Starting phenix.real_space_refine on Tue Nov 18 20:21:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rd8_4809/11_2025/6rd8_4809.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rd8_4809/11_2025/6rd8_4809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rd8_4809/11_2025/6rd8_4809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rd8_4809/11_2025/6rd8_4809.map" model { file = "/net/cci-nas-00/data/ceres_data/6rd8_4809/11_2025/6rd8_4809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rd8_4809/11_2025/6rd8_4809.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 58 5.16 5 C 11231 2.51 5 N 2862 2.21 5 O 3160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17312 Number of models: 1 Model: "" Number of chains: 26 Chain: "0" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 605 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "A" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 515 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 4.54, per 1000 atoms: 0.26 Number of scatterers: 17312 At special positions: 0 Unit cell: (131.625, 117.936, 220.077, 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) Zn 1 29.99 S 58 16.00 O 3160 8.00 N 2862 7.00 C 11231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 9 69 " - pdb=" SG CYS 9 79 " distance=2.21 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: 1.63 Conformation dependent library (CDL) restraints added in 771.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 2 sheets defined 79.1% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain '0' and resid 3 through 10 removed outlier: 3.901A pdb=" N ALA 0 10 " --> pdb=" O TYR 0 6 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 31 Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 51 through 56 Processing helix chain '0' and resid 57 through 61 removed outlier: 3.518A pdb=" N GLN 0 60 " --> pdb=" O SER 0 57 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 74 Processing helix chain '1' and resid 106 through 143 removed outlier: 4.229A pdb=" N LYS 1 143 " --> pdb=" O ALA 1 139 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 177 Processing helix chain '1' and resid 190 through 205 Processing helix chain '1' and resid 209 through 223 Processing helix chain '1' and resid 241 through 271 removed outlier: 3.573A pdb=" N ARG 1 267 " --> pdb=" O LEU 1 263 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 3.694A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE 1 276 " --> pdb=" O GLU 1 273 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL 1 277 " --> pdb=" O LEU 1 274 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 272 through 277' Processing helix chain '1' and resid 278 through 282 Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 306 Processing helix chain '1' and resid 310 through 317 Processing helix chain '1' and resid 318 through 322 removed outlier: 3.616A pdb=" N PHE 1 321 " --> pdb=" O SER 1 318 " (cutoff:3.500A) Processing helix chain '1' and resid 323 through 327 removed outlier: 3.784A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 338 through 351 Processing helix chain '1' and resid 353 through 363 Processing helix chain '1' and resid 364 through 367 removed outlier: 3.505A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 364 through 367' Processing helix chain '1' and resid 375 through 388 Processing helix chain '1' and resid 392 through 421 removed outlier: 3.659A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.871A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 446 removed outlier: 3.716A pdb=" N ASN 1 446 " --> pdb=" O ASP 1 442 " (cutoff:3.500A) Processing helix chain '1' and resid 446 through 461 removed outlier: 3.820A pdb=" N ALA 1 459 " --> pdb=" O ALA 1 455 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 479 removed outlier: 3.935A pdb=" N ASP 1 479 " --> pdb=" O GLU 1 475 " (cutoff:3.500A) Processing helix chain '1' and resid 480 through 483 removed outlier: 3.603A pdb=" N ILE 1 483 " --> pdb=" O PRO 1 480 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 480 through 483' Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 515 removed outlier: 4.214A pdb=" N ASP 1 504 " --> pdb=" O LEU 1 500 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE 1 505 " --> pdb=" O GLU 1 501 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 540 removed outlier: 3.647A pdb=" N LEU 1 522 " --> pdb=" O GLU 1 518 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLY 1 537 " --> pdb=" O GLN 1 533 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE 1 538 " --> pdb=" O LYS 1 534 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU 1 540 " --> pdb=" O PHE 1 536 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 Processing helix chain '1' and resid 549 through 562 removed outlier: 3.594A pdb=" N GLU 1 559 " --> pdb=" O LYS 1 555 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 