Starting phenix.real_space_refine on Mon Aug 10 02:01:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9okl_70568/08_2026/9okl_70568.cif Found real_map, /net/cci-nas-00/data/ceres_data/9okl_70568/08_2026/9okl_70568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9okl_70568/08_2026/9okl_70568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9okl_70568/08_2026/9okl_70568.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9okl_70568/08_2026/9okl_70568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9okl_70568/08_2026/9okl_70568.map" } resolution = 3.0 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 ------------------------------------------------------------------------------- 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= 0.010 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: 5 Type Number sf(0) Gaussians S 94 5.16 5 C 13176 2.51 5 N 3530 2.21 5 O 3847 1.98 5 H 18862 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39509 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1108 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "B" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 907 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain: "C" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 880 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1050 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "H" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3517 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 223} Chain breaks: 1 Chain: "I" Number of atoms: 8726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8726 Classifications: {'peptide': 534} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 509} Chain breaks: 1 Chain: "K" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3282 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain breaks: 1 Chain: "L" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3880 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 4 Chain: "M" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 2626 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 159} Chain: "N" Number of atoms: 5105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 5105 Classifications: {'peptide': 319} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 301} Chain breaks: 1 Chain: "O" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3317 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 2 Chain: "P" Number of atoms: 3868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 3868 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 12, 'TRANS': 242} Chain breaks: 1 Chain: "T" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1243 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain breaks: 1 Time building chain proxies: 6.80, per 1000 atoms: 0.17 Number of scatterers: 39509 At special positions: 0 Unit cell: (113.13, 165.086, 176.818, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 O 3847 8.00 N 3530 7.00 C 13176 6.00 H 18862 1.00 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: 4.17 Conformation dependent library (CDL) restraints added in 1.4 seconds 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4990 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 9 sheets defined 66.8% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 8 through 41 Processing helix chain 'A' and resid 45 through 66 Processing helix chain 'B' and resid 19 through 57 Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.526A pdb=" N GLN B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 70 Processing helix chain 'D' and resid 11 through 66 removed outlier: 3.951A pdb=" N SER D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG D 56 " --> pdb=" O GLU D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'H' and resid 3 through 24 removed outlier: 3.621A pdb=" N VAL H 24 " --> pdb=" O GLN H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 61 removed outlier: 3.591A pdb=" N LYS H 40 " --> pdb=" O ASP H 36 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 63 through 68 Processing helix chain 'H' and resid 73 through 108 removed outlier: 3.855A pdb=" N LYS H 77 " --> pdb=" O GLU H 73 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS H 90 " --> pdb=" O LYS H 86 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS H 100 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 114 through 170 removed outlier: 3.896A pdb=" N LYS H 170 " --> pdb=" O LEU H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 207 Processing helix chain 'H' and resid 212 through 215 Processing helix chain 'H' and resid 216 through 229 removed outlier: 4.243A pdb=" N ALA H 220 " --> pdb=" O ASP H 216 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN H 229 " --> pdb=" O LYS H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 237 removed outlier: 3.714A pdb=" N PHE H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 53 Processing helix chain 'I' and resid 57 through 68 removed outlier: 4.002A pdb=" N CYS I 67 " --> pdb=" O SER I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.775A pdb=" N VAL I 79 " --> pdb=" O GLU I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 111 removed outlier: 4.277A pdb=" N THR I 97 " --> pdb=" O GLN I 93 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS I 98 " --> pdb=" O ASN I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 122 removed outlier: 3.871A pdb=" N LEU I 120 " --> pdb=" O ASP I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 132 removed outlier: 4.024A pdb=" N THR I 132 " --> pdb=" O TYR I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 148 removed outlier: 4.348A pdb=" N LYS I 142 " --> pdb=" O PRO I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 154 through 168 removed outlier: 4.062A pdb=" N ILE I 161 " --> pdb=" O ARG I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 189 removed outlier: 3.617A pdb=" N PHE I 175 " --> pdb=" O LYS I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 193 Processing helix chain 'I' and resid 201 through 205 removed outlier: 3.981A pdb=" N THR I 204 " --> pdb=" O CYS I 201 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA I 205 " --> pdb=" O VAL I 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 201 through 205' Processing helix chain 'I' and resid 210 through 220 Processing helix chain 'I' and resid 309 through 313 Processing helix chain 'I' and resid 315 through 334 removed outlier: 3.681A pdb=" N HIS I 328 " --> pdb=" O HIS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 360 Processing helix chain 'I' and resid 363 through 374 Processing helix chain 'I' and resid 375 through 377 No H-bonds generated for 'chain 'I' and resid 375 through 377' Processing helix chain 'I' and resid 382 through 391 removed outlier: 3.672A pdb=" N GLU I 391 " --> pdb=" O LEU I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 