan': 7, 'HIS:plan': 1, 'ASN:plan1': 8} Unresolved non-hydrogen planarities: 352 Chain: "c" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "n" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 498 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "X" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 641 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "h" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 817 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "o" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "a" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 834 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 8, 'TRANS': 90} Chain: "m" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "i" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 419 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "b" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 913 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "Z" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "d" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1105 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 4, 'TRANS': 137} Chain: "e" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "f" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1176 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 3, 'TRANS': 138} Chain: "V" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1461 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 1 Chain: "k" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 435 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain breaks: 1 Chain: "Y" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1124 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "A" Number of atoms: 10672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 10672 Classifications: {'RNA': 3, 'RNAv2': 498} Modifications used: {'rna2p_pur': 45, 'rna2p_pyr': 44, 'rna3p': 3, 'rna3p_pur': 206, 'rna3p_pyr': 202} Link IDs: {'rna2p': 88, 'rna3p': 412} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Unusual residues: {' MG': 28} Classifications: {'undetermined': 28} Link IDs: {None: 27} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16675 SG CYS k 121 93.746 165.640 39.991 1.00104.69 S ATOM 16711 SG CYS k 126 90.181 164.946 40.787 1.00109.17 S ATOM 16829 SG CYS k 141 93.957 165.708 43.630 1.00 95.97 S ATOM 16848 SG CYS k 144 94.487 162.654 41.866 1.00 99.65 S Time building chain proxies: 5.62, per 1000 atoms: 0.20 Number of scatterers: 28732 At special positions: 0 Unit cell: (148.212, 207.282, 131.028, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 85 16.00 P 501 15.00 Mg 29 11.99 O 6764 8.00 N 5248 7.00 C 16104 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: 2.47 Conformation dependent library (CDL) restraints added in 804.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN k 201 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 121 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 141 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 144 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 126 " Number of angles added : 6 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4342 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 27 sheets defined 35.8% alpha, 18.2% beta 142 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'x' and resid 177 through 182 removed outlier: 3.700A pdb=" N LYS x 182 " --> pdb=" O PRO x 178 " (cutoff:3.500A) Processing helix chain 'x' and resid 204 through 209 Processing helix chain 'x' and resid 233 through 238 Processing helix chain 'x' and resid 309 through 324 Processing helix chain 'x' and resid 325 through 327 No H-bonds generated for 'chain 'x' and resid 325 through 327' Processing helix chain 'x' and resid 409 through 414 removed outlier: 3.668A pdb=" N LYS x 413 " --> pdb=" O ASP x 409 " (cutoff:3.500A) Processing helix chain 'x' and resid 417 through 429 removed outlier: 3.550A pdb=" N VAL x 421 " --> pdb=" O GLN x 417 " (cutoff:3.500A) Processing helix chain 'x' and resid 430 through 443 removed outlier: 3.677A pdb=" N CYS x 439 " --> pdb=" O ARG x 435 " (cutoff:3.500A) Processing helix chain 'x' and resid 475 through 480 Processing helix chain 'x' and resid 484 through 499 Processing helix chain 'X' and resid 6 through 21 Processing helix chain 'X' and resid 22 through 24 No H-bonds generated for 'chain 'X' and resid 22 through 24' Processing helix chain 'X' and resid 27 through 38 Processing helix chain 'X' and resid 44 through 62 removed outlier: 3.702A pdb=" N ARG X 60 " --> pdb=" O HIS X 56 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN X 62 " --> pdb=" O MET X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 71 through 75 Processing helix chain 'h' and resid 28 through 46 removed outlier: 3.690A pdb=" N LEU h 32 " --> pdb=" O ASN h 28 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS h 46 " --> pdb=" O GLY h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 102 removed outlier: 3.568A pdb=" N VAL h 98 " --> pdb=" O PRO h 94 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN h 100 " --> pdb=" O GLU h 96 " (cutoff:3.500A) Processing helix chain 'o' and resid 251 through 260 removed outlier: 3.658A pdb=" N LEU o 255 " --> pdb=" O ARG o 251 " (cutoff:3.500A) Processing helix chain 'o' and resid 261 through 263 No H-bonds generated for 'chain 'o' and resid 261 through 263' Processing helix chain 'o' and resid 291 through 297 Processing helix chain 'a' and resid 4 through 19 Processing helix chain 'a' and resid 35 through 39 Processing helix chain 'a' and resid 41 through 54 Processing helix chain 'a' and resid 72 through 83 removed outlier: 3.867A pdb=" N GLN a 77 " --> pdb=" O ASN a 73 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 28 Processing helix chain 'm' and resid 35 through 44 Processing helix chain 'm' and resid 58 through 73 removed outlier: 3.966A pdb=" N VAL m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS m 72 " --> pdb=" O LEU m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 81 through 90 Processing helix chain 'm' and resid 120 through 132 removed outlier: 4.343A pdb=" N ILE m 124 " --> pdb=" O ALA m 120 " (cutoff:3.500A) Processing helix chain 'i' and resid 32 through 36 Processing helix chain 'i' and resid 40 through 51 removed outlier: 5.952A pdb=" N LYS i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASP i 49 " --> pdb=" O GLN i 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 28 Processing helix chain 'b' and resid 29 through 35 removed outlier: 3.925A pdb=" N GLN b 35 " --> pdb=" O GLU b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 47 Processing helix chain 'b' and resid 50 through 65 Processing helix chain 'b' and resid 108 through 112 removed outlier: 3.805A pdb=" N ILE b 112 " --> pdb=" O PRO b 109 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 120 Processing helix chain 'Z' and resid 6 through 29 Processing helix chain 'Z' and resid 30 through 32 No H-bonds generated for 'chain 'Z' and resid 30 through 32' Processing helix chain 'Z' and resid 54 through 60 removed outlier: 3.590A pdb=" N VAL Z 58 " --> pdb=" O ARG Z 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 78 Processing helix chain 'Z' and resid 97 through 111 Processing helix chain 'Z' and resid 114 through 129 Processing helix chain 'Z' and resid 162 through 166 Processing helix chain 'd' and resid 5 through 9 removed outlier: 3.850A pdb=" N VAL d 9 " --> pdb=" O VAL d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 10 through 25 removed outlier: 3.933A pdb=" N ARG d 16 " --> pdb=" O GLN d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 33 through 37 removed outlier: 4.012A pdb=" N VAL d 37 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 66 removed outlier: 3.786A pdb=" N THR d 55 " --> pdb=" O ASN d 51 " (cutoff:3.500A) Processing helix chain 'd' and resid 71 through 79 Processing helix chain 'd' and resid 96 through 110 removed outlier: 3.665A pdb=" N ALA d 100 " --> pdb=" O SER d 96 " (cutoff:3.500A) Processing helix chain 'd' and resid 124 through 143 removed outlier: 3.630A pdb=" N LYS d 143 " --> pdb=" O ALA d 139 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 62 removed outlier: 3.579A pdb=" N VAL e 62 " --> pdb=" O LEU e 58 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 65 No H-bonds generated for 'chain 'e' and resid 63 through 65' Processing helix chain 'e' and resid 72 through 77 Processing helix chain 'e' and resid 80 through 95 Processing helix chain 'f' and resid 25 through 30 removed outlier: 3.612A pdb=" N ILE f 30 " --> pdb=" O ILE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 33 No H-bonds generated for 'chain 'f' and resid 31 through 33' Processing helix chain 'f' and resid 37 through 48 Processing helix chain 'f' and resid 55 through 59 Processing helix chain 'f' and resid 60 through 73 Processing helix chain 'f' and resid 74 through 78 Processing helix chain 'f' and resid 80 through 84 Processing helix chain 'f' and resid 101 through 117 removed outlier: 3.507A pdb=" N ILE f 117 " --> pdb=" O ARG f 113 " (cutoff:3.500A) Processing helix chain 'f' and