588 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 592 through 606 Processing helix chain '3' and resid 78 through 87 removed outlier: 3.638A pdb=" N ASN 3 87 " --> pdb=" O SER 3 83 " (cutoff:3.500A) Processing helix chain '3' and resid 91 through 99 Processing helix chain '3' and resid 102 through 114 Processing helix chain '3' and resid 117 through 129 removed outlier: 3.516A pdb=" N PHE 3 121 " --> pdb=" O SER 3 117 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU 3 126 " --> pdb=" O VAL 3 122 " (cutoff:3.500A) Processing helix chain '3' and resid 136 through 151 Processing helix chain '3' and resid 154 through 168 Processing helix chain '3' and resid 173 through 187 Processing helix chain '3' and resid 191 through 204 Processing helix chain '3' and resid 215 through 229 removed outlier: 3.514A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 241 Processing helix chain '3' and resid 245 through 251 Processing helix chain '3' and resid 253 through 272 Processing helix chain '3' and resid 275 through 277 No H-bonds generated for 'chain '3' and resid 275 through 277' Processing helix chain '3' and resid 278 through 287 Processing helix chain '3' and resid 293 through 312 Processing helix chain '5' and resid 7 through 29 Processing helix chain '5' and resid 29 through 59 removed outlier: 4.150A pdb=" N THR 5 33 " --> pdb=" O GLN 5 29 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 68 Processing helix chain '5' and resid 72 through 81 removed outlier: 3.541A pdb=" N PHE 5 81 " --> pdb=" O LEU 5 77 " (cutoff:3.500A) Processing helix chain '5' and resid 87 through 107 removed outlier: 4.324A pdb=" N HIS 5 91 " --> pdb=" O ALA 5 87 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 Processing helix chain '6' and resid 30 through 42 Processing helix chain '6' and resid 46 through 58 removed outlier: 5.092A pdb=" N LYS 6 52 " --> pdb=" O LEU 6 48 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N THR 6 53 " --> pdb=" O SER 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 72 through 96 Processing helix chain '6' and resid 98 through 120 removed outlier: 3.618A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 133 removed outlier: 3.721A pdb=" N ALA 6 133 " --> pdb=" O PHE 6 129 " (cutoff:3.500A) Processing helix chain '6' and resid 133 through 138 removed outlier: 3.874A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '8' and resid 5 through 9 removed outlier: 3.901A pdb=" N LYS 8 9 " --> pdb=" O VAL 8 6 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 31 Processing helix chain '8' and resid 31 through 39 removed outlier: 3.582A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 79 removed outlier: 3.656A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) Processing helix chain '9' and resid 2 through 17 removed outlier: 4.050A pdb=" N PHE 9 6 " --> pdb=" O ALA 9 2 " (cutoff:3.500A) Processing helix chain '9' and resid 32 through 56 removed outlier: 3.512A pdb=" N ASN 9 56 " --> pdb=" O LEU 9 52 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 95 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 69 through 92 removed outlier: 4.042A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 126 removed outlier: 3.887A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 69 through 92 removed outlier: 4.165A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 125 removed outlier: 3.601A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 69 Processing helix chain 'C' and resid 70 through 92 removed outlier: 3.917A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 3.773A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.864A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 3.573A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 3.900A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 92 removed outlier: 3.739A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 126 removed outlier: 3.673A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 69 removed outlier: 4.137A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 92 removed outlier: 3.938A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 126 removed outlier: 3.592A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.598A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 92 removed outlier: 4.142A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 126 removed outlier: 4.044A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 69 removed outlier: 3.864A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 92 removed outlier: 4.119A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 127 removed outlier: 4.171A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 Processing helix chain 'I' and resid 70 through 92 removed outlier: 3.668A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 127 removed outlier: 4.536A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 