413 removed outlier: 4.208A pdb=" N LEU I 401 " --> pdb=" O SER I 397 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY I 402 " --> pdb=" O PRO I 398 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR I 403 " --> pdb=" O ASP I 399 " (cutoff:3.500A) Proline residue: I 407 - end of helix Processing helix chain 'I' and resid 416 through 440 removed outlier: 3.665A pdb=" N THR I 439 " --> pdb=" O VAL I 435 " (cutoff:3.500A) Processing helix chain 'I' and resid 444 through 448 removed outlier: 3.684A pdb=" N ILE I 448 " --> pdb=" O PHE I 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 477 removed outlier: 4.019A pdb=" N TYR I 455 " --> pdb=" O PRO I 451 " (cutoff:3.500A) Proline residue: I 460 - end of helix removed outlier: 3.653A pdb=" N TYR I 476 " --> pdb=" O LYS I 472 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN I 477 " --> pdb=" O ALA I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 480 through 502 Processing helix chain 'I' and resid 510 through 520 removed outlier: 3.902A pdb=" N LEU I 514 " --> pdb=" O GLY I 510 " (cutoff:3.500A) Proline residue: I 517 - end of helix Processing helix chain 'I' and resid 522 through 547 removed outlier: 3.887A pdb=" N ILE I 526 " --> pdb=" O SER I 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 550 through 573 removed outlier: 3.723A pdb=" N LEU I 570 " --> pdb=" O ASP I 566 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR I 571 " --> pdb=" O LEU I 567 " (cutoff:3.500A) Processing helix chain 'I' and resid 578 through 582 Processing helix chain 'I' and resid 584 through 588 Processing helix chain 'I' and resid 589 through 600 Processing helix chain 'I' and resid 603 through 608 removed outlier: 3.640A pdb=" N SER I 608 " --> pdb=" O THR I 605 " (cutoff:3.500A) Processing helix chain 'I' and resid 612 through 624 removed outlier: 4.094A pdb=" N ALA I 617 " --> pdb=" O VAL I 613 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TYR I 618 " --> pdb=" O ALA I 614 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL I 621 " --> pdb=" O ALA I 617 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA I 622 " --> pdb=" O TYR I 618 " (cutoff:3.500A) Processing helix chain 'I' and resid 629 through 632 Processing helix chain 'I' and resid 633 through 645 Processing helix chain 'I' and resid 645 through 656 Processing helix chain 'I' and resid 656 through 661 removed outlier: 3.628A pdb=" N ARG I 660 " --> pdb=" O VAL I 656 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET I 661 " --> pdb=" O PRO I 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 656 through 661' Processing helix chain 'K' and resid 3 through 34 Processing helix chain 'K' and resid 42 through 62 Processing helix chain 'K' and resid 71 through 123 removed outlier: 3.737A pdb=" N LYS K 84 " --> pdb=" O LEU K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 159 Processing helix chain 'K' and resid 162 through 179 Processing helix chain 'K' and resid 192 through 202 Processing helix chain 'L' and resid 50 through 67 Processing helix chain 'L' and resid 142 through 158 Processing helix chain 'L' and resid 167 through 182 Processing helix chain 'L' and resid 211 through 221 Processing helix chain 'L' and resid 227 through 248 Processing helix chain 'L' and resid 276 through 289 removed outlier: 3.843A pdb=" N GLU L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 49 Processing helix chain 'M' and resid 62 through 73 removed outlier: 4.046A pdb=" N VAL M 66 " --> pdb=" O HIS M 62 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP M 71 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU M 72 " --> pdb=" O LYS M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 102 removed outlier: 3.626A pdb=" N GLN M 102 " --> pdb=" O LYS M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 108 removed outlier: 5.980A pdb=" N ASP M 106 " --> pdb=" O VAL M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 125 removed outlier: 3.912A pdb=" N MET M 125 " --> pdb=" O VAL M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 139 Processing helix chain 'M' and resid 150 through 170 Processing helix chain 'N' and resid 2 through 17 Processing helix chain 'N' and resid 18 through 25 Processing helix chain 'N' and resid 25 through 30 Processing helix chain 'N' and resid 33 through 44 Processing helix chain 'N' and resid 49 through 65 removed outlier: 3.697A pdb=" N VAL N 53 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS N 63 " --> pdb=" O ARG N 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER N 64 " --> pdb=" O HIS N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 83 Processing helix chain 'N' and resid 102 through 120 Proline residue: N 111 - end of helix Processing helix chain 'N' and resid 173 through 185 Processing helix chain 'N' and resid 198 through 207 Processing helix chain 'N' and resid 238 through 251 Processing helix chain 'N' and resid 288 through 299 Processing helix chain 'N' and resid 306 through 312 removed outlier: 3.868A pdb=" N PHE N 309 " --> pdb=" O SER N 306 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE N 311 " --> pdb=" O PHE N 308 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 52 removed outlier: 3.880A pdb=" N LYS O 32 " --> pdb=" O ASP O 28 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU O 33 " --> pdb=" O GLU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 93 Processing helix chain 'O' and resid 128 through 131 Processing helix chain 'O' and resid 144 through 150 removed outlier: 3.966A pdb=" N VAL O 148 " --> pdb=" O ASN O 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 186 Processing helix chain 'O' and resid 254 through 258 Processing helix chain 'O' and resid 260 through 270 Processing helix chain 'P' and resid 21 through 44 removed outlier: 3.928A pdb=" N LEU P 26 " --> pdb=" O GLU P 22 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS P 44 " --> pdb=" O LEU P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 87 Processing helix chain 'P' and resid 157 through 166 removed outlier: 4.294A pdb=" N LYS P 166 " --> pdb=" O THR P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 172 Proline residue: P 170 - end of helix No H-bonds generated for 'chain 'P' and resid 167 through 172' Processing helix chain 'P' and resid 174 through 204 Processing helix chain 'P' and resid 253 through 267 removed outlier: 3.806A pdb=" N ALA P 263 " --> pdb=" O LYS P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 291 removed outlier: 3.896A pdb=" N VAL P 291 " --> pdb=" O VAL P 287 " (cutoff:3.500A) Processing helix chain 'T' and resid 813 through 836 Processing helix chain 'T' and resid 907 through 922 removed outlier: 3.633A pdb=" N LYS T 911 " --> pdb=" O LYS T 907 " (cutoff:3.500A) Proline residue: T 919 - end of helix Processing helix chain 'T' and resid 923 through 946 removed outlier: 4.331A pdb=" N