resid 119 through 128 Processing helix chain 'V' and resid 18 through 22 Processing helix chain 'V' and resid 61 through 66 removed outlier: 3.637A pdb=" N CYS V 66 " --> pdb=" O LYS V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 75 Processing helix chain 'V' and resid 85 through 104 removed outlier: 3.657A pdb=" N THR V 89 " --> pdb=" O LYS V 85 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 120 Processing helix chain 'V' and resid 142 through 162 Processing helix chain 'V' and resid 168 through 183 Processing helix chain 'V' and resid 187 through 203 removed outlier: 3.707A pdb=" N LYS V 191 " --> pdb=" O SER V 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 42 No H-bonds generated for 'chain 'Y' and resid 40 through 42' Processing helix chain 'Y' and resid 44 through 46 No H-bonds generated for 'chain 'Y' and resid 44 through 46' Processing helix chain 'Y' and resid 47 through 59 removed outlier: 4.013A pdb=" N LEU Y 51 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) Proline residue: Y 54 - end of helix Processing helix chain 'Y' and resid 76 through 100 Processing helix chain 'Y' and resid 101 through 116 removed outlier: 3.699A pdb=" N LYS Y 105 " --> pdb=" O ASP Y 101 " (cutoff:3.500A) Processing helix chain 'Y' and resid 117 through 120 Processing sheet with id=AA1, first strand: chain 'x' and resid 170 through 176 removed outlier: 5.696A pdb=" N VAL x 171 " --> pdb=" O SER x 522 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N SER x 522 " --> pdb=" O VAL x 171 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU x 173 " --> pdb=" O VAL x 520 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE x 278 " --> pdb=" O GLN x 271 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL x 246 " --> pdb=" O ILE x 373 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N ARG x 375 " --> pdb=" O VAL x 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'x' and resid 392 through 396 removed outlier: 6.204A pdb=" N ASN x 393 " --> pdb=" O LYS x 449 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLY x 451 " --> pdb=" O ASN x 393 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS x 395 " --> pdb=" O GLY x 451 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL x 453 " --> pdb=" O LYS x 395 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU x 448 " --> pdb=" O GLN x 471 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN x 471 " --> pdb=" O LEU x 448 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU x 450 " --> pdb=" O THR x 469 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR x 469 " --> pdb=" O LEU x 450 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR x 452 " --> pdb=" O LEU x 467 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 5 through 7 removed outlier: 4.051A pdb=" N SER c 288 " --> pdb=" O GLY c 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 18 through 22 removed outlier: 6.158A pdb=" N LYS c 44 " --> pdb=" O PRO c 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 66 through 71 removed outlier: 6.179A pdb=" N LEU c 87 " --> pdb=" O ARG c 100 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG c 100 " --> pdb=" O LEU c 87 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU c 89 " --> pdb=" O THR c 98 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR c 96 " --> pdb=" O ASP c 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 108 through 113 removed outlier: 3.589A pdb=" N LYS c 130 " --> pdb=" O SER c 122 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE c 129 " --> pdb=" O VAL c 142 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR c 140 " --> pdb=" O LEU c 131 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN c 133 " --> pdb=" O CYS c 138 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N CYS c 138 " --> pdb=" O ASN c 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 151 through 155 removed outlier: 5.587A pdb=" N ASN c 178 " --> pdb=" O LEU c 184 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU c 184 " --> pdb=" O ASN c 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 195 through 200 removed outlier: 3.582A pdb=" N THR c 197 " --> pdb=" O GLY c 210 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY c 211 " --> pdb=" O GLN c 215 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN c 215 " --> pdb=" O GLY c 211 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR c 228 " --> pdb=" O LEU c 218 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP c 220 " --> pdb=" O HIS c 226 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N HIS c 226 " --> pdb=" O ASP c 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 236 through 241 removed outlier: 4.194A pdb=" N ALA c 238 " --> pdb=" O ALA c 251 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP c 268 " --> pdb=" O ILE c 258 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP c 260 " --> pdb=" O ILE c 266 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE c 266 " --> pdb=" O ASP c 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'n' and resid 55 through 58 removed outlier: 7.020A pdb=" N ARG n 31 " --> pdb=" O THR n 15 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL n 17 " --> pdb=" O GLN n 29 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLN n 29 " --> pdb=" O VAL n 17 " (cutoff:3.500A) removed outlier: 12.276A pdb=" N ALA V 138 " --> pdb=" O ILE n 43 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN n 45 " --> pdb=" O ALA V 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'X' and resid 39 through 40 removed outlier: 3.759A pdb=" N SER Z 209 " --> pdb=" O ILE X 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 51 through 55 removed outlier: 6.066A pdb=" N LEU h 88 " --> pdb=" O PRO h 53 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ARG h 55 " --> pdb=" O LYS h 86 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS h 86 " --> pdb=" O ARG h 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 51 through 55 removed outlier: 6.066A pdb=" N LEU h 88 " --> pdb=" O PRO h 53 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ARG h 55 " --> pdb=" O LYS h 86 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS h 86 " --> pdb=" O ARG h 55 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'o' and resid 267 through 273 removed outlier: 6.752A pdb=" N ARG o 267 " --> pdb=" O PHE o 284 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE o 284 " --> pdb=" O ARG o 267 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N TYR o 269 " --> pdb=" O PHE o 282 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N PHE o 282 " --> pdb=" O TYR o 269 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ALA o 271 " --> pdb=" O LYS o 280 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLN o 278 " --> pdb=" O ASP o 273 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'o' and resid 302 through 305 removed outlier: 4.290A pdb=" N GLY o 304 " --> pdb=" O LEU o 308 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU o 308 " --> pdb=" O GLY o 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'a' and resid 20 through 24 Processing sheet with id=AB8, first strand: chain 'm' and resid 31 through 33 removed outlier: 3.957A pdb=" N LEU m 49 " --> pdb=" O VAL m 111 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE m 77 " --> pdb=" O CYS m 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU m 52 " --> pdb=" O ILE m 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'i' and resid 30 through 31 Processing sheet with id=AC1, first strand: chain 'b' and resid 76 through 78 removed outlier: 6.240A pdb=" N VAL b 76 " --> pdb=" O GLY b 95 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TYR b 97 " --> pdb=" O VAL b 76 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR b 78 " --> pdb=" O TYR b 97 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Z' and resid 34 through 41 removed outlier: 6.757A pdb=" N LEU Z 51 " --> pdb=" O SER Z 35 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL Z 37 " --> pdb=" O ILE Z 49 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE Z 49 " --> pdb=" O VAL Z 37 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL Z 39 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU Z 47 " --> pdb=" O VAL Z 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Z' and resid 148 through 155 removed outlier: 3.660A pdb=" N GLY Z 133 " --> pdb=" O MET Z 189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 81 through 85 removed outlier: 4.411A pdb=" N ASN d 85 " --> pdb=" O PRO d 89 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'd' and resid 113 through 115 Processing sheet with id=AC6, first strand: chain 'e' and resid 99 through 102 removed outlier: 6.727A pdb=" N ILE e 108 " --> pdb=" O VAL e 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'f' and resid 12 through 13 Processing sheet with id=AC8, first strand: chain 'k' and resid 119 through 120 removed outlier: 4.526A pdb=" N ARG k 119 " --> pdb=" O MET k 132 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 9 through 16 removed outlier: 3.522A pdb=" N LYS Y 16 " --> pdb=" O ALA Y 19 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU Y 31 " --> pdb=" O ILE Y 68 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL Y 70 " --> pdb=" O LEU Y 31 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS Y 33 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL Y 72 " --> pdb=" O LYS Y 33 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 2070 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 570 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 8.75 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5421 1.33 - 1.45: 9596 1.45 - 1.57: 14104 1.57 - 1.69: 1002 1.69 - 1.82: 127 Bond restraints: 30250 Sorted by residual: bond pdb=" P A2M A1678 " pdb=" O5' A2M A1678 " ideal model delta sigma weight residual 1.722 1.607 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C4 JMH A1219 " pdb=" C5 JMH A1219 " ideal model delta sigma weight residual 1.442 1.373 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O5' A2M A1678 " pdb=" C5' A2M A1678 " ideal model delta sigma weight residual 1.388 1.448 -0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" C VAL e 62 " pdb=" N PRO e 63 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.46e+00 bond pdb=" CB GLU o 313 " pdb=" CG GLU o 313 " ideal model delta sigma weight residual 1.520 1.582 -0.062 3.00e-02 1.11e+03 4.26e+00 ... (remaining 30245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 42090 3.22 - 6.44: 1096 6.44 - 9.66: 63 9.66 - 12.89: 6 12.89 - 16.11: 3 Bond angle restraints: 43258 Sorted by residual: angle pdb=" C3' G A1600 " pdb=" O3' G A1600 " pdb=" P A A1601 " ideal model delta sigma weight residual 119.70 128.82 -9.12 1.20e+00 6.94e-01 5.77e+01 angle pdb=" CG1 ILE x 481 " pdb=" CB ILE x 481 " pdb=" CG2 ILE x 481 " ideal model delta sigma weight residual 110.70 94.59 16.11 3.00e+00 1.11e-01 2.88e+01 angle pdb=" CG1 ILE c 189 " pdb=" CB ILE c 189 " pdb=" CG2 ILE c 189 " ideal model delta sigma weight residual 110.70 96.47 14.23 3.00e+00 1.11e-01 2.25e+01 angle pdb=" C3' C A1434 " pdb=" O3' C A1434 " pdb=" P C A1435 " ideal model delta sigma weight residual 119.70 125.27 -5.57 1.20e+00 6.94e-01 2.15e+01 angle pdb=" C LYS V 42 " pdb=" N GLU V 43 " pdb=" CA GLU V 43 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 ... (remaining 43253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 15228 25.61 - 51.22: 1439 51.22 - 76.83: 549 76.83 - 102.44: 11 102.44 - 128.05: 1 Dihedral angle restraints: 17228 sinusoidal: 10506 harmonic: 6722 Sorted by residual: dihedral pdb=" C4' A A1344 " pdb=" C3' A A1344 " pdb=" C2' A A1344 " pdb=" C1' A A1344 " ideal model delta sinusoidal sigma weight residual 36.35 -40.37 76.72 1 3.10e+00 1.04e-01 7.69e+02 dihedral pdb=" C4' G A1648 " pdb=" C3' G A1648 " pdb=" C2' G A1648 " pdb=" C1' G A1648 " ideal model delta sinusoidal sigma weight residual 36.35 -38.76 75.11 1 3.10e+00 1.04e-01 7.42e+02 dihedral pdb=" C4' G A1302 " pdb=" C3' G A1302 " pdb=" C2' G A1302 " pdb=" C1' G A1302 " ideal model delta sinusoidal sigma weight residual 36.34 -38.40 74.75 1 3.10e+00 1.04e-01 7.36e+02 ... (remaining 17225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4056 0.085 - 0.171: 525 0.171 - 0.256: 511 0.256 - 0.342: 174 0.342 - 0.427: 12 Chirality restraints: 5278 Sorted by residual: chirality pdb=" P C A1435 " pdb=" OP1 C A1435 " pdb=" OP2 C A1435 " pdb=" O5' C A1435 " both_signs ideal model delta sigma weight residual True 2.17 -2.60 -0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" C3' U A1242 " pdb=" C4' U A1242 " pdb=" O3' U A1242 " pdb=" C2' U A1242 " both_signs ideal model delta sigma weight residual False -2.50 -2.89 0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C2' C A1521 " pdb=" C3' C A1521 " pdb=" O2' C A1521 " pdb=" C1' C A1521 " both_signs ideal model delta sigma weight residual False -2.79 -2.40 -0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 5275 not shown) Planarity restraints: 3667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' JMH A1219 " -0.108 2.00e-02 2.50e+03 8.87e-02 1.97e+02 pdb=" N1 JMH A1219 " 0.023 2.00e-02 2.50e+03 pdb=" C2 JMH A1219 " -0.006 2.00e-02 2.50e+03 pdb=" O2 JMH A1219 " -0.047 2.00e-02 2.50e+03 pdb=" N3 JMH A1219 " 0.030 2.00e-02 2.50e+03 pdb=" C4 JMH A1219 " -0.037 2.00e-02 2.50e+03 pdb=" N4 JMH A1219 " -0.166 2.00e-02 2.50e+03 pdb=" C5 JMH A1219 " 0.064 2.00e-02 2.50e+03 pdb=" C6 JMH A1219 " 0.125 2.00e-02 2.50e+03 pdb=" C31 JMH A1219 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU f 103 " 0.021 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C LEU f 103 " -0.072 2.00e-02 2.50e+03 pdb=" O LEU f 103 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP f 104 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU Z 218 " 0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO Z 219 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO Z 219 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO Z 219 " 0.050 5.00e-02 4.00e+02 ... (remaining 3664 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 501 2.61 - 3.19: 21919 3.19 - 3.76: 50069 3.76 - 4.33: 69138 4.33 - 4.90: 103006 Nonbonded interactions: 244633 Sorted by model distance: nonbonded pdb=" O6 G A1517 " pdb="MG MG A1909 " model vdw 2.044 2.170 nonbonded pdb=" O6 G A1387 " pdb="MG MG A1918 " model vdw 2.050 2.170 nonbonded pdb=" OP2 G A1385 " pdb="MG MG A1918 " model vdw 2.053 2.170 nonbonded pdb=" OP2 C A1262 " pdb="MG MG A1909 " model vdw 2.061 2.170 nonbonded pdb=" OP2 A A1217 " pdb="MG MG A1901 " model vdw 2.071 2.170 ... (remaining 244628 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 12.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 34.050 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 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 : 0.007 0.399 30254 Z= 0.322 Angle : 1.157 29.256 43264 Z= 0.534 Chirality : 0.100 0.427 5278 Planarity : 0.007 0.091 3667 Dihedral : 19.674 128.047 12886 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.92 % Allowed : 17.10 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.15), residues: 2292 helix: -0.96 (0.17), residues: 723 sheet: -1.56 (0.23), residues: 428 loop : -2.25 (0.15), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG V 71 TYR 0.034 0.002 TYR Z 107 PHE 0.032 0.003 PHE m 128 TRP 0.025 0.002 TRP i 8 HIS 0.016 0.001 HIS o 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.30 (30250) covalent geometry : angle 1.12891 / 0.53 (43258) hydrogen bonds : bond 0.12978 / 9.45 ( 1090) hydrogen bonds : angle 5.53628 / 3.93 ( 2640) metal coordination : bond 0.26831 / 13.12 ( 4) metal coordination : angle 21.49834 / 11.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 552 time to evaluate : 0.828 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: x 391 PHE cc_start: 0.4619 (m-80) cc_final: 0.4093 (m-10) REVERT: x 418 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7723 (ttm-80) REVERT: x 446 GLU cc_start: 0.8293 (tp30) cc_final: 0.7817 (tp30) REVERT: c 291 TRP cc_start: 0.8488 (m100) cc_final: 0.8158 (m100) REVERT: c 302 TYR cc_start: 0.9125 (m-80) cc_final: 0.8674 (m-80) REVERT: n 31 ARG cc_start: 0.8233 (ptm160) cc_final: 0.7762 (ttp80) REVERT: n 60 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7865 (tm-30) REVERT: h 19 ARG cc_start: 0.7516 (mtp180) cc_final: 0.7107 (mpt90) REVERT: a 53 LYS cc_start: 0.9262 (tmmt) cc_final: 0.9059 (ttpp) REVERT: a 73 ASN cc_start: 0.9030 (m-40) cc_final: 0.8806 (m-40) REVERT: m 71 GLU cc_start: 0.8341 (tt0) cc_final: 0.7862 (tt0) REVERT: i 54 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8752 (ttmt) REVERT: b 58 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8456 (mttp) REVERT: b 62 LYS cc_start: 0.9164 (tttm) cc_final: 0.8314 (tttm) REVERT: b 64 LYS cc_start: 0.8453 (tttt) cc_final: 0.8105 (ttpp) REVERT: b 82 ASP cc_start: 0.8170 (p0) cc_final: 0.7913 (p0) REVERT: Z 40 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7780 (ttp-170) REVERT: Z 193 ASP cc_start: 0.8049 (p0) cc_final: 0.7835 (p0) REVERT: d 29 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7468 (tptt) REVERT: e 66 LYS cc_start: 0.8939 (mttt) cc_final: 0.7725 (mmpt) REVERT: e 94 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8415 (mtmm) REVERT: f 83 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8129 (t80) REVERT: V 36 GLN cc_start: 0.8150 (tp-100) cc_final: 0.7876 (tp40) REVERT: V 65 GLN cc_start: 0.8462 (mp10) cc_final: 0.8261 (mm-40) REVERT: V 194 ASP cc_start: 0.7949 (m-30) cc_final: 0.7665 (m-30) REVERT: k 107 LYS cc_start: 0.6524 (pttt) cc_final: 0.5755 (ptmt) REVERT: k 114 ILE cc_start: 0.7073 (mp) cc_final: 0.6830 (mp) REVERT: k 144 CYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8266 (p) REVERT: Y 106 LYS cc_start: 0.8135 (tttt) cc_final: 0.7887 (ttpp) outliers start: 54 outliers final: 38 residues processed: 593 average time/residue: 0.1975 time to fit residues: 180.2185 Evaluate side-chains 541 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 501 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 369 ASP Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 467 LEU Chi-restraints excluded: chain x residue 472 PHE Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 72 SER Chi-restraints excluded: chain