Processing helix chain 'J' and resid 70 through 92 removed outlier: 4.068A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 126 removed outlier: 4.378A pdb=" N SER J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL J 120 " --> pdb=" O PHE J 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 120 Processing helix chain 'M' and resid 134 through 145 Processing helix chain 'M' and resid 147 through 166 Processing helix chain 'M' and resid 177 through 200 removed outlier: 3.522A pdb=" N ALA M 181 " --> pdb=" O GLY M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 264 removed outlier: 3.891A pdb=" N LEU M 224 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 270 through 309 removed outlier: 3.936A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 183 through 184 Processing sheet with id=AA2, first strand: chain '3' and resid 315 through 317 1317 hydrogen bonds defined for protein. 3915 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: 3.12 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4003 1.33 - 1.45: 3604 1.45 - 1.57: 9932 1.57 - 1.69: 0 1.69 - 1.81: 97 Bond restraints: 17636 Sorted by residual: bond pdb=" C VAL M 271 " pdb=" N PRO M 272 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.20e-02 6.94e+03 1.72e+01 bond pdb=" C VAL 1 107 " pdb=" N PRO 1 108 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.23e-02 6.61e+03 1.41e+01 bond pdb=" N LEU M 265 " pdb=" CA LEU M 265 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.00e-02 1.00e+04 1.05e+01 bond pdb=" N VAL 9 78 " pdb=" CA VAL 9 78 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" C ILE 8 41 " pdb=" N PRO 8 42 " ideal model delta sigma weight residual 1.336 1.375 -0.039 1.23e-02 6.61e+03 1.03e+01 ... (remaining 17631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 23123 2.17 - 4.34: 716 4.34 - 6.50: 68 6.50 - 8.67: 21 8.67 - 10.84: 5 Bond angle restraints: 23933 Sorted by residual: angle pdb=" N PRO 3 77 " pdb=" CA PRO 3 77 " pdb=" CB PRO 3 77 " ideal model delta sigma weight residual 103.00 110.50 -7.50 1.10e+00 8.26e-01 4.65e+01 angle pdb=" N GLY 1 231 " pdb=" CA GLY 1 231 " pdb=" C GLY 1 231 " ideal model delta sigma weight residual 115.80 107.66 8.14 1.74e+00 3.30e-01 2.19e+01 angle pdb=" C ASN 9 60 " pdb=" N PRO 9 61 " pdb=" CA PRO 9 61 " ideal model delta sigma weight residual 120.38 124.76 -4.38 1.03e+00 9.43e-01 1.81e+01 angle pdb=" N LYS 3 129 " pdb=" CA LYS 3 129 " pdb=" C LYS 3 129 " ideal model delta sigma weight residual 109.81 119.01 -9.20 2.21e+00 2.05e-01 1.73e+01 angle pdb=" N PRO 9 58 " pdb=" CA PRO 9 58 " pdb=" CB PRO 9 58 " ideal model delta sigma weight residual 103.25 98.92 4.33 1.05e+00 9.07e-01 1.70e+01 ... (remaining 23928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.49: 9954 26.49 - 52.99: 429 52.99 - 79.48: 44 79.48 - 105.97: 7 105.97 - 132.46: 1 Dihedral angle restraints: 10435 sinusoidal: 3837 harmonic: 6598 Sorted by residual: dihedral pdb=" CA PHE 9 57 " pdb=" C PHE 9 57 " pdb=" N PRO 9 58 " pdb=" CA PRO 9 58 " ideal model delta harmonic sigma weight residual 180.00 47.54 132.46 0 5.00e+00 4.00e-02 7.02e+02 dihedral pdb=" CB CYS 9 69 " pdb=" SG CYS 9 69 " pdb=" SG CYS 9 79 " pdb=" CB CYS 9 79 " ideal model delta sinusoidal sigma weight residual 93.00 -179.66 -87.34 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CA LEU 8 8 " pdb=" C LEU 8 8 " pdb=" N LYS 8 9 " pdb=" CA LYS 8 9 " ideal model delta harmonic sigma weight residual 180.00 -155.26 -24.74 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 10432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2385 0.064 - 0.127: 381 0.127 - 0.191: 50 0.191 - 0.254: 11 0.254 - 0.318: 2 Chirality restraints: 2829 Sorted by residual: chirality pdb=" CB ILE H 95 " pdb=" CA ILE H 95 " pdb=" CG1 ILE H 95 " pdb=" CG2 ILE H 95 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB ILE 3 101 " pdb=" CA ILE 3 101 " pdb=" CG1 ILE 3 101 " pdb=" CG2 ILE 3 101 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA ALA 9 71 " pdb=" N ALA 9 71 " pdb=" C ALA 9 71 " pdb=" CB ALA 9 71 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 2826 not shown) Planarity restraints: 3017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE 9 59 " -0.019 2.00e-02 2.50e+03 4.04e-02 1.64e+01 pdb=" C PHE 9 59 " 0.070 2.00e-02 2.50e+03 pdb=" O PHE 9 59 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN 9 60 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 108 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.58e+00 pdb=" C ALA B 108 " 0.054 2.00e-02 2.50e+03 pdb=" O ALA B 108 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU B 109 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 107 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.29e+00 pdb=" C PHE C 107 " 0.053 2.00e-02 2.50e+03 pdb=" O PHE C 107 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA C 108 " -0.018 2.00e-02 2.50e+03 ... (remaining 3014 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 49 2.41 - 3.03: 9415 3.03 - 3.66: 27967 3.66 - 4.28: 40865 4.28 - 4.90: 67856 Nonbonded interactions: 146152 Sorted by model distance: nonbonded pdb=" O ASN 9 56 " pdb=" OD1 ASN 9 56 " model vdw 1.790 3.040 nonbonded pdb=" OE2 GLU A 111 " pdb=" OD1 ASN M 243 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR 5 62 " pdb=" O PHE 6 146 " model vdw 2.241 3.040 nonbonded pdb=" O ALA C 64 " pdb=" OG1 THR C 68 " model vdw 2.266 3.040 nonbonded pdb=" O ILE 6 100 " pdb=" ND2 ASN 6 104 " model vdw 2.272 3.120 ... (remaining 146147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 54 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 11.510 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.850 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.009 0.352 17639 Z= 0.393 Angle : 0.912 21.320 23935 Z= 0.539 Chirality : 0.050 0.318 2829 Planarity : 0.008 0.071 3017 Dihedral : 14.783 132.463 6184 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.38 % Favored : 97.53 % Rotamer: Outliers : 0.45 % Allowed : 8.20 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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 (0.14), residues: 2271 helix: -1.46 (0.10), residues: 1701 sheet: None (None), residues: 0 loop : -1.93 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 1 434 TYR 0.015 0.002 TYR 5 51 PHE 0.026 0.002 PHE 9 63 TRP 0.015 0.002 TRP 3 109 HIS 0.008 0.002 HIS 9 41 Details of bonding type rmsd covalent geometry : bond 0.00839 (17636) covalent geometry : angle 0.90048 (23933) SS BOND : bond 0.17894 ( 1) SS BOND : angle 15.85384 ( 2) hydrogen bonds : bond 0.14445 ( 1317) hydrogen bonds : angle 6.45810 ( 3915) metal coordination : bond 0.26969 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 383 time to evaluate : 0.661 Fit side-chains REVERT: 0 40 LYS cc_start: 0.8920 (ttpt) cc_final: 0.7407 (mptt) REVERT: 0 41 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6950 (pm20) REVERT: 1 34 GLU cc_start: 0.5822 (tp30) cc_final: 0.5082 (mm-30) REVERT: 1 150 ARG cc_start: 0.7728 (mmp-170) cc_final: 0.6729 (tpt170) REVERT: 1 194 LYS cc_start: 0.7777 (ttmt) cc_final: 0.7561 (tttp) REVERT: 1 441 PHE cc_start: 0.8693 (m-80) cc_final: 0.8380 (m-80) REVERT: 5 94 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7338 (pttt) REVERT: 5 111 LYS cc_start: 0.6493 (tptt) cc_final: 0.5432 (mmtp) REVERT: 8 70 LYS cc_start: 0.8579 (ttpp) cc_final: 0.7225 (mptt) REVERT: A 81 MET cc_start: 0.8621 (ttp) cc_final: 0.8374 (ttp) REVERT: C 87 ASN cc_start: 0.8351 (t0) cc_final: 0.8080 (t0) REVERT: C 97 LYS cc_start: 0.8342 (tptt) cc_final: 0.7857 (tptt) REVERT: E 91 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.7684 (mtt180) REVERT: F 86 ILE cc_start: 0.8997 (mt) cc_final: 0.8707 (mp) REVERT: H 86 ILE cc_start: 0.9192 (mt) cc_final: 0.8968 (mt) REVERT: I 61 MET cc_start: 0.7296 (mmt) cc_final: 0.6993 (mmm) REVERT: I 98 GLN cc_start: 0.7874 (tt0) cc_final: 0.7570 (tt0) REVERT: M 257 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7343 (mpt) REVERT: M 313 ASP cc_start: 0.7818 (t0) cc_final: 0.7584 (t0) REVERT: M 321 LYS cc_start: 0.8209 (ptmt) cc_final: 0.7958 (ptpt) outliers start: 8 outliers final: 6 residues processed: 388 average time/residue: 0.1563 time to fit residues: 88.3239 Evaluate side-chains 339 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 332 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 264 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.5980 chunk 212 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 1 166 ASN 1 285 GLN 1 313 GLN 1 316 ASN 1 430 GLN 1 482 ASN 3 179 GLN 3 206 ASN 5 29 GLN 5 79 ASN 6 40 ASN 8 26 HIS 9 35 GLN A 98 GLN B 94 ASN I 87 ASN M 163 ASN M 243 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093256 restraints weight = 26271.118| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.79 r_work: 0.2892 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17639 Z= 0.145 Angle : 0.534 7.845 23935 Z= 0.280 Chirality : 0.036 0.162 2829 Planarity : 0.005 0.056 3017 Dihedral : 5.360 91.934 2424 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.08 % Allowed : 11.96 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.17), residues: 2271 helix: 0.58 (0.12), residues: 1715 sheet: None (None), residues: 0 loop : -1.02 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 91 TYR 0.012 0.001 TYR 5 51 PHE 0.016 0.001 PHE D 122 TRP 0.013 0.001 TRP 3 109 HIS 0.006 0.001 HIS 8 44 Details of bonding type rmsd covalent geometry : bond 0.00308 (17636) covalent geometry : angle 0.53344 (23933) SS BOND : bond 0.00458 ( 1) SS BOND : angle 2.42185 ( 2) hydrogen bonds : bond 0.04796 ( 1317) hydrogen bonds : angle 4.32327 ( 3915) metal coordination : bond 0.01195 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 357 time to evaluate : 0.667 Fit side-chains REVERT: 0 