VAL T 927 " --> pdb=" O TYR T 923 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS T 945 " --> pdb=" O LYS T 941 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS T 946 " --> pdb=" O GLU T 942 " (cutoff:3.500A) Processing helix chain 'T' and resid 950 through 964 removed outlier: 3.576A pdb=" N VAL T 954 " --> pdb=" O PRO T 950 " (cutoff:3.500A) Processing helix chain 'T' and resid 969 through 981 Processing helix chain 'T' and resid 982 through 990 Processing sheet with id=AA1, first strand: chain 'K' and resid 185 through 187 Processing sheet with id=AA2, first strand: chain 'L' and resid 35 through 37 removed outlier: 4.197A pdb=" N GLY L 271 " --> pdb=" O LYS L 267 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL L 193 " --> pdb=" O SER L 257 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE L 259 " --> pdb=" O THR L 191 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR L 191 " --> pdb=" O ILE L 259 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP L 210 " --> pdb=" O ASN N 279 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ASN N 279 " --> pdb=" O ASP L 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 77 through 84 removed outlier: 6.246A pdb=" N SER L 103 " --> pdb=" O VAL L 113 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL L 113 " --> pdb=" O SER L 103 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET L 137 " --> pdb=" O ASN L 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 54 through 60 removed outlier: 6.492A pdb=" N LEU M 23 " --> pdb=" O VAL M 56 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU M 58 " --> pdb=" O LEU M 23 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA M 25 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N SER M 60 " --> pdb=" O ALA M 25 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL M 27 " --> pdb=" O SER M 60 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N PHE M 80 " --> pdb=" O SER M 22 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR M 24 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ILE M 82 " --> pdb=" O THR M 24 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE M 26 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ALA M 84 " --> pdb=" O ILE M 26 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU M 28 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 127 through 135 removed outlier: 6.453A pdb=" N LEU N 139 " --> pdb=" O ALA N 158 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA N 158 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE N 141 " --> pdb=" O TYR N 156 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR N 156 " --> pdb=" O ILE N 141 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL N 143 " --> pdb=" O THR N 154 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR N 154 " --> pdb=" O VAL N 143 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU N 145 " --> pdb=" O GLY N 152 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU N 194 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASN N 93 " --> pdb=" O ALA N 192 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA N 192 " --> pdb=" O ASN N 93 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER N 95 " --> pdb=" O GLU N 190 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLU N 190 " --> pdb=" O SER N 95 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLN N 97 " --> pdb=" O LYS N 188 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LYS N 188 " --> pdb=" O GLN N 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 94 through 100 removed outlier: 6.750A pdb=" N CYS O 106 " --> pdb=" O GLN O 97 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR O 99 " --> pdb=" O HIS O 104 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N HIS O 104 " --> pdb=" O TYR O 99 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY O 122 " --> pdb=" O SER O 137 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER O 137 " --> pdb=" O GLY O 122 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG O 124 " --> pdb=" O SER O 135 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL O 133 " --> pdb=" O GLU O 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 190 through 192 removed outlier: 3.663A pdb=" N ASP O 223 " --> pdb=" O GLN O 233 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN O 233 " --> pdb=" O ASP O 223 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 89 through 97 removed outlier: 6.775A pdb=" N ASP P 122 " --> pdb=" O LEU P 91 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER P 93 " --> pdb=" O THR P 120 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR P 120 " --> pdb=" O SER P 93 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL P 95 " --> pdb=" O GLU P 118 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU P 118 " --> pdb=" O VAL P 95 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL P 97 " --> pdb=" O TRP P 116 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TRP P 116 " --> pdb=" O VAL P 97 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR P 135 " --> pdb=" O LYS P 150 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS P 150 " --> pdb=" O TYR P 135 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N HIS P 137 " --> pdb=" O TYR P 148 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TYR P 148 " --> pdb=" O HIS P 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 207 through 211 1366 hydrogen bonds defined for protein. 3990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.40 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18828 1.03 - 1.23: 36 1.23 - 1.42: 8413 1.42 - 1.62: 12423 1.62 - 1.81: 153 Bond restraints: 39853 Sorted by residual: bond pdb=" N MET N 1 " pdb=" H3 MET N 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N MET N 1 " pdb=" H2 MET N 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N MET N 1 " pdb=" CA MET N 1 " ideal model delta sigma weight residual 1.491 1.457 0.034 2.10e-02 2.27e+03 2.57e+00 bond pdb=" N MET N 1 " pdb=" H1 MET N 1 " ideal model delta sigma weight residual 0.890 0.861 0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" CA VAL P 97 " pdb=" CB VAL P 97 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 7.10e-01 ... (remaining 39848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.96: 71220 4.96 - 9.92: 1 9.92 - 14.88: 0 14.88 - 19.85: 1 19.85 - 24.81: 1 Bond angle restraints: 71223 Sorted by residual: angle pdb=" H1 MET N 1 " pdb=" N MET N 1 " pdb=" H3 MET N 1 " ideal model delta sigma weight residual 109.47 84.66 24.81 3.00e+00 1.11e-01 6.84e+01 angle pdb=" H1 MET N 1 " pdb=" N MET N 1 " pdb=" H2 MET N 1 " ideal model delta sigma weight residual 109.47 125.92 -16.45 3.00e+00 1.11e-01 3.01e+01 angle pdb=" N GLN O 70 " pdb=" CA GLN O 70 " pdb=" C GLN O 70 " ideal model delta sigma weight residual 113.18 110.04 3.14 1.33e+00 5.65e-01 