c residue 107 ASP Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 275 ILE Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 286 SER Chi-restraints excluded: chain a residue 51 SER Chi-restraints excluded: chain m residue 15 ASN Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 123 VAL Chi-restraints excluded: chain m residue 132 LYS Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 144 CYS Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 129 SER Chi-restraints excluded: chain Y residue 143 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.0570 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 305 ASN x 312 ASN x 327 GLN x 406 ASN x 429 ASN c 162 ASN X 31 ASN X 62 GLN h 92 HIS m 46 GLN i 16 GLN i 26 ASN i 45 GLN b 32 GLN b 41 GLN b 103 ASN Z 145 GLN d 85 ASN e 46 ASN e 106 GLN f 72 GLN f 76 GLN f 105 ASN V 31 ASN V 36 GLN V 82 ASN V 148 ASN V 165 ASN V 179 ASN V 203 ASN Y 11 GLN Y 35 ASN Y 86 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.120644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.085783 restraints weight = 47347.639| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.63 r_work: 0.2832 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30254 Z= 0.206 Angle : 1.105 18.652 43264 Z= 0.455 Chirality : 0.095 1.190 5278 Planarity : 0.005 0.070 3667 Dihedral : 17.857 162.225 8652 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.87 % Allowed : 19.86 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.16), residues: 2292 helix: 0.36 (0.19), residues: 734 sheet: -1.28 (0.23), residues: 442 loop : -1.93 (0.16), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG k 116 TYR 0.029 0.001 TYR x 319 PHE 0.017 0.001 PHE a 67 TRP 0.019 0.001 TRP c 177 HIS 0.005 0.001 HIS c 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.21 (30250) covalent geometry : angle 1.09904 / 0.45 (43258) hydrogen bonds : bond 0.06020 / 4.17 ( 1090) hydrogen bonds : angle 4.05328 / 2.88 ( 2640) metal coordination : bond 0.01806 / 0.87 ( 4) metal coordination : angle 9.61983 / 5.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 504 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 371 ASP cc_start: 0.5029 (OUTLIER) cc_final: 0.4808 (t0) REVERT: x 391 PHE cc_start: 0.4312 (m-80) cc_final: 0.3839 (m-10) REVERT: x 418 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7394 (ttm-80) REVERT: x 446 GLU cc_start: 0.7994 (tp30) cc_final: 0.7627 (tp30) REVERT: x 480 GLN cc_start: 0.6149 (OUTLIER) cc_final: 0.5837 (mt0) REVERT: c 113 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8320 (t80) REVERT: n 31 ARG cc_start: 0.8509 (ptm160) cc_final: 0.8128 (ttm110) REVERT: n 60 GLU cc_start: 0.8504 (tm-30) cc_final: 0.7937 (tm-30) REVERT: h 19 ARG cc_start: 0.8312 (mtp180) cc_final: 0.7391 (mmt180) REVERT: h 75 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8932 (mttp) REVERT: o 306 ASP cc_start: 0.8037 (m-30) cc_final: 0.7535 (t0) REVERT: a 3 MET cc_start: 0.9305 (ptp) cc_final: 0.8977 (ptp) REVERT: a 73 ASN cc_start: 0.9291 (m-40) cc_final: 0.9064 (m-40) REVERT: m 18 LEU cc_start: 0.9206 (tp) cc_final: 0.8926 (tp) REVERT: i 54 LYS cc_start: 0.9209 (ttmt) cc_final: 0.8801 (ttmt) REVERT: b 58 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8564 (mttp) REVERT: b 64 LYS cc_start: 0.8469 (tttt) cc_final: 0.8114 (ttpp) REVERT: b 82 ASP cc_start: 0.8750 (p0) cc_final: 0.8451 (p0) REVERT: b 110 GLU cc_start: 0.8781 (mp0) cc_final: 0.8482 (mp0) REVERT: Z 40 ARG cc_start: 0.8428 (ttm170) cc_final: 0.8215 (ttm170) REVERT: Z 143 ARG cc_start: 0.8256 (tpt170) cc_final: 0.8050 (tpp-160) REVERT: Z 179 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: d 29 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7473 (tptt) REVERT: d 126 GLN cc_start: 0.8674 (tp40) cc_final: 0.8468 (tp40) REVERT: e 94 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8417 (mtmm) REVERT: f 83 PHE cc_start: 0.9494 (OUTLIER) cc_final: 0.8437 (t80) REVERT: f 97 GLN cc_start: 0.8603 (tp40) cc_final: 0.8358 (tp40) REVERT: V 37 ASP cc_start: 0.8479 (t0) cc_final: 0.8228 (t0) REVERT: V 65 GLN cc_start: 0.8730 (mp10) cc_final: 0.8517 (mm-40) REVERT: V 194 ASP cc_start: 0.8385 (m-30) cc_final: 0.8147 (m-30) REVERT: V 203 ASN cc_start: 0.8754 (t0) cc_final: 0.8474 (t0) REVERT: k 107 LYS cc_start: 0.6427 (pttt) cc_final: 0.5699 (ptmt) REVERT: k 114 ILE cc_start: 0.7308 (mp) cc_final: 0.6879 (mp) outliers start: 53 outliers final: 30 residues processed: 540 average time/residue: 0.1886 time to fit residues: 155.9812 Evaluate side-chains 521 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 485 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 371 ASP Chi-restraints excluded: chain x residue 429 ASN Chi-restraints excluded: chain x residue 472 PHE Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain x residue 480 GLN Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 75 LYS Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain Z residue 216 GLU Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 66 LEU Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain d residue 138 VAL Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: [121, 153, 236, 129, 141, 26, 88, 0, 240, 44, 193] chunk 121 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 240 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 429 ASN c 147 HIS c 159 ASN X 62 GLN b 32 GLN d 85 ASN Y 86 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.083089 restraints weight = 47684.167| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.64 r_work: 0.2779 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 30254 Z= 0.271 Angle : 1.024 19.892 43264 Z= 0.426 Chirality : 0.088 1.124 5278 Planarity : 0.005 0.063 3667 Dihedral : 18.157 170.357 8602 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.41 % Allowed : 20.45 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.17), residues: 2292 helix: 0.72 (0.19), residues: 739 sheet: -1.24 (0.22), residues: 444 loop : -1.79 (0.16), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 45 TYR 0.017 0.001 TYR Z 107 PHE 0.021 0.001 PHE b 119 TRP 0.018 0.002 TRP c 177 HIS 0.004 0.001 HIS h 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.27 (30250) covalent geometry : angle 1.01988 / 0.43 (43258) hydrogen bonds : bond 0.05681 / 4.06 ( 1090) hydrogen bonds : angle 3.95024 / 2.81 ( 2640) metal coordination : bond 0.01210 / 0.60 ( 4) metal coordination : angle 7.83186 / 4.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 516 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 319 TYR cc_start: 0.6829 (t80) cc_final: 0.6611 (t80) REVERT: x 391 PHE cc_start: 0.4139 (m-80) cc_final: 0.3714 (m-10) REVERT: x 399 GLU cc_start: 0.6304 (tt0) cc_final: 0.5965 (tt0) REVERT: x 414 LEU cc_start: 0.8651 (tp) cc_final: 0.8410 (tp) REVERT: x 418 ARG cc_start: 0.7687 (ttm-80) cc_final: 0.7247 (ttm-80) REVERT: x 446 GLU cc_start: 0.8010 (tp30) cc_final: 0.7725 (tp30) REVERT: c 113 PHE cc_start: 0.9347 (OUTLIER) cc_final: 0.8192 (t80) REVERT: c 132 TRP cc_start: 0.9229 (OUTLIER) cc_final: 0.8298 (m100) REVERT: c 139 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8227 (ttpp) REVERT: n 31 ARG cc_start: 0.8520 (ptm160) cc_final: 0.8104 (ttm110) REVERT: X 72 LYS cc_start: 0.8286 (tppt) cc_final: 0.7916 (tppt) REVERT: X 76 GLU cc_start: 0.7426 (mp0) cc_final: 0.7166 (mp0) REVERT: h 19 ARG cc_start: 0.8258 (mtp180) cc_final: 0.7420 (mmt180) REVERT: h 75 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8930 (mttp) REVERT: o 306 ASP cc_start: 0.8047 (m-30) cc_final: 0.7470 (t0) REVERT: a 73 ASN cc_start: 0.9293 (m-40) cc_final: 0.9072 (m-40) REVERT: m 18 LEU cc_start: 0.9199 (tp) cc_final: 0.8989 (tt) REVERT: i 54 LYS cc_start: 0.9248 (ttmt) cc_final: 0.8893 (ttmt) REVERT: b 34 MET cc_start: 0.8963 (mtt) cc_final: 0.8714 (mtm) REVERT: b 58 LYS cc_start: 0.8944 (mmmt) cc_final: 0.8634 (mttp) REVERT: b 64 LYS cc_start: 0.8498 (tttt) cc_final: 0.8142 (ttpp) REVERT: b 110 GLU cc_start: 0.8719 (mp0) cc_final: 0.8501 (mp0) REVERT: Z 143 ARG cc_start: 0.8224 (tpt170) cc_final: 0.8018 (tpp-160) REVERT: Z 179 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: d 29 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7422 (tptt) REVERT: e 94 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8450 (mtmm) REVERT: f 83 PHE cc_start: 0.9536 (OUTLIER) cc_final: 0.8442 (t80) REVERT: f 97 GLN cc_start: 0.8719 (tp40) cc_final: 0.8463 (tp40) REVERT: V 16 ASP cc_start: 0.7990 (p0) cc_final: 0.7738 (p0) REVERT: V 37 ASP cc_start: 0.8467 (t0) cc_final: 0.8149 (t0) REVERT: V 44 LYS cc_start: 0.9090 (ttpp) cc_final: 0.8828 (ttpp) REVERT: V 136 ARG cc_start: 0.8250 (mtp85) cc_final: 0.8007 (mtp85) REVERT: V 194 ASP cc_start: 0.8427 (m-30) cc_final: 0.8178 (m-30) REVERT: V 203 ASN cc_start: 0.8703 (t0) cc_final: 0.8426 (t0) REVERT: k 107 LYS cc_start: 0.6832 (pttt) cc_final: 0.5981 (ptmt) REVERT: k 114 ILE cc_start: 0.7308 (mp) cc_final: 0.6778 (mp) outliers start: 63 outliers final: 43 residues processed: 555 average time/residue: 0.1935 time to fit residues: 164.1793 Evaluate side-chains 544 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 495 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 