40 LYS cc_start: 0.8886 (ttpt) cc_final: 0.7203 (mptt) REVERT: 0 41 GLU cc_start: 0.7683 (mt-10) cc_final: 0.6922 (pm20) REVERT: 1 34 GLU cc_start: 0.5763 (tp30) cc_final: 0.5038 (mm-30) REVERT: 1 150 ARG cc_start: 0.8395 (mmp-170) cc_final: 0.6692 (tpt170) REVERT: 1 604 ARG cc_start: 0.8542 (tpp-160) cc_final: 0.8299 (ttm170) REVERT: 3 271 PHE cc_start: 0.8846 (m-80) cc_final: 0.8348 (m-80) REVERT: 3 297 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8490 (mt) REVERT: 5 94 LYS cc_start: 0.8660 (mtpt) cc_final: 0.7481 (pttt) REVERT: 8 67 SER cc_start: 0.8931 (m) cc_final: 0.8674 (m) REVERT: 8 70 LYS cc_start: 0.8668 (ttpp) cc_final: 0.7168 (mptt) REVERT: 8 78 HIS cc_start: 0.7732 (OUTLIER) cc_final: 0.7516 (t-170) REVERT: 9 35 GLN cc_start: 0.8232 (mt0) cc_final: 0.7948 (tt0) REVERT: B 69 ILE cc_start: 0.9149 (mt) cc_final: 0.8797 (mp) REVERT: C 97 LYS cc_start: 0.8272 (tptt) cc_final: 0.7659 (tptt) REVERT: D 109 LEU cc_start: 0.8081 (mt) cc_final: 0.7880 (mp) REVERT: D 126 PHE cc_start: 0.8270 (m-80) cc_final: 0.7973 (m-80) REVERT: E 91 ARG cc_start: 0.8591 (ttm-80) cc_final: 0.8034 (mtt180) REVERT: F 60 LYS cc_start: 0.8505 (mttm) cc_final: 0.8294 (mmtp) REVERT: H 95 ILE cc_start: 0.8373 (tp) cc_final: 0.8146 (tp) REVERT: I 61 MET cc_start: 0.7681 (mmt) cc_final: 0.7181 (mmm) outliers start: 37 outliers final: 18 residues processed: 379 average time/residue: 0.1412 time to fit residues: 80.6322 Evaluate side-chains 360 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 340 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 605 LYS Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 8 residue 52 THR Chi-restraints excluded: chain 8 residue 78 HIS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 271 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 27 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 162 optimal weight: 5.9990 chunk 181 optimal weight: 0.0980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 0 56 GLN 1 257 HIS 1 531 HIS 3 179 GLN 3 189 HIS 9 60 ASN 9 80 GLN C 98 GLN I 98 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.094226 restraints weight = 26406.300| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.90 r_work: 0.2870 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17639 Z= 0.145 Angle : 0.514 8.215 23935 Z= 0.266 Chirality : 0.037 0.169 2829 Planarity : 0.004 0.063 3017 Dihedral : 4.798 81.031 2415 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.64 % Allowed : 14.60 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.17), residues: 2271 helix: 1.27 (0.12), residues: 1726 sheet: None (None), residues: 0 loop : -0.73 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 91 TYR 0.010 0.001 TYR 9 14 PHE 0.018 0.001 PHE D 122 TRP 0.011 0.001 TRP 3 109 HIS 0.005 0.001 HIS 8 44 Details of bonding type rmsd covalent geometry : bond 0.00316 (17636) covalent geometry : angle 0.51364 (23933) SS BOND : bond 0.00273 ( 1) SS BOND : angle 0.96687 ( 2) hydrogen bonds : bond 0.04518 ( 1317) hydrogen bonds : angle 4.07567 ( 3915) metal coordination : bond 0.00186 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 351 time to evaluate : 0.652 Fit side-chains REVERT: 0 40 LYS cc_start: 0.8916 (ttpt) cc_final: 0.7241 (mptt) REVERT: 0 41 GLU cc_start: 0.7715 (mt-10) cc_final: 0.6958 (pm20) REVERT: 1 34 GLU cc_start: 0.5854 (tp30) cc_final: 0.5036 (mm-30) REVERT: 1 150 ARG cc_start: 0.8646 (mmp-170) cc_final: 0.7092 (mmm160) REVERT: 3 271 PHE cc_start: 0.8891 (m-80) cc_final: 0.8344 (m-80) REVERT: 3 297 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8512 (mt) REVERT: 5 94 LYS cc_start: 0.8763 (mtpt) cc_final: 0.7610 (pttt) REVERT: 8 67 SER cc_start: 0.8943 (m) cc_final: 0.8720 (m) REVERT: 8 70 LYS cc_start: 0.8643 (ttpp) cc_final: 0.7206 (mptt) REVERT: 9 35 GLN cc_start: 0.8249 (mt0) cc_final: 0.7983 (tt0) REVERT: B 60 LYS cc_start: 0.8293 (mttp) cc_final: 0.7974 (mmtt) REVERT: C 97 LYS cc_start: 0.8312 (tptt) cc_final: 0.7661 (tptt) REVERT: D 118 LEU cc_start: 0.7648 (mt) cc_final: 0.7303 (mt) REVERT: D 126 PHE cc_start: 0.8283 (m-80) cc_final: 0.7999 (m-80) REVERT: E 91 ARG cc_start: 0.8652 (ttm-80) cc_final: 0.8104 (mtt180) REVERT: I 61 MET cc_start: 0.7698 (mmt) cc_final: 0.7212 (mmm) REVERT: M 267 PHE cc_start: 0.6953 (m-10) cc_final: 0.6593 (m-10) outliers start: 47 outliers final: 35 residues processed: 371 average time/residue: 0.1402 time to fit residues: 78.1796 Evaluate side-chains 367 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 331 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 39 LYS Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 350 GLU Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 605 LYS Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 314 GLU Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 8 residue 78 HIS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 87 