5.58e+00 angle pdb=" C THR L 199 " pdb=" N GLU L 200 " pdb=" CA GLU L 200 " ideal model delta sigma weight residual 121.54 125.85 -4.31 1.91e+00 2.74e-01 5.09e+00 angle pdb=" CA TYR B 26 " pdb=" CB TYR B 26 " pdb=" CG TYR B 26 " ideal model delta sigma weight residual 113.90 117.59 -3.69 1.80e+00 3.09e-01 4.19e+00 ... (remaining 71218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 17953 17.69 - 35.38: 710 35.38 - 53.08: 211 53.08 - 70.77: 66 70.77 - 88.46: 18 Dihedral angle restraints: 18958 sinusoidal: 10367 harmonic: 8591 Sorted by residual: dihedral pdb=" CA ASP O 196 " pdb=" C ASP O 196 " pdb=" N ALA O 197 " pdb=" CA ALA O 197 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CB GLU K 214 " pdb=" CG GLU K 214 " pdb=" CD GLU K 214 " pdb=" OE1 GLU K 214 " ideal model delta sinusoidal sigma weight residual 0.00 83.80 -83.80 1 3.00e+01 1.11e-03 9.51e+00 dihedral pdb=" CB ARG N 208 " pdb=" CG ARG N 208 " pdb=" CD ARG N 208 " pdb=" NE ARG N 208 " ideal model delta sinusoidal sigma weight residual 180.00 120.45 59.55 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 18955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2308 0.027 - 0.055: 630 0.055 - 0.082: 223 0.082 - 0.110: 97 0.110 - 0.137: 52 Chirality restraints: 3310 Sorted by residual: chirality pdb=" CA ILE N 141 " pdb=" N ILE N 141 " pdb=" C ILE N 141 " pdb=" CB ILE N 141 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA VAL M 112 " pdb=" N VAL M 112 " pdb=" C VAL M 112 " pdb=" CB VAL M 112 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE L 161 " pdb=" N ILE L 161 " pdb=" C ILE L 161 " pdb=" CB ILE L 161 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 3307 not shown) Planarity restraints: 5781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG O 68 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.71e+00 pdb=" N PRO O 69 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO O 69 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO O 69 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 57 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO B 58 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 58 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 58 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 56 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO I 57 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO I 57 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 57 " 0.025 5.00e-02 4.00e+02 ... (remaining 5778 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 972 2.15 - 2.76: 73339 2.76 - 3.37: 109207 3.37 - 3.99: 134591 3.99 - 4.60: 215846 Nonbonded interactions: 533955 Sorted by model distance: nonbonded pdb=" OD1 ASP I 116 " pdb=" H ALA I 119 " model vdw 1.534 2.450 nonbonded pdb=" OE1 GLU H 35 " pdb=" H GLU H 35 " model vdw 1.567 2.450 nonbonded pdb=" OE1 GLU I 191 " pdb=" H GLU I 191 " model vdw 1.573 2.450 nonbonded pdb=" HZ1 LYS N 6 " pdb=" O ALA N 67 " model vdw 1.583 2.450 nonbonded pdb=" OE1 GLU I 658 " pdb=" H GLU I 658 " model vdw 1.601 2.450 ... (remaining 533950 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: 6.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.240 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 40.660 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 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:9.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.002 0.034 20991 Z= 0.106 Angle : 0.403 4.990 28355 Z= 0.222 Chirality : 0.035 0.137 3310 Planarity : 0.003 0.060 3575 Dihedral : 9.930 84.822 7984 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.22 % Favored : 97.70 % Rotamer: Outliers : 0.90 % Allowed : 3.45 % Favored : 95.65 % 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: 3.15 (0.18), residues: 2519 helix: 3.37 (0.13), residues: 1522 sheet: 0.84 (0.33), residues: 261 loop : -0.32 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 39 TYR 0.018 0.001 TYR B 26 PHE 0.006 0.001 PHE I 373 TRP 0.007 0.001 TRP I 61 HIS 0.002 0.000 HIS O 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (20991) covalent geometry : angle 0.40317 / 0.22 (28355) hydrogen bonds : bond 0.12336 / 8.01 ( 1366) hydrogen bonds : angle 5.10611 / 3.76 ( 3990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 456 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 435 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 ASP cc_start: 0.8078 (t0) cc_final: 0.7751 (t0) REVERT: I 127 PHE cc_start: 0.6571 (m-80) cc_final: 0.6370 (m-80) REVERT: I 143 LEU cc_start: 0.6011 (tt) cc_final: 0.5504 (tt) REVERT: I 640 PHE cc_start: 0.6859 (OUTLIER) cc_final: 0.6429 (t80) REVERT: M 36 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6835 (mp0) REVERT: P 141 ARG cc_start: 0.6988 (ttp80) cc_final: 0.6762 (ttp-110) outliers start: 21 outliers final: 4 residues processed: 446 average time/residue: 1.2126 time to fit residues: 620.7795 Evaluate side-chains 252 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 247 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 640 PHE Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 158 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 ASN A 39 ASN A 63 ASN B 62 GLN B 74 ASN C 20 GLN C 52 ASN C 68 ASN D 43 ASN D 72 GLN I 93 GLN I 346 GLN I 350 GLN L 48 GLN L 63 GLN N 20 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 190 GLN ** T 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 819 ASN T 828 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.150829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.116631 restraints weight = 115735.849| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.24 r_work: 0.3712 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20991 Z= 0.138 Angle : 0.501 6.213 28355 Z= 0.268 Chirality : 0.037 0.171 3310 Planarity : 0.004 0.068 3575 Dihedral : 4.143 71.840 2774 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.54 % Favored : 97.30 % Rotamer: Outliers : 1.85 % Allowed : 11.85 % Favored : 86.30 % 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: 3.07 (0.17), residues: 2519 helix: 3.30 (0.13), residues: 1546 sheet: 0.76 (0.32), residues: 267 loop : -0.47 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 210 TYR 0.018 0.001 TYR B 26 PHE 0.012 0.001 PHE T 973 TRP 0.005 0.001 TRP I 61 HIS 0.004 0.001 HIS T 978 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (20991) covalent geometry : angle 0.50093 / 0.27 (28355) hydrogen bonds : bond 0.04676 / 3.10 ( 1366) hydrogen bonds : angle 4.12353 / 3.07 ( 3990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 320 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 277 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6934 (tm-30) REVERT: A 52 LYS cc_start: 0.9011 (mptm) cc_final: 0.8713 (mptm) REVERT: C 25 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8116 (mpp) REVERT: D 51 