291 THR Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 469 THR Chi-restraints excluded: chain x residue 480 GLN Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 75 LYS Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 60 GLU Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain i residue 9 SER Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain Z residue 216 GLU Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain d residue 138 VAL Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain f residue 68 ILE Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: [199, 90, 194, 156, 248, 186, 89, 164, 151, 106, 228] chunk 199 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 186 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 327 GLN x 417 GLN x 429 ASN x 482 ASN X 62 GLN m 46 GLN d 137 GLN f 101 ASN f 135 HIS Y 11 GLN Y 86 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.083407 restraints weight = 47423.103| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.64 r_work: 0.2787 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30254 Z= 0.254 Angle : 0.992 17.570 43264 Z= 0.412 Chirality : 0.085 1.067 5278 Planarity : 0.004 0.059 3667 Dihedral : 18.131 175.846 8597 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.38 % Allowed : 21.27 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.17), residues: 2292 helix: 0.88 (0.19), residues: 747 sheet: -1.13 (0.22), residues: 456 loop : -1.71 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 45 TYR 0.017 0.001 TYR Z 107 PHE 0.019 0.001 PHE b 119 TRP 0.017 0.001 TRP c 177 HIS 0.003 0.001 HIS x 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 (30250) covalent geometry : angle 0.98858 / 0.41 (43258) hydrogen bonds : bond 0.05512 / 3.92 ( 1090) hydrogen bonds : angle 3.83152 / 2.73 ( 2640) metal coordination : bond 0.00933 / 0.46 ( 4) metal coordination : angle 6.62874 / 3.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 503 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 391 PHE cc_start: 0.3886 (m-80) cc_final: 0.3673 (m-10) REVERT: x 414 LEU cc_start: 0.8566 (tp) cc_final: 0.8352 (tp) REVERT: x 418 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.7060 (ttm-80) REVERT: x 446 GLU cc_start: 0.7965 (tp30) cc_final: 0.7582 (tp30) REVERT: x 459 LYS cc_start: 0.5080 (mtpt) cc_final: 0.4748 (mtpt) REVERT: x 460 ASP cc_start: 0.4730 (OUTLIER) cc_final: 0.4306 (m-30) REVERT: x 480 GLN cc_start: 0.6076 (mt0) cc_final: 0.5573 (mt0) REVERT: c 113 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.8228 (t80) REVERT: c 132 TRP cc_start: 0.9226 (OUTLIER) cc_final: 0.8313 (m100) REVERT: c 139 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8210 (ttpp) REVERT: n 31 ARG cc_start: 0.8477 (ptm160) cc_final: 0.8038 (ttm110) REVERT: X 72 LYS cc_start: 0.8243 (tppt) cc_final: 0.7868 (tppt) REVERT: X 76 GLU cc_start: 0.7400 (mp0) cc_final: 0.7124 (mp0) REVERT: h 19 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7401 (mmt180) REVERT: h 75 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8963 (mttp) REVERT: o 306 ASP cc_start: 0.8308 (m-30) cc_final: 0.7699 (t0) REVERT: a 3 MET cc_start: 0.9222 (ptp) cc_final: 0.8858 (ptp) REVERT: m 19 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8508 (mm110) REVERT: m 88 TRP cc_start: 0.8574 (m-10) cc_final: 0.8229 (m-10) REVERT: i 54 LYS cc_start: 0.9251 (ttmt) cc_final: 0.8986 (ttpt) REVERT: b 34 MET cc_start: 0.8992 (mtt) cc_final: 0.8734 (mtm) REVERT: b 58 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8626 (mttp) REVERT: b 64 LYS cc_start: 0.8556 (tttt) cc_final: 0.8223 (ttmm) REVERT: b 110 GLU cc_start: 0.8719 (mp0) cc_final: 0.8474 (mp0) REVERT: Z 143 ARG cc_start: 0.8198 (tpt170) cc_final: 0.7991 (tpp-160) REVERT: Z 179 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: Z 216 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8076 (pp20) REVERT: d 29 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7436 (tptt) REVERT: e 94 LYS cc_start: 0.8825 (mtpt) cc_final: 0.8457 (mtmm) REVERT: f 83 PHE cc_start: 0.9530 (OUTLIER) cc_final: 0.8384 (t80) REVERT: V 36 GLN cc_start: 0.8865 (tp40) cc_final: 0.8543 (tp40) REVERT: V 37 ASP cc_start: 0.8346 (t0) cc_final: 0.8062 (t0) REVERT: V 44 LYS cc_start: 0.9092 (ttpp) cc_final: 0.8859 (ttpp) REVERT: V 136 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7980 (mtp85) REVERT: V 194 ASP cc_start: 0.8423 (m-30) cc_final: 0.8191 (m-30) REVERT: k 107 LYS cc_start: 0.6593 (pttt) cc_final: 0.5767 (ptmt) REVERT: k 114 ILE cc_start: 0.7327 (mp) cc_final: 0.6758 (mp) outliers start: 81 outliers final: 51 residues processed: 552 average time/residue: 0.1948 time to fit residues: 165.5044 Evaluate side-chains 552 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 493 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 417 GLN Chi-restraints excluded: chain x residue 429 ASN Chi-restraints excluded: chain x residue 460 ASP Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain x residue 482 ASN Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 75 LYS Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 60 GLU Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain Z residue 216 GLU Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 66 LEU Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 76 ARG Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain V residue 202 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: [243, 138, 31, 100, 94, 41, 260, 144, 200, 142, 229] chunk 243 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 260 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 327 GLN x 429 ASN x 482 ASN X 62 GLN b 32 GLN V 114 ASN Y 11 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.083331 restraints weight = 47479.478| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.63 r_work: 0.2784 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30254 Z= 0.255 Angle : 0.990 17.422 43264 Z= 0.412 Chirality : 0.084 1.003 5278 Planarity : 0.004 0.057 3667 Dihedral : 18.115 173.706 8597 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.44 % Allowed : 21.75 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.17), residues: 2292 helix: 0.96 (0.19), residues: 748 sheet: -1.04 (0.22), residues: 454 loop : -1.60 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 45 TYR 0.020 0.001 TYR x 431 PHE 0.019 0.001 PHE b 119 TRP 0.016 0.001 TRP c 177 HIS 0.004 0.001 HIS c 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 (30250) covalent geometry : angle 0.98764 / 0.41 (43258) hydrogen bonds : bond 0.05496 / 3.92 ( 1090) hydrogen bonds : angle 3.80462 / 2.70 ( 2640) metal coordination : bond 0.00801 / 0.41 ( 4) metal coordination : angle 6.31926 / 3.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 499 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 399 GLU cc_start: 0.6334 (tt0) cc_final: 0.5880 (tt0) REVERT: x 446 GLU cc_start: 0.8158 (tp30) cc_final: 0.7840 (tp30) REVERT: x 459 LYS cc_start: 0.5118 (mtpt) cc_final: 0.4792 (mtpt) REVERT: x 460 ASP cc_start: 0.4758 (t70) cc_final: 0.4323 (m-30) REVERT: x 480 GLN cc_start: 0.6088 (mt0) cc_final: 0.5549 (mt0) REVERT: c 113 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8226 (t80) REVERT: c 132 TRP cc_start: 0.9225 (OUTLIER) cc_final: 0.8307 (m100) REVERT: c 139 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8231 (ttpp) REVERT: n 31 ARG cc_start: 0.8446 (ptm160) cc_final: 0.8033 (ttm110) REVERT: X 72 LYS cc_start: 0.8252 (tppt) cc_final: 0.8000 (tppt) REVERT: X 76 GLU cc_start: 0.7387 (mp0) cc_final: 0.7160 (mp0) REVERT: h 19 ARG cc_start: 0.8102 (mtp180) cc_final: 0.7315 (mmt180) REVERT: h 75 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8972 (mttp) REVERT: o 306 ASP cc_start: 0.8350 (m-30) cc_final: 0.7784 (t0) REVERT: a 3 MET cc_start: 0.9221 (ptp) cc_final: 0.8844 (ptp) REVERT: m 19 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8250 (mm-40) REVERT: m 88 TRP cc_start: 0.8605 (m-10) cc_final: 0.8129 (m-10) REVERT: i 54 LYS cc_start: 0.9248 (ttmt) cc_final: 0.8982 (ttpt) REVERT: b 34 MET cc_start: 0.8996 (mtt) cc_final: 0.8738 (mtm) REVERT: b 58 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8641 (mttp) REVERT: b 64 LYS cc_start: 0.8525 (tttt) cc_final: 0.8096 (ttpp) REVERT: b 110 GLU cc_start: 0.8737 (mp0) cc_final: 0.8501 (mp0) REVERT: Z 143 ARG cc_start: 0.8228 (tpt170) cc_final: 0.8022 (tpp-160) REVERT: Z 216 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8031 (pp20) REVERT: d 29 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7437 (tptt) REVERT: e 94 LYS cc_start: 0.8831 (mtpt) cc_final: 0.8459 (mtmm) REVERT: f 83 PHE cc_start: 0.9528 (OUTLIER) cc_final: 0.8444 (t80) REVERT: V 36 GLN cc_start: 0.8878 (tp40) cc_final: 0.8545 (tp40) REVERT: V 37 ASP cc_start: 0.8384 (t0) cc_final: 0.8110 (t0) REVERT: V 44 LYS cc_start: 0.9079 (ttpp) cc_final: 0.8842 (ttpp) REVERT: V 136 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7831 (mtp85) REVERT: V 194 ASP cc_start: 0.8413 (m-30) cc_final: 0.8185 (m-30) REVERT: V 203 ASN cc_start: 0.8835 (t0) cc_final: 0.8406 (t0) REVERT: k 107 LYS cc_start: 0.6629 (pttt) cc_final: 0.5820 (ptmt) REVERT: k 114 ILE cc_start: 0.7197 (mp) cc_final: 0.6744 (mp) REVERT: k 132 MET cc_start: 0.7847 (mtp) cc_final: 0.7605 (mtp) outliers start: 82 outliers final: 57 residues processed: 551 average time/residue: 0.1929 time to fit residues: 164.2785 Evaluate side-chains 556 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 493 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain x residue 482 ASN Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain c residue 277 THR Chi-restraints excluded: chain c residue 287 THR Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 61 LEU Chi-restraints excluded: chain h residue 75 LYS Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 60 GLU Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain Z residue 216 GLU Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 66 LEU Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain d residue 138 VAL Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: [268, 41, 203, 252, 11, 229, 55, 44, 96, 1, 108] chunk 268 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 203 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 96 optimal weight: 0.0770 chunk 1 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 overall best weight: 1.