ASN Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 271 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 52 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 3 309 ASN 6 106 ASN J 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.091968 restraints weight = 26622.605| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.83 r_work: 0.2869 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17639 Z= 0.184 Angle : 0.532 9.195 23935 Z= 0.274 Chirality : 0.038 0.145 2829 Planarity : 0.004 0.063 3017 Dihedral : 4.686 75.900 2415 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.26 % Allowed : 15.44 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.17), residues: 2271 helix: 1.56 (0.12), residues: 1734 sheet: None (None), residues: 0 loop : -0.55 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 91 TYR 0.014 0.001 TYR F 102 PHE 0.018 0.002 PHE D 122 TRP 0.012 0.001 TRP 3 109 HIS 0.003 0.001 HIS 9 41 Details of bonding type rmsd covalent geometry : bond 0.00419 (17636) covalent geometry : angle 0.53232 (23933) SS BOND : bond 0.00246 ( 1) SS BOND : angle 0.73378 ( 2) hydrogen bonds : bond 0.04590 ( 1317) hydrogen bonds : angle 3.99918 ( 3915) metal coordination : bond 0.00176 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 346 time to evaluate : 0.738 Fit side-chains REVERT: 0 40 LYS cc_start: 0.8941 (ttpt) cc_final: 0.7256 (mptt) REVERT: 0 41 GLU cc_start: 0.7698 (mt-10) cc_final: 0.6936 (pm20) REVERT: 1 34 GLU cc_start: 0.5982 (tp30) cc_final: 0.5134 (mm-30) REVERT: 1 150 ARG cc_start: 0.9109 (mmp-170) cc_final: 0.7203 (mmm160) REVERT: 3 297 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8498 (mp) REVERT: 5 94 LYS cc_start: 0.8772 (mtpt) cc_final: 0.7561 (pttt) REVERT: 8 67 SER cc_start: 0.8944 (m) cc_final: 0.8710 (m) REVERT: 8 70 LYS cc_start: 0.8658 (ttpp) cc_final: 0.7224 (mptt) REVERT: 9 35 GLN cc_start: 0.8237 (mt0) cc_final: 0.7989 (tt0) REVERT: 9 66 ILE cc_start: 0.8945 (mm) cc_final: 0.8652 (mm) REVERT: 9 92 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 115 LEU cc_start: 0.8701 (mt) cc_final: 0.8483 (mt) REVERT: B 87 ASN cc_start: 0.8452 (m-40) cc_final: 0.8065 (m-40) REVERT: C 97 LYS cc_start: 0.8207 (tptt) cc_final: 0.7404 (tptt) REVERT: D 118 LEU cc_start: 0.7630 (mt) cc_final: 0.7262 (mt) REVERT: D 119 LEU cc_start: 0.7868 (mt) cc_final: 0.7651 (mt) REVERT: F 92 ASN cc_start: 0.8508 (p0) cc_final: 0.8236 (p0) REVERT: G 122 PHE cc_start: 0.7840 (t80) cc_final: 0.7612 (t80) REVERT: I 61 MET cc_start: 0.7674 (mmt) cc_final: 0.7201 (mmm) REVERT: J 115 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8541 (mt) REVERT: M 321 LYS cc_start: 0.8383 (ptmt) cc_final: 0.8090 (ptpt) outliers start: 58 outliers final: 38 residues processed: 376 average time/residue: 0.1377 time to fit residues: 78.6019 Evaluate side-chains 374 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 333 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 350 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 605 LYS Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 314 GLU Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 105 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 8 residue 52 THR Chi-restraints excluded: chain 8 residue 78 HIS Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 294 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 195 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 48 optimal weight: 0.0030 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 199 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 3 179 GLN ** I 94 ASN ** 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 = 0.3458 r_free = 0.3458 target = 0.120286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.092459 restraints weight = 26308.016| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.62 r_work: 0.2918 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17639 Z= 0.137 Angle : 0.501 7.988 23935 Z= 0.259 Chirality : 0.037 0.234 2829 Planarity : 0.004 0.058 3017 Dihedral : 4.475 69.537 2415 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 3.20 % Allowed : 16.00 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.18), residues: 2271 helix: 1.82 (0.12), residues: 1733 sheet: None (None), residues: 0 loop : -0.40 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 91 TYR 0.012 0.001 TYR 9 14 PHE 0.020 0.001 PHE E 122 TRP 0.010 0.001 TRP 3 109 HIS 0.004 0.001 HIS 8 44 Details of bonding type rmsd covalent geometry : bond 0.00299 (17636) covalent geometry : angle 0.50100 (23933) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.42074 ( 2) hydrogen bonds : bond 0.04279 ( 1317) hydrogen bonds : angle 3.87300 ( 3915) metal coordination : bond 0.00090 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 345 time to evaluate : 0.678 Fit side-chains REVERT: 0 40 LYS cc_start: 0.8923 (ttpt) cc_final: 0.7187 (mptt) REVERT: 0 41 GLU cc_start: 0.7601 (mt-10) cc_final: 0.6811 (pm20) REVERT: 1 34 GLU cc_start: 0.5827 (tp30) cc_final: 0.5063 (mm-30) REVERT: 1 194 LYS cc_start: 0.7838 (ttmt) cc_final: 0.7592 (ttmm) REVERT: 1 456 LYS cc_start: 0.8761 (tmtt) cc_final: 0.8026 (mtmt) REVERT: 3 271 PHE cc_start: 0.8827 (m-80) cc_final: 0.8312 (m-80) REVERT: 3 297 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8465 (mt) REVERT: 5 94 LYS cc_start: 0.8702 (mtpt) cc_final: 0.7491 (pttt) REVERT: 8 67 SER cc_start: 0.8893 (m) cc_final: 0.8631 (m) REVERT: 9 35 GLN cc_start: 0.8190 (mt0) cc_final: 0.7921 (tt0) REVERT: 9 66 ILE cc_start: 0.8882 (mm) cc_final: 0.8577 (mm) REVERT: 9 92 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: B 60 LYS cc_start: 0.8108 (mttp) cc_final: 0.7857 (mmtt) REVERT: C 97 LYS cc_start: 0.8266 (tptt) cc_final: 0.7362 (tptt) REVERT: D 118 LEU cc_start: 0.7500 (mt) cc_final: 0.7099 (mt) REVERT: D 119 LEU cc_start: 0.7862 (mt) cc_final: 0.7645 (mt) REVERT: F 60 LYS cc_start: 0.8472 (mttm) cc_final: 0.8138 (mmtp) REVERT: F 92 ASN cc_start: 0.8442 (p0) cc_final: 0.8178 (p0) REVERT: F 123 LEU cc_start: 0.8350 (mt) cc_final: 0.8084 (mp) REVERT: I 61 MET cc_start: 0.7579 (mmt) cc_final: 0.7111 (mmm) REVERT: M 321 LYS cc_start: 0.8320 (ptmt) cc_final: 0.7881 (pttt) outliers start: 57 outliers final: 39 residues processed: 378 average time/residue: 0.1374 time to fit residues: 78.7393 Evaluate side-chains 374 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 333 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 48 ASN Chi-restraints excluded: chain 1 residue 39 LYS Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 350 GLU Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 519 GLU Chi-restraints excluded: chain 1 residue 605 LYS Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 314 GLU Chi-restraints excluded: chain 6 residue 71 TYR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 105 LEU Chi-restraints excluded: chain 8 residue 52 THR Chi-restraints excluded: chain 8 residue 78 HIS Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 271 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 71 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 72 optimal weight: 0.1980 chunk 156 optimal weight: 6.9990 chunk 130 optimal weight: 0.2980 chunk 164 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 86 optimal weight: 0.2980 chunk 35 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 423 ASN ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.092836 restraints weight = 26098.079| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.63 r_work: 0.2955 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17639 Z= 0.116 Angle : 0.490 7.929 23935 Z= 0.253 Chirality : 0.036 0.208 2829 Planarity : 0.004 0.056 3017 Dihedral : 4.133 63.094 2412 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.75 % Allowed : 17.69 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: 2.20 (0.18), residues: 2271 helix: 2.02 (0.12), residues: 1738 sheet: None (None), residues: 0 loop : -0.37 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 0 34 TYR 0.013 0.001 TYR 9 14 PHE 0.026 0.001 PHE D 122 TRP 0.009 0.001 TRP 8 45 HIS 0.003 0.000 HIS 9 41 Details of bonding type rmsd covalent geometry : bond 0.00238 (17636) covalent geometry : angle 0.48952 (23933) SS BOND : bond 0.00014 ( 1) SS BOND : angle 0.23637 ( 2) hydrogen bonds : bond 0.04051 ( 1317) hydrogen bonds : angle 3.78454 ( 3915) metal coordination : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 340 time to evaluate : 0.715 Fit side-chains REVERT: 0 40 LYS cc_start: 0.8920 (ttpt) cc_final: 0.7184 (mptt) REVERT: 0 41 GLU cc_start: 0.7562 (mt-10) cc_final: 0.6871 (pm20) REVERT: 1 34 GLU cc_start: 0.5690 (tp30) cc_final: 0.4964 (mm-30) REVERT: 1 456 LYS cc_start: 0.8761 (tmtt) cc_final: 0.8063 (mtmt) REVERT: 3 297 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8438 (mt) REVERT: 5 94 LYS cc_start: 0.8667 (mtpt) cc_final: 0.7486 (pttt) REVERT: 9 35 GLN cc_start: 0.8069 (mt0) cc_final: 0.7864 (tt0) REVERT: 9 66 ILE cc_start: 0.8830 (mm) cc_final: 0.8591 (mm) REVERT: 9 92 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: C 97 LYS cc_start: 0.8217 (tptt) cc_final: 0.7342 (tptt) REVERT: F 60 LYS cc_start: 0.8507 (mttm) cc_final: 0.8230 (mmtp) REVERT: F 91 ARG cc_start: 0.8152 (mmm160) cc_final: 0.6247 (tpt90) REVERT: F 92 ASN cc_start: 0.8416 (p0) cc_final: 0.8202 (p0) REVERT: F 123 LEU cc_start: 0.8310 (mt) cc_final: 0.8051 (mp) REVERT: G 102 TYR cc_start: 0.7727 (m-10) cc_final: 0.7516 (m-80) REVERT: I 61 MET cc_start: 0.7605 (mmt) cc_final: 0.7148 (mmm) REVERT: M 321 LYS cc_start: 0.8289 (ptmt) cc_final: 0.7843 (pttt) outliers start: 49 outliers final: 36 residues processed: 368 average time/residue: 0.1401 time to fit residues: 77.8660 Evaluate side-chains 360 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 322 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 