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7348 (mp10) REVERT: D 67 ASP cc_start: 0.8473 (t0) cc_final: 0.8100 (t0) REVERT: H 237 MET cc_start: 0.5178 (mmm) cc_final: 0.2323 (ppp) REVERT: I 127 PHE cc_start: 0.7115 (m-80) cc_final: 0.6869 (m-80) REVERT: I 640 PHE cc_start: 0.6085 (OUTLIER) cc_final: 0.5689 (t80) REVERT: K 170 MET cc_start: 0.8344 (mmm) cc_final: 0.6513 (pp-130) REVERT: K 216 LYS cc_start: 0.5714 (tmmt) cc_final: 0.5443 (ttpp) REVERT: L 31 TYR cc_start: 0.7873 (p90) cc_final: 0.7668 (OUTLIER) REVERT: L 139 GLU cc_start: 0.7655 (pt0) cc_final: 0.7367 (pt0) REVERT: L 248 TYR cc_start: 0.6409 (OUTLIER) cc_final: 0.5990 (m-10) REVERT: M 36 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7127 (mp0) REVERT: M 40 GLU cc_start: 0.7946 (mp0) cc_final: 0.7386 (mp0) REVERT: N 38 PHE cc_start: 0.6537 (t80) cc_final: 0.6284 (t80) REVERT: O 103 GLU cc_start: 0.7847 (mp0) cc_final: 0.7644 (mp0) REVERT: O 156 MET cc_start: 0.6286 (tpt) cc_final: 0.6064 (tpt) REVERT: P 141 ARG cc_start: 0.6781 (ttp80) cc_final: 0.6472 (ttp-110) REVERT: T 825 ARG cc_start: 0.8286 (tmm-80) cc_final: 0.8077 (tmm-80) REVERT: T 904 TRP cc_start: 0.6953 (OUTLIER) cc_final: 0.6645 (p-90) REVERT: T 912 TYR cc_start: 0.8983 (t80) cc_final: 0.8618 (t80) REVERT: T 944 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7319 (mtmt) REVERT: T 997 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7097 (tp) outliers start: 43 outliers final: 15 residues processed: 299 average time/residue: 1.1516 time to fit residues: 395.9998 Evaluate side-chains 251 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 231 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 640 PHE Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain L residue 248 TYR Chi-restraints excluded: chain M residue 136 TYR Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain P residue 248 ASP Chi-restraints excluded: chain T residue 820 MET Chi-restraints excluded: chain T residue 904 TRP Chi-restraints excluded: chain T residue 933 VAL Chi-restraints excluded: chain T residue 985 ILE Chi-restraints excluded: chain T residue 997 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 57 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 147 optimal weight: 0.0980 chunk 190 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 225 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 ASN A 63 ASN A 65 GLN B 74 ASN C 20 GLN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN D 43 ASN O 76 ASN P 228 HIS ** T 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.142574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.106819 restraints weight = 114725.242| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.25 r_work: 0.3591 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20991 Z= 0.205 Angle : 0.571 6.877 28355 Z= 0.308 Chirality : 0.039 0.149 3310 Planarity : 0.005 0.084 3575 Dihedral : 4.286 68.136 2769 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 2.37 % Allowed : 11.68 % Favored : 85.95 % 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: 2.45 (0.17), residues: 2519 helix: 2.80 (0.13), residues: 1559 sheet: 0.33 (0.33), residues: 269 loop : -0.69 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG P 198 TYR 0.025 0.002 TYR N 140 PHE 0.021 0.002 PHE I 373 TRP 0.011 0.001 TRP I 85 HIS 0.006 0.001 HIS I 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (20991) covalent geometry : angle 0.57133 / 0.31 (28355) hydrogen bonds : bond 0.04990 / 3.37 ( 1366) hydrogen bonds : angle 4.15642 / 3.08 ( 3990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 319 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6855 (tm-30) REVERT: A 39 ASN cc_start: 0.8144 (m-40) cc_final: 0.7934 (m110) REVERT: C 25 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8137 (mpp) REVERT: D 51 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7288 (mp10) REVERT: D 67 ASP cc_start: 0.8490 (t0) cc_final: 0.8087 (t0) REVERT: I 640 PHE cc_start: 0.6054 (OUTLIER) cc_final: 0.5632 (t80) REVERT: L 31 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.7573 (p90) REVERT: L 248 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.6279 (m-10) REVERT: O 103 GLU cc_start: 0.7862 (mp0) cc_final: 0.7615 (mp0) REVERT: O 156 MET cc_start: 0.6473 (tpt) cc_final: 0.5925 (tpt) REVERT: T 914 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8372 (tp30) REVERT: T 931 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7407 (mtpp) outliers start: 55 outliers final: 20 residues processed: 298 average time/residue: 1.0746 time to fit residues: 376.6434 Evaluate side-chains 257 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 640 PHE Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 248 TYR Chi-restraints excluded: chain M residue 136 TYR Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 248 ASP Chi-restraints excluded: chain T residue 820 MET Chi-restraints excluded: chain T residue 931 LYS Chi-restraints excluded: chain T residue 985 ILE Chi-restraints excluded: chain T residue 989 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 200 optimal weight: 0.0570 chunk 48 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 ASN A 63 ASN C 20 GLN C 68 ASN H 13 ASN I 346 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.141858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.106714 restraints weight = 114508.204| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.22 r_work: 0.3567 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20991 Z= 0.160 Angle : 0.505 5.585 28355 Z= 0.269 Chirality : 0.037 0.153 3310 Planarity : 0.004 0.061 3575 Dihedral : 4.173 69.455 2769 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.82 % Favored : 97.06 % Rotamer: Outliers : 1.98 % Allowed : 13.83 % Favored : 84.19 % 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: 2.56 (0.17), residues: 2519 helix: 2.90 (0.13), residues: 1565 sheet: 0.38 (0.33), residues: 268 loop : -0.68 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 87 TYR 0.022 0.002 TYR B 26 PHE 0.020 0.001 PHE I 101 TRP 0.007 0.001 TRP L 36 HIS 0.002 0.001 HIS D 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (20991) covalent geometry : angle 0.50493 / 0.27 (28355) hydrogen bonds : bond 0.04551 / 3.05 ( 1366) hydrogen bonds : angle 3.97813 / 2.95 ( 3990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6843 (tm-30) REVERT: B 28 TYR cc_start: 0.8221 (m-80) cc_final: 0.7889 (m-80) REVERT: C 21 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: C 25 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8025 (mpp) REVERT: D 51 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: D 67 ASP cc_start: 0.8470 (t0) cc_final: 0.8069 (t0) REVERT: H 237 MET cc_start: 0.5981 (mmm) cc_final: 0.5485 (mmt) REVERT: I 640 PHE cc_start: 0.5895 (OUTLIER) cc_final: 0.5282 (t80) REVERT: L 31 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7577 (p90) REVERT: O 103 GLU cc_start: 0.7849 (mp0) cc_final: 0.7572 (mp0) REVERT: O 156 MET cc_start: 0.6458 (tpt) cc_final: 0.5951 (tpt) REVERT: T 914 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8479 (tp30) REVERT: T 977 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.8034 (m-80) outliers start: 46 outliers final: 18 residues processed: 265 average time/residue: 1.1111 time to fit residues: 342.2436 Evaluate side-chains 247 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 557 ILE Chi-restraints excluded: chain I residue 640 PHE Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 136 TYR Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 171 TYR Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain T residue 820 MET Chi-restraints excluded: chain T residue 977 PHE Chi-restraints excluded: chain T residue 983 ARG Chi-restraints excluded: chain T residue 985 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 189 optimal weight: 7.9990 chunk 143 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 229 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 ASN A 63 ASN C 20 GLN C 68 ASN M 139 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.141831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.106670 restraints weight = 113837.803| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.24 r_work: 0.3576 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20991 Z= 0.137 Angle : 0.485 6.285 28355 Z= 0.257 Chirality : 0.036 0.150 3310 Planarity : 0.004 0.063 3575 Dihedral : 4.043 66.963 2767 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.82 % Favored : 97.02 % Rotamer: Outliers : 1.77 % Allowed : 14.22 % Favored : 84.02 % 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: 2.67 (0.17), residues: 2519 helix: 3.01 (0.13), residues: 1566 sheet: 0.34 (0.33), residues: 269 loop : -0.69 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 218 TYR 0.022 0.001 TYR B 26 PHE 0.013 0.001 PHE I 101 TRP 0.012 0.001 TRP I 51 HIS 0.003 0.000 HIS I 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (20991) covalent geometry : angle 0.48461 / 0.26 (28355) hydrogen bonds : bond 0.04348 / 2.93 ( 1366) hydrogen bonds : angle 3.87244 / 2.88 ( 3990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6950 (tm-30) REVERT: C 25 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8252 (mpp) REVERT: D 51 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: D 67 ASP cc_start: 0.8510 (t0) cc_final: 0.8114 (t0) REVERT: H 237 MET cc_start: 0.6045 (mmm) cc_final: 0.5660 (mmt) REVERT: I 558 GLN cc_start: 0.7696 (tp40) cc_final: 0.7296 (tp-100) REVERT: I 640 PHE cc_start: 0.5942 (OUTLIER) cc_final: 0.5374 (t80) REVERT: L 31 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7651 (p90) REVERT: O 103 GLU cc_start: 0.7811 (mp0) cc_final: 0.7559 (mp0) REVERT: O 156 MET cc_start: 0.6459 (tpt) cc_final: 0.5881 (tpt) REVERT: T 814 LYS cc_start: 0.5884 (pmtt) cc_final: 0.5179 (ptmt) REVERT: T 901 ASN cc_start: 0.8131 (m-40) cc_final: 0.7925 (p0) REVERT: T 977 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8082 (m-80) outliers start: 41 outliers final: 19 residues processed: 262 average time/residue: 1.0708 time to fit residues: 329.3458 Evaluate side-chains 246 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain I residue 446 MET Chi-restraints excluded: chain I residue 640 PHE Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 136 TYR Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain O residue 171 TYR Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain T residue 820 MET Chi-restraints excluded: chain T residue 966 ILE Chi-restraints excluded: chain T residue 977 PHE Chi-restraints excluded: chain T residue 985 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 65 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 159 optimal weight: 0.4980 chunk 136 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 ASN A 63 ASN A 66 GLN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN O 128 GLN T 959 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.140357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.105102 restraints weight = 114099.662| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.21 r_work: 0.3544 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20991 Z= 0.148 Angle : 0.498 6.642 28355 Z= 0.263 Chirality : 0.037 0.149 3310 Planarity : 0.004 0.059 3575 Dihedral : 4.056 68.324 2767 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 1.98 % Allowed : 14.52 % Favored : 83.50 % 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: 2.66 (0.17), residues: 2519 helix: 3.00 (0.13), residues: 1567 sheet: 0.32 (0.33), residues: 269 loop : -0.70 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 177 TYR 0.022 0.001 TYR B 26 PHE 0.014 0.001 PHE I 101 TRP 0.011 0.001 TRP I 51 HIS 0.003 0.001 HIS N 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (20991) covalent geometry : angle 0.49754 / 0.26 (28355) hydrogen bonds : bond 0.04318 / 2.90 ( 1366) hydrogen bonds : angle 3.85647 / 2.87 ( 3990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6891 (tm-30) REVERT: C 25 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8234 (mpp) REVERT: D 51 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: H 237 MET cc_start: 0.6200 (mmm) cc_final: 0.5928 (mmt) REVERT: I 189 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.6153 (tptm) REVERT: I 640 PHE cc_start: 0.5804 (OUTLIER) cc_final: 0.5189 (t80) REVERT: K 197 GLU cc_start: 0.5805 (tp30) cc_final: 0.5585 (mm-30) REVERT: L 31 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7596 (p90) REVERT: O 103 GLU cc_start: 0.7859 (mp0) cc_final: 0.7613 (mp0) REVERT: O 156 MET cc_start: 0.6406 (tpt) cc_final: 0.5845 (tpt) REVERT: P 256 TYR cc_start: 0.5624 (m-80) cc_final: 0.5170 (m-80) REVERT: T 814 LYS cc_start: 0.6023 (OUTLIER) cc_final: 0.5366 (ptmt) REVERT: T 977 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8104 (t80) outliers start: 46 outliers final: 23 residues processed: 259 average time/residue: 1.0675 time to fit residues: 322.6147 Evaluate side-chains 252 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 640 PHE Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 136 TYR Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 171 TYR Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain P residue 248 ASP Chi-restraints excluded: chain T residue 814 LYS Chi-restraints excluded: chain T residue 820 MET Chi-restraints excluded: chain T residue 959 HIS Chi-restraints excluded: chain T residue 977 PHE Chi-restraints excluded: chain T residue 983 ARG Chi-restraints excluded: chain T residue 985 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 71 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 208 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 ASN A 63 ASN ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.139838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.104584 restraints weight = 113621.471| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.22 r_work: 0.3520 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20991 Z= 0.157 Angle : 0.501 6.724 28355 Z= 0.265 Chirality : 0.037 0.148 3310 Planarity : 0.004 0.057 3575 Dihedral : 4.080 67.859 2767 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.14 % Favored : 96.71 % Rotamer: Outliers : 1.68 % Allowed : 15.12 % Favored : 83.20 % 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: 2.63 (0.17), residues: 2519 helix: 2.99 (0.13), residues: 1568 sheet: 0.27 (0.34), residues: 269 loop : -0.75 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 218 TYR 0.022 0.001 TYR B 26 PHE 0.013 0.001 PHE I 373 TRP 0.011 0.001 TRP I 51 HIS 0.034 0.001 HIS T 959 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (20991) covalent geometry : angle 0.50093 / 0.27 (28355) hydrogen bonds : bond 0.04376 / 2.93 ( 1366) hydrogen bonds : angle 3.85575 / 2.87 ( 3990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6953 (tm-30) REVERT: A 59 LYS cc_start: 0.9134 (ptmm) cc_final: 0.8899 (ptmm) REVERT: A 63 ASN cc_start: 0.8672 (m-40) cc_final: 0.8304 (m110) REVERT: C 25 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8237 (mpp) REVERT: D 51 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7393 (mp10) REVERT: H 237 MET cc_start: 0.6021 (mmm) cc_final: 0.5698 (mmt) REVERT: I 558 GLN cc_start: 0.7760 (tp40) cc_final: 0.7399 (tp-100) REVERT: I 640 PHE cc_start: 0.5944 (OUTLIER) cc_final: 0.5244 (t80) REVERT: K 197 GLU cc_start: 0.5934 (tp30) cc_final: 0.5664 (mm-30) REVERT: O 103 GLU cc_start: 0.7848 (mp0) cc_final: 0.7524 (mp0) REVERT: O 114 ASP cc_start: 0.8343 (m-30) cc_final: 0.8118 (m-30) REVERT: O 156 MET cc_start: 0.6505 (tpt) cc_final: 0.5919 (tpt) REVERT: P 256 TYR cc_start: 0.5533 (m-80) cc_final: 0.5068 (m-80) REVERT: T 814 LYS cc_start: 0.6220 (OUTLIER) cc_final: 0.5608 (ptmt) REVERT: T 977 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8233 (t80) outliers start: 39 outliers final: 24 residues processed: 251 average time/residue: 1.0534 time to fit residues: 309.3443 Evaluate side-chains 247 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain I residue 640 PHE Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 155 ILE Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 136 TYR Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain O residue 171 TYR Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain P residue 248 ASP Chi-restraints excluded: chain T residue 814 LYS Chi-restraints excluded: chain T residue 820 MET Chi-restraints excluded: chain T residue 977 PHE Chi-restraints excluded: chain T residue 983 ARG Chi-restraints excluded: chain T residue 985 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 196 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 ASN A 66 GLN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN I 93 GLN ** M 69 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 = 0.4199 r_free = 0.4199 target = 0.138731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.103448 restraints weight = 113788.808| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.23 r_work: 0.3528 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20991 Z= 0.159 Angle : 0.506 6.343 28355 Z= 0.269 Chirality : 0.037 0.145 3310 Planarity : 0.004 0.063 3575 Dihedral : 4.148 68.440 2767 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.33 % Favored : 96.51 % Rotamer: Outliers : 1.94 % Allowed : 15.42 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.17), residues: 2519 helix: 2.99 (0.13), residues: 1568 sheet: 0.26 (0.34), residues: 269 loop : -0.83 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 218 TYR 0.023 0.001 TYR N 189 PHE 0.015 0.001 PHE I 44 TRP 0.015 0.001 TRP I 51 HIS 0.003 0.001 HIS N 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (20991) covalent geometry : angle 0.50596 / 0.27 (28355) hydrogen bonds : bond 0.04401 / 2.95 ( 1366) hydrogen bonds : angle 3.87190 / 2.89 ( 3990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6975 (tm-30) REVERT: C 25 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8234 (mpp) REVERT: D 51 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: H 237 MET cc_start: 0.6051 (mmm) cc_final: 0.5670 (mmt) REVERT: I 195 GLU cc_start: 0.8112 (tp30) cc_final: 0.7874 (tp30) REVERT: I 558 GLN cc_start: 0.7809 (tp40) cc_final: 0.7437 (tp-100) REVERT: I 640 PHE cc_start: 0.5915 (OUTLIER) cc_final: 0.5159 (t80) REVERT: K 197 GLU cc_start: 0.6181 (tp30) cc_final: 0.5834 (mm-30) REVERT: O 62 LYS cc_start: 0.6224 (OUTLIER) cc_final: 0.5667 (mptp) REVERT: O 103 GLU cc_start: 0.7850 (mp0) cc_final: 0.7513 (mp0) REVERT: O 156 MET cc_start: 0.6574 (tpt) cc_final: 0.5956 (tpt) REVERT: P 256 TYR cc_start: 0.5593 (m-80) cc_final: 0.5130 (m-80) REVERT: T 814 LYS cc_start: 0.6378 (OUTLIER) cc_final: 0.5762 (ptmt) REVERT: T 901 ASN cc_start: 0.8138 (m-40) cc_final: 0.7758 (p0) REVERT: T 977 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8287 (t80) REVERT: T 983 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6418 (tmm-80) outliers start: 45 outliers final: 22 residues processed: 259 average time/residue: 1.0521 time to fit residues: 318.6444 Evaluate side-chains 252 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain I residue 640 PHE Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 136 TYR Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain O residue 171 TYR Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain P residue 248 ASP Chi-restraints excluded: chain T residue 814 LYS Chi-restraints excluded: chain T residue 820 MET Chi-restraints excluded: chain T residue 977 PHE Chi-restraints excluded: chain T residue 983 ARG Chi-restraints excluded: chain T residue 985 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 50 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 234 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 ASN ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.139534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.104534 restraints weight = 113503.292| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 3.22 r_work: 0.3533 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20991 Z= 0.118 Angle : 0.489 6.663 28355 Z= 0.256 Chirality : 0.036 0.195 3310 Planarity : 0.004 0.065 3575 Dihedral : 4.062 65.837 2767 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.82 % Favored : 97.02 % Rotamer: Outliers : 1.51 % Allowed : 16.20 % Favored : 82.29 % 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: 2.74 (0.17), residues: 2519 helix: 3.09 (0.13), residues: 1570 sheet: 0.31 (0.34), residues: 269 loop : -0.73 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 218 TYR 0.022 0.001 TYR B 26 PHE 0.015 0.001 PHE H 236 TRP 