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 327 GLN x 429 ASN X 62 GLN b 114 HIS d 137 GLN Y 86 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.081907 restraints weight = 47505.583| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.63 r_work: 0.2757 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 30254 Z= 0.304 Angle : 1.033 18.378 43264 Z= 0.430 Chirality : 0.087 0.972 5278 Planarity : 0.005 0.056 3667 Dihedral : 18.128 176.045 8597 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.17 % Allowed : 22.56 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.17), residues: 2292 helix: 0.90 (0.19), residues: 748 sheet: -1.00 (0.22), residues: 453 loop : -1.57 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Z 45 TYR 0.021 0.002 TYR x 431 PHE 0.020 0.002 PHE b 119 TRP 0.016 0.001 TRP c 177 HIS 0.005 0.001 HIS c 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.30 (30250) covalent geometry : angle 1.03022 / 0.43 (43258) hydrogen bonds : bond 0.05675 / 4.05 ( 1090) hydrogen bonds : angle 3.87995 / 2.76 ( 2640) metal coordination : bond 0.00859 / 0.44 ( 4) metal coordination : angle 6.24875 / 3.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 496 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 391 PHE cc_start: 0.4113 (m-10) cc_final: 0.3750 (m-80) REVERT: x 399 GLU cc_start: 0.6380 (tt0) cc_final: 0.5854 (tt0) REVERT: x 446 GLU cc_start: 0.8210 (tp30) cc_final: 0.7882 (tp30) REVERT: x 480 GLN cc_start: 0.6094 (OUTLIER) cc_final: 0.5682 (mt0) REVERT: c 132 TRP cc_start: 0.9234 (OUTLIER) cc_final: 0.8201 (m100) REVERT: c 139 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8327 (ttpp) REVERT: n 31 ARG cc_start: 0.8434 (ptm160) cc_final: 0.8028 (ttm110) REVERT: h 19 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7327 (mmt180) REVERT: h 75 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9050 (mttp) REVERT: o 306 ASP cc_start: 0.8357 (m-30) cc_final: 0.7793 (t0) REVERT: a 3 MET cc_start: 0.9227 (ptp) cc_final: 0.8892 (ptp) REVERT: m 88 TRP cc_start: 0.8587 (m-10) cc_final: 0.8255 (m-10) REVERT: i 54 LYS cc_start: 0.9244 (ttmt) cc_final: 0.8962 (ttpt) REVERT: b 58 LYS cc_start: 0.8935 (mmmt) cc_final: 0.8656 (mttp) REVERT: b 64 LYS cc_start: 0.8530 (tttt) cc_final: 0.8090 (ttpp) REVERT: b 71 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7904 (pm20) REVERT: Z 216 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8007 (pp20) REVERT: d 13 GLU cc_start: 0.8980 (tp30) cc_final: 0.8690 (tp30) REVERT: d 29 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7442 (tptt) REVERT: e 94 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8528 (mtmm) REVERT: f 83 PHE cc_start: 0.9552 (OUTLIER) cc_final: 0.8371 (t80) REVERT: V 37 ASP cc_start: 0.8488 (t0) cc_final: 0.8174 (t0) REVERT: V 44 LYS cc_start: 0.9043 (ttpp) cc_final: 0.8809 (ttpp) REVERT: V 136 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7795 (mtp85) REVERT: V 194 ASP cc_start: 0.8457 (m-30) cc_final: 0.8216 (m-30) REVERT: V 203 ASN cc_start: 0.8794 (t0) cc_final: 0.8355 (t0) REVERT: k 107 LYS cc_start: 0.6931 (pttt) cc_final: 0.6043 (ptmt) REVERT: k 114 ILE cc_start: 0.7132 (mp) cc_final: 0.6644 (mp) REVERT: k 132 MET cc_start: 0.8031 (mtp) cc_final: 0.7758 (mtp) outliers start: 77 outliers final: 60 residues processed: 541 average time/residue: 0.1945 time to fit residues: 162.3070 Evaluate side-chains 559 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 492 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 360 ARG Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain x residue 480 GLN Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 61 ILE Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 75 LYS Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 60 GLU Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 123 VAL Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain b residue 71 GLU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain Z residue 216 GLU Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 63 HIS Chi-restraints excluded: chain d residue 66 LEU Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain d residue 138 VAL Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: [27, 238, 91, 177, 68, 243, 118, 101, 254, 232, 214] chunk 27 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 118 optimal weight: 0.0670 chunk 101 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 327 GLN Z 159 HIS f 76 GLN Y 11 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.085404 restraints weight = 47086.972| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.62 r_work: 0.2819 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30254 Z= 0.194 Angle : 0.947 15.692 43264 Z= 0.395 Chirality : 0.079 0.811 5278 Planarity : 0.004 0.054 3667 Dihedral : 18.048 176.559 8597 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.57 % Allowed : 24.13 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 2292 helix: 1.09 (0.19), residues: 750 sheet: -0.90 (0.23), residues: 451 loop : -1.50 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 45 TYR 0.021 0.001 TYR x 431 PHE 0.017 0.001 PHE b 119 TRP 0.015 0.001 TRP c 177 HIS 0.003 0.001 HIS c 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (30250) covalent geometry : angle 0.94539 / 0.39 (43258) hydrogen bonds : bond 0.05334 / 3.78 ( 1090) hydrogen bonds : angle 3.76533 / 2.68 ( 2640) metal coordination : bond 0.00686 / 0.35 ( 4) metal coordination : angle 4.89206 / 2.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 499 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 316 GLU cc_start: 0.5325 (tt0) cc_final: 0.5029 (tt0) REVERT: x 391 PHE cc_start: 0.4076 (m-10) cc_final: 0.3770 (m-80) REVERT: x 399 GLU cc_start: 0.6167 (tt0) cc_final: 0.5707 (tt0) REVERT: x 446 GLU cc_start: 0.8149 (tp30) cc_final: 0.7804 (tp30) REVERT: x 460 ASP cc_start: 0.5069 (t70) cc_final: 0.4552 (m-30) REVERT: x 480 GLN cc_start: 0.5695 (mt0) cc_final: 0.5243 (mt0) REVERT: c 113 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.8220 (t80) REVERT: c 132 TRP cc_start: 0.9208 (OUTLIER) cc_final: 0.8300 (m100) REVERT: c 139 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8282 (ttpp) REVERT: c 217 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8432 (mtm) REVERT: n 31 ARG cc_start: 0.8363 (ptm160) cc_final: 0.7979 (ttm110) REVERT: n 60 GLU cc_start: 0.8497 (tm-30) cc_final: 0.7846 (tm-30) REVERT: h 19 ARG cc_start: 0.8014 (mtp180) cc_final: 0.7318 (mmt180) REVERT: h 75 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8912 (mttp) REVERT: o 306 ASP cc_start: 0.8327 (m-30) cc_final: 0.7859 (t0) REVERT: a 3 MET cc_start: 0.9199 (ptp) cc_final: 0.8787 (ptp) REVERT: m 88 TRP cc_start: 0.8671 (m-10) cc_final: 0.8327 (m-10) REVERT: i 54 LYS cc_start: 0.9200 (ttmt) cc_final: 0.8944 (ttpt) REVERT: b 34 MET cc_start: 0.9014 (mtt) cc_final: 0.8743 (mtm) REVERT: b 58 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8644 (mttp) REVERT: b 64 LYS cc_start: 0.8524 (tttt) cc_final: 0.8105 (ttpp) REVERT: b 71 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7890 (pm20) REVERT: Z 179 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: Z 216 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7997 (pp20) REVERT: d 29 LYS cc_start: 0.8093 (ttmt) cc_final: 0.7436 (tptt) REVERT: e 94 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8465 (mtmm) REVERT: f 63 GLU cc_start: 0.8643 (mp0) cc_final: 0.8201 (pm20) REVERT: f 83 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.8164 (t80) REVERT: V 36 GLN cc_start: 0.8809 (tp40) cc_final: 0.8607 (tp40) REVERT: V 37 ASP cc_start: 0.8282 (t0) cc_final: 0.8039 (t0) REVERT: V 44 LYS cc_start: 0.9066 (ttpp) cc_final: 0.8849 (ttpp) REVERT: V 65 GLN cc_start: 0.8762 (mp10) cc_final: 0.8543 (mm-40) REVERT: V 136 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7815 (mtp85) REVERT: V 194 ASP cc_start: 0.8410 (m-30) cc_final: 