0.008 0.001 TRP I 51 HIS 0.003 0.000 HIS D 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (20991) covalent geometry : angle 0.48913 / 0.26 (28355) hydrogen bonds : bond 0.04135 / 2.77 ( 1366) hydrogen bonds : angle 3.76734 / 2.81 ( 3990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7394 (tm-30) cc_final: 0.6947 (tm-30) REVERT: C 25 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8211 (mpp) REVERT: D 51 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: H 237 MET cc_start: 0.5802 (mmm) cc_final: 0.5457 (mmt) REVERT: I 558 GLN cc_start: 0.7779 (tp40) cc_final: 0.7410 (tp-100) REVERT: I 640 PHE cc_start: 0.5890 (OUTLIER) cc_final: 0.5192 (t80) REVERT: K 197 GLU cc_start: 0.6130 (tp30) cc_final: 0.5849 (mm-30) REVERT: L 29 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8294 (tt) REVERT: O 103 GLU cc_start: 0.7825 (mp0) cc_final: 0.7499 (mp0) REVERT: O 156 MET cc_start: 0.6507 (tpt) cc_final: 0.5893 (tpt) REVERT: T 814 LYS cc_start: 0.6467 (OUTLIER) cc_final: 0.5876 (ptmt) REVERT: T 901 ASN cc_start: 0.8035 (m-40) cc_final: 0.7661 (p0) REVERT: T 977 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8269 (t80) REVERT: T 983 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6262 (tmm-80) outliers start: 35 outliers final: 21 residues processed: 252 average time/residue: 1.0547 time to fit residues: 312.8601 Evaluate side-chains 251 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 640 PHE Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 136 TYR Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain P residue 248 ASP Chi-restraints excluded: chain T residue 814 LYS Chi-restraints excluded: chain T residue 820 MET Chi-restraints excluded: chain T residue 977 PHE Chi-restraints excluded: chain T residue 983 ARG Chi-restraints excluded: chain T residue 985 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 209 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 63 optimal weight: 0.2980 chunk 134 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 ASN ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.139122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.104129 restraints weight = 113523.677| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.21 r_work: 0.3545 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20991 Z= 0.125 Angle : 0.492 7.549 28355 Z= 0.258 Chirality : 0.036 0.181 3310 Planarity : 0.004 0.066 3575 Dihedral : 4.061 66.674 2767 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.02 % Favored : 96.82 % Rotamer: Outliers : 1.38 % Allowed : 16.42 % Favored : 82.21 % 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: 2.75 (0.17), residues: 2519 helix: 3.12 (0.13), residues: 1569 sheet: 0.33 (0.34), residues: 269 loop : -0.79 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 218 TYR 0.022 0.001 TYR B 26 PHE 0.014 0.001 PHE I 44 TRP 0.019 0.001 TRP I 51 HIS 0.002 0.000 HIS D 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (20991) covalent geometry : angle 0.49247 / 0.26 (28355) hydrogen bonds : bond 0.04095 / 2.74 ( 1366) hydrogen bonds : angle 3.76096 / 2.81 ( 3990) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5038 Ramachandran restraints generated. 2519 Oldfield, 0 Emsley, 2519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 51 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 246 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6837 (tm-30) REVERT: A 39 ASN cc_start: 0.8157 (m-40) cc_final: 0.7934 (m110) REVERT: C 25 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8188 (mpp) REVERT: D 51 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7384 (mp10) REVERT: H 237 MET cc_start: 0.5850 (mmm) cc_final: 0.5591 (mmt) REVERT: I 195 GLU cc_start: 0.8203 (tp30) cc_final: 0.7950 (tp30) REVERT: I 558 GLN cc_start: 0.7745 (tp40) cc_final: 0.7345 (tp-100) REVERT: I 640 PHE cc_start: 0.5701 (OUTLIER) cc_final: 0.5053 (t80) REVERT: K 197 GLU cc_start: 0.6312 (tp30) cc_final: 0.5998 (mm-30) REVERT: L 139 GLU cc_start: 0.7679 (pt0) cc_final: 0.7358 (pt0) REVERT: O 62 LYS cc_start: 0.6229 (OUTLIER) cc_final: 0.5695 (mptp) REVERT: O 103 GLU cc_start: 0.7848 (mp0) cc_final: 0.7504 (mp0) REVERT: O 156 MET cc_start: 0.6464 (tpt) cc_final: 0.5881 (tpt) REVERT: P 256 TYR cc_start: 0.5588 (m-80) cc_final: 0.5054 (m-80) REVERT: T 814 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6035 (ptmt) REVERT: T 901 ASN cc_start: 0.7980 (m-40) cc_final: 0.7562 (p0) REVERT: T 977 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8242 (t80) REVERT: T 983 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6206 (tmm-80) outliers start: 32 outliers final: 22 residues processed: 255 average time/residue: 1.0616 time to fit residues: 315.8432 Evaluate side-chains 253 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 51 GLN Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain I residue 640 PHE Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain M residue 40 GLU Chi-restraints excluded: chain M residue 136 TYR Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 62 LYS Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain P residue 248 ASP Chi-restraints excluded: chain T residue 814 LYS Chi-restraints excluded: chain T residue 820 MET Chi-restraints excluded: chain T residue 909 LEU Chi-restraints excluded: chain T residue 977 PHE Chi-restraints excluded: chain T residue 983 ARG Chi-restraints excluded: chain T residue 985 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 221 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 ASN ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** M 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.137966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.102815 restraints weight = 114414.419| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.22 r_work: 0.3528 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20991 Z= 0.159 Angle : 0.523 8.924 28355 Z= 0.277 Chirality : 0.037 0.167 3310 Planarity : 0.004 0.064 3575 Dihedral : 4.179 68.881 2767 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.33 % Favored : 96.51 % Rotamer: Outliers : 1.46 % Allowed : 16.67 % Favored : 81.86 % 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: 2.60 (0.17), residues: 2519 helix: 3.02 (0.13), residues: 1567 sheet: 0.23 (0.34), residues: 266 loop : -0.88 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 219 TYR 0.023 0.002 TYR N 189 PHE 0.014 0.001 PHE I 44 TRP 0.017 0.001 TRP I 51 HIS 0.004 0.001 HIS K 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (20991) covalent geometry : angle 0.52343 / 0.28 (28355) hydrogen bonds : bond 0.04324 / 2.90 ( 1366) hydrogen bonds : angle 3.83338 / 2.86 ( 3990) =============================================================================== Job complete usr+sys time: 13040.84 seconds wall clock time: 221 minutes 12.31 seconds (13272.31 seconds total)