0.8181 (m-30) REVERT: V 203 ASN cc_start: 0.8730 (t0) cc_final: 0.8346 (t0) REVERT: k 107 LYS cc_start: 0.6575 (pttt) cc_final: 0.5748 (ptmt) REVERT: k 114 ILE cc_start: 0.7185 (mp) cc_final: 0.6718 (mp) REVERT: k 132 MET cc_start: 0.7914 (mtp) cc_final: 0.7637 (mtp) REVERT: Y 101 ASP cc_start: 0.8116 (t70) cc_final: 0.7570 (p0) outliers start: 66 outliers final: 47 residues processed: 535 average time/residue: 0.1916 time to fit residues: 157.7889 Evaluate side-chains 543 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 487 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 360 ARG Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain c residue 277 THR Chi-restraints excluded: chain c residue 287 THR Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 61 ILE Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 75 LYS Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain b residue 71 GLU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain Z residue 216 GLU Chi-restraints excluded: chain d residue 66 LEU Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: [164, 172, 240, 228, 68, 37, 43, 177, 207, 248, 192] chunk 164 optimal weight: 0.0470 chunk 172 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 177 optimal weight: 0.0980 chunk 207 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 327 GLN a 32 HIS b 41 GLN Z 165 ASN d 137 GLN f 76 GLN Y 86 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.086428 restraints weight = 47443.845| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.63 r_work: 0.2837 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30254 Z= 0.188 Angle : 0.930 15.056 43264 Z= 0.388 Chirality : 0.077 0.750 5278 Planarity : 0.004 0.057 3667 Dihedral : 17.938 174.537 8595 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.73 % Allowed : 24.73 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.17), residues: 2292 helix: 1.18 (0.20), residues: 751 sheet: -0.77 (0.23), residues: 445 loop : -1.47 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 45 TYR 0.020 0.001 TYR x 431 PHE 0.017 0.001 PHE b 119 TRP 0.015 0.001 TRP c 177 HIS 0.004 0.001 HIS V 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (30250) covalent geometry : angle 0.92854 / 0.39 (43258) hydrogen bonds : bond 0.05259 / 3.72 ( 1090) hydrogen bonds : angle 3.71835 / 2.64 ( 2640) metal coordination : bond 0.00588 / 0.30 ( 4) metal coordination : angle 4.35850 / 2.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 498 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 316 GLU cc_start: 0.5339 (tt0) cc_final: 0.5041 (tt0) REVERT: x 391 PHE cc_start: 0.3966 (m-10) cc_final: 0.3626 (m-80) REVERT: x 399 GLU cc_start: 0.6193 (tt0) cc_final: 0.5733 (tt0) REVERT: x 446 GLU cc_start: 0.8090 (tp30) cc_final: 0.7747 (tp30) REVERT: x 459 LYS cc_start: 0.5177 (mtpt) cc_final: 0.4811 (mtpt) REVERT: x 460 ASP cc_start: 0.5052 (t70) cc_final: 0.4560 (m-30) REVERT: x 480 GLN cc_start: 0.5679 (mt0) cc_final: 0.5238 (mt0) REVERT: c 113 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8204 (t80) REVERT: c 132 TRP cc_start: 0.9207 (OUTLIER) cc_final: 0.8270 (m100) REVERT: c 139 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8230 (ttpp) REVERT: c 217 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8436 (mtm) REVERT: n 31 ARG cc_start: 0.8349 (ptm160) cc_final: 0.7977 (ttm110) REVERT: n 60 GLU cc_start: 0.8500 (tm-30) cc_final: 0.7882 (tm-30) REVERT: h 19 ARG cc_start: 0.8124 (mtp180) cc_final: 0.7425 (mpt90) REVERT: h 75 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8909 (mttp) REVERT: o 306 ASP cc_start: 0.8313 (m-30) cc_final: 0.7864 (t0) REVERT: a 3 MET cc_start: 0.9197 (ptp) cc_final: 0.8810 (ptp) REVERT: m 61 TYR cc_start: 0.9131 (t80) cc_final: 0.8845 (t80) REVERT: m 88 TRP cc_start: 0.8665 (m-10) cc_final: 0.8440 (m-10) REVERT: i 54 LYS cc_start: 0.9167 (ttmt) cc_final: 0.8912 (ttpt) REVERT: b 34 MET cc_start: 0.9015 (mtt) cc_final: 0.8796 (mtp) REVERT: b 58 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8642 (mttp) REVERT: b 64 LYS cc_start: 0.8493 (tttt) cc_final: 0.8081 (ttpp) REVERT: b 71 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: Z 179 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: Z 216 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7944 (pp20) REVERT: d 29 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7454 (tptt) REVERT: e 94 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8453 (mtmm) REVERT: f 63 GLU cc_start: 0.8561 (mp0) cc_final: 0.8136 (pm20) REVERT: f 83 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8166 (t80) REVERT: V 36 GLN cc_start: 0.8811 (tp40) cc_final: 0.8592 (tp40) REVERT: V 37 ASP cc_start: 0.8275 (t0) cc_final: 0.8036 (t0) REVERT: V 44 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8881 (ttpp) REVERT: V 65 GLN cc_start: 0.8743 (mp10) cc_final: 0.8529 (mm-40) REVERT: V 136 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7813 (mtp85) REVERT: V 194 ASP cc_start: 0.8414 (m-30) cc_final: 0.8198 (m-30) REVERT: V 203 ASN cc_start: 0.8736 (t0) cc_final: 0.8361 (t0) REVERT: k 107 LYS cc_start: 0.6524 (pttt) cc_final: 0.5734 (ptmt) REVERT: k 114 ILE cc_start: 0.7315 (mp) cc_final: 0.6863 (mp) REVERT: k 132 MET cc_start: 0.7896 (mtp) cc_final: 0.7628 (mtp) outliers start: 69 outliers final: 48 residues processed: 537 average time/residue: 0.1906 time to fit residues: 157.9966 Evaluate side-chains 539 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 482 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 360 ARG Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain c residue 287 THR Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 61 ILE Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 75 LYS Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 60 GLU Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain b residue 71 GLU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain Z residue 216 GLU Chi-restraints excluded: chain d residue 66 LEU Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: [142, 155, 25, 57, 165, 255, 249, 40, 203, 164, 122] chunk 142 optimal weight: 0.7980 chunk 155 optimal weight: 0.0370 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 40 optimal weight: 0.0570 chunk 203 optimal weight: 1.9990 chunk 164 optimal weight: 0.1980 chunk 122 optimal weight: 0.9980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 327 GLN h 100 GLN m 28 HIS b 32 GLN Y 86 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.090007 restraints weight = 47162.881| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.63 r_work: 0.2899 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30254 Z= 0.149 Angle : 0.890 14.034 43264 Z= 0.373 Chirality : 0.073 0.625 5278 Planarity : 0.004 0.062 3667 Dihedral : 17.846 174.036 8595 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.92 % Allowed : 25.60 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.17), residues: 2292 helix: 1.37 (0.20), residues: 746 sheet: -0.67 (0.23), residues: 441 loop : -1.37 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 51 TYR 0.019 0.001 TYR x 431 PHE 0.015 0.001 PHE a 67 TRP 0.015 0.001 TRP c 177 HIS 0.005 0.001 HIS d 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (30250) covalent geometry : angle 0.88898 / 0.37 (43258) hydrogen bonds : bond 0.05147 / 3.63 ( 1090) hydrogen bonds : angle 3.61902 / 2.57 ( 2640) metal coordination : bond 0.00507 / 0.26 ( 4) metal coordination : angle 3.53236 / 1.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 494 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 302 ASP cc_start: 0.5520 (m-30) cc_final: 0.4747 (t0) REVERT: x 316 GLU cc_start: 0.5325 (tt0) cc_final: 0.5036 (tt0) REVERT: x 391 PHE cc_start: 0.3919 (m-10) cc_final: 0.3594 (m-80) REVERT: x 399 GLU cc_start: 0.6152 (tt0) cc_final: 0.5696 (tt0) REVERT: x 446 GLU cc_start: 0.8085 (tp30) cc_final: 0.7725 (tp30) REVERT: x 459 LYS cc_start: 0.5305 (mtpt) cc_final: 0.4961 (mtpt) REVERT: x 460 ASP cc_start: 0.5034 (t70) cc_final: 0.4402 (m-30) REVERT: x 480 GLN cc_start: 0.5605 (mt0) cc_final: 0.5210 (mt0) REVERT: c 113 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8238 (t80) REVERT: c 132 TRP cc_start: 0.9173 (OUTLIER) cc_final: 0.8361 (m100) REVERT: c 139 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8199 (ttpp) REVERT: c 217 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8394 (mtm) REVERT: n 31 ARG cc_start: 0.8302 (ptm160) cc_final: 0.7958 (ttm110) REVERT: n 60 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7936 (tm-30) REVERT: X 62 GLN cc_start: 0.8445 (mp10) cc_final: 0.7968 (mp10) REVERT: X 72 LYS cc_start: 0.8609 (tppt) cc_final: 0.8315 (tppt) REVERT: h 19 ARG cc_start: 0.8078 (mtp180) cc_final: 0.7375 (mmt180) REVERT: h 38 ASP cc_start: 0.7706 (m-30) cc_final: 0.7496 (m-30) REVERT: h 99 LYS cc_start: 0.8286 (mttm) cc_final: 0.7590 (mmtt) REVERT: o 306 ASP cc_start: 0.8286 (m-30) cc_final: 0.7849 (t0) REVERT: a 3 MET cc_start: 0.9152 (ptp) cc_final: 0.8774 (ptp) REVERT: m 19 GLN cc_start: 0.8835 (mm110) cc_final: 0.8522 (mm110) REVERT: m 61 TYR cc_start: 0.9115 (t80) cc_final: 0.8910 (t80) REVERT: m 88 TRP cc_start: 0.8623 (m-10) cc_final: 0.8375 (m-10) REVERT: i 54 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8822 (ttpt) REVERT: b 34 MET cc_start: 0.9020 (mtt) cc_final: 0.8815 (mtp) REVERT: b 58 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8629 (mttp) REVERT: b 64 LYS cc_start: 0.8453 (tttt) cc_final: 0.8054 (ttpp) REVERT: b 71 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: Z 179 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: Z 216 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7935 (pp20) REVERT: d 29 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7428 (tptt) REVERT: e 94 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8351 (mtmm) REVERT: f 63 GLU cc_start: 0.8563 (mp0) cc_final: 0.8181 (pm20) REVERT: f 83 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8067 (t80) REVERT: f 112 GLU cc_start: 0.8305 (pp20) cc_final: 0.8085 (pp20) REVERT: V 37 ASP cc_start: 0.8114 (t0) cc_final: 0.7874 (t0) REVERT: V 65 GLN cc_start: 0.8736 (mp10) cc_final: 0.8525 (mm-40) REVERT: V 136 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7820 (mtp85) REVERT: V 203 ASN cc_start: 0.8758 (t0) cc_final: 0.8474 (t0) REVERT: k 104 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7722 (mmtm) REVERT: k 107 LYS cc_start: 0.6483 (pttt) cc_final: 0.5638 (ptmt) REVERT: k 114 ILE cc_start: 0.7220 (mp) cc_final: 0.6809 (mp) REVERT: Y 106 LYS cc_start: 0.8360 (ttpp) cc_final: 0.8003 (tptp) outliers start: 54 outliers final: 43 residues processed: 523 average time/residue: 0.1846 time to fit residues: 149.5528 Evaluate side-chains 546 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 495 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 360 ARG Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain c residue 277 THR Chi-restraints excluded: chain c residue 287 THR Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain n residue 6 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 61 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 123 VAL Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain b residue 71 GLU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain Z residue 197 LYS Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain Z residue 216 GLU Chi-restraints excluded: chain d residue 66 LEU Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain f residue 68 ILE Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: [117, 31, 234, 114, 143, 111, 246, 74, 127, 16, 120] chunk 117 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 234 optimal weight: 1.9990 chunk 114 optimal weight: 0.0040 chunk 143 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 120 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 327 GLN b 41 GLN f 76 GLN f 101 ASN Y 86 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.089303 restraints weight = 47103.844| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.63 r_work: 0.2886 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30254 Z= 0.160 Angle : 0.895 14.163 43264 Z= 0.375 Chirality : 0.073 0.643 5278 Planarity : 0.004 0.064 3667 Dihedral : 17.796 173.792 8593 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.92 % Allowed : 25.76 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2292 helix: 1.44 (0.20), residues: 744 sheet: -0.58 (0.23), residues: 445 loop : -1.32 (0.17), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 51 TYR 0.031 0.001 TYR x 319 PHE 0.015 0.001 PHE a 67 TRP 0.014 0.001 TRP c 177 HIS 0.005 0.001 HIS d 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (30250) covalent geometry : angle 0.89378 / 0.38 (43258) hydrogen bonds : bond 0.05132 / 3.62 ( 1090) hydrogen bonds : angle 3.61110 / 2.56 ( 2640) metal coordination : bond 0.00505 / 0.26 ( 4) metal coordination : angle 4.26632 / 2.25 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 486 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 302 ASP cc_start: 0.5571 (m-30) cc_final: 0.5230 (t0) REVERT: x 330 ARG cc_start: 0.5580 (mmm160) cc_final: 0.5334 (mmm160) REVERT: x 391 PHE cc_start: 0.4012 (m-10) cc_final: 0.3683 (m-80) REVERT: x 399 GLU cc_start: 0.6107 (tt0) cc_final: 0.5649 (tt0) REVERT: x 446 GLU cc_start: 0.8092 (tp30) cc_final: 0.7750 (tp30) REVERT: x 459 LYS cc_start: 0.5315 (mtpt) cc_final: 0.4970 (mtpt) REVERT: x 460 ASP cc_start: 0.4888 (t70) cc_final: 0.4373 (m-30) REVERT: x 480 GLN cc_start: 0.5601 (mt0) cc_final: 0.5160 (mt0) REVERT: c 113 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8289 (t80) REVERT: c 132 TRP cc_start: 0.9186 (OUTLIER) cc_final: 0.8272 (m100) REVERT: c 139 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8155 (ttpp) REVERT: c 217 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8424 (mtm) REVERT: n 31 ARG cc_start: 0.8288 (ptm160) cc_final: 0.7953 (ttm110) REVERT: n 60 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7896 (tm-30) REVERT: X 72 LYS cc_start: 0.8617 (tppt) cc_final: 0.8379 (tppt) REVERT: h 19 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7368 (mmt180) REVERT: h 38 ASP cc_start: 0.7683 (m-30) cc_final: 0.7479 (m-30) REVERT: h 68 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9036 (t) REVERT: h 99 LYS cc_start: 0.8310 (mttm) cc_final: 0.7614 (mmtt) REVERT: o 306 ASP cc_start: 0.8281 (m-30) cc_final: 0.7833 (t0) REVERT: a 3 MET cc_start: 0.9106 (ptp) cc_final: 0.8742 (ptp) REVERT: m 19 GLN cc_start: 0.8788 (mm110) cc_final: 0.8447 (mm-40) REVERT: m 88 TRP cc_start: 0.8687 (m-10) cc_final: 0.8437 (m-10) REVERT: i 54 LYS cc_start: 0.9100 (ttmt) cc_final: 0.8845 (ttpt) REVERT: b 34 MET cc_start: 0.9030 (mtt) cc_final: 0.8829 (mtp) REVERT: b 58 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8634 (mttp) REVERT: b 64 LYS cc_start: 0.8440 (tttt) cc_final: 0.8049 (ttpp) REVERT: b 71 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: Z 143 ARG cc_start: 0.8137 (tpt170) cc_final: 0.7836 (tpt170) REVERT: Z 179 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: Z 216 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7951 (pp20) REVERT: d 29 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7446 (tptt) REVERT: e 94 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8334 (mtmm) REVERT: f 63 GLU cc_start: 0.8573 (mp0) cc_final: 0.8177 (pm20) REVERT: f 83 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.8043 (t80) REVERT: V 36 GLN cc_start: 0.8790 (tp40) cc_final: 0.8571 (tp40) REVERT: V 37 ASP cc_start: 0.8143 (t0) cc_final: 0.7866 (t0) REVERT: V 65 GLN cc_start: 0.8705 (mp10) cc_final: 0.8494 (mm-40) REVERT: V 136 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7819 (mtp85) REVERT: V 203 ASN cc_start: 0.8767 (t0) cc_final: 0.8465 (t0) REVERT: k 104 LYS cc_start: 0.8153 (mmtm) cc_final: 0.7755 (mmtm) REVERT: k 107 LYS cc_start: 0.6806 (pttt) cc_final: 0.5969 (ptmt) REVERT: k 114 ILE cc_start: 0.7230 (mp) cc_final: 0.6815 (mp) outliers start: 54 outliers final: 42 residues processed: 514 average time/residue: 0.1881 time to fit residues: 149.7354 Evaluate side-chains 535 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 484 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 360 ARG Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain c residue 287 THR Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain n residue 6 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 61 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 68 THR Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 123 VAL Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain b residue 71 GLU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain Z residue 197 LYS Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain Z residue 216 GLU Chi-restraints excluded: chain d residue 66 LEU Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: [48, 270, 159, 57, 45, 124, 269, 197, 194, 132, 60] chunk 48 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 269 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 132 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 327 GLN f 101 ASN Y 86 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.085380 restraints weight = 47403.092| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.64 r_work: 0.2818 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30254 Z= 0.228 Angle : 0.955 16.030 43264 Z= 0.400 Chirality : 0.079 0.798 5278 Planarity : 0.004 0.069 3667 Dihedral : 17.864 173.384 8593 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.03 % Allowed : 26.14 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2292 helix: 1.26 (0.19), residues: 752 sheet: -0.65 (0.23), residues: 449 loop : -1.37 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 51 TYR 0.019 0.001 TYR x 431 PHE 0.017 0.001 PHE b 119 TRP 0.014 0.001 TRP c 177 HIS 0.006 0.001 HIS d 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.23 (30250) covalent geometry : angle 0.95318 / 0.40 (43258) hydrogen bonds : bond 0.05339 / 3.77 ( 1090) hydrogen bonds : angle 3.68251 / 2.61 ( 2640) metal coordination : bond 0.00614 / 0.31 ( 4) metal coordination : angle 4.65767 / 2.53 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8444.59 seconds wall clock time: 145 minutes 0.68 seconds (8700.68 seconds total)