48 ASN Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 350 GLU Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 519 GLU Chi-restraints excluded: chain 1 residue 605 LYS Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 314 GLU Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 8 residue 78 HIS Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 271 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 7 optimal weight: 0.0470 chunk 186 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 1 423 ASN C 94 ASN ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.121064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.091579 restraints weight = 26262.816| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.64 r_work: 0.2931 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17639 Z= 0.134 Angle : 0.507 7.621 23935 Z= 0.260 Chirality : 0.037 0.271 2829 Planarity : 0.004 0.052 3017 Dihedral : 4.082 58.642 2412 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.26 % Allowed : 17.46 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: 2.35 (0.18), residues: 2271 helix: 2.11 (0.12), residues: 1729 sheet: None (None), residues: 0 loop : -0.19 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 91 TYR 0.013 0.001 TYR 9 14 PHE 0.031 0.001 PHE E 122 TRP 0.010 0.001 TRP 3 109 HIS 0.003 0.001 HIS 9 41 Details of bonding type rmsd covalent geometry : bond 0.00295 (17636) covalent geometry : angle 0.50671 (23933) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.26263 ( 2) hydrogen bonds : bond 0.04123 ( 1317) hydrogen bonds : angle 3.78642 ( 3915) metal coordination : bond 0.00108 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 343 time to evaluate : 0.670 Fit side-chains REVERT: 0 40 LYS cc_start: 0.8905 (ttpt) cc_final: 0.7162 (mptt) REVERT: 0 41 GLU cc_start: 0.7708 (mt-10) cc_final: 0.6927 (pm20) REVERT: 1 34 GLU cc_start: 0.5760 (tp30) cc_final: 0.5014 (mm-30) REVERT: 1 194 LYS cc_start: 0.7818 (ttmt) cc_final: 0.7592 (ttmm) REVERT: 5 74 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8665 (t0) REVERT: 5 94 LYS cc_start: 0.8681 (mtpt) cc_final: 0.7469 (pttt) REVERT: 9 35 GLN cc_start: 0.8130 (mt0) cc_final: 0.7928 (tt0) REVERT: 9 92 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: B 60 LYS cc_start: 0.7850 (mmtp) cc_final: 0.7649 (mmtt) REVERT: C 61 MET cc_start: 0.8258 (mmm) cc_final: 0.7907 (mmm) REVERT: C 97 LYS cc_start: 0.8151 (tptt) cc_final: 0.7219 (tptt) REVERT: F 91 ARG cc_start: 0.8151 (mmm160) cc_final: 0.6152 (tpt90) REVERT: F 92 ASN cc_start: 0.8379 (p0) cc_final: 0.8174 (p0) REVERT: F 123 LEU cc_start: 0.8294 (mt) cc_final: 0.8036 (mp) REVERT: G 102 TYR cc_start: 0.7771 (m-10) cc_final: 0.7522 (m-80) REVERT: I 61 MET cc_start: 0.7611 (mmt) cc_final: 0.7066 (mmt) REVERT: J 115 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8446 (mt) REVERT: M 321 LYS cc_start: 0.8294 (ptmt) cc_final: 0.7879 (pttt) outliers start: 58 outliers final: 47 residues processed: 375 average time/residue: 0.1365 time to fit residues: 77.9060 Evaluate side-chains 387 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 337 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 48 ASN Chi-restraints excluded: chain 1 residue 39 LYS Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 350 GLU Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 519 GLU Chi-restraints excluded: chain 1 residue 605 LYS Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 3 residue 314 GLU Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 122 LEU Chi-restraints excluded: chain 6 residue 71 TYR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 105 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 8 residue 78 HIS Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 271 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 165 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 174 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 37 optimal weight: 0.0470 chunk 123 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 33 optimal weight: 0.0010 chunk 135 optimal weight: 3.9990 overall best weight: 0.6486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 423 ASN ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.093797 restraints weight = 26298.291| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.56 r_work: 0.2939 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17639 Z= 0.128 Angle : 0.513 8.378 23935 Z= 0.260 Chirality : 0.037 0.301 2829 Planarity : 0.004 0.052 3017 Dihedral : 4.044 55.457 2412 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.09 % Allowed : 17.97 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: 2.36 (0.17), residues: 2271 helix: 2.12 (0.12), residues: 1737 sheet: None (None), residues: 0 loop : -0.26 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 0 34 TYR 0.014 0.001 TYR 9 14 PHE 0.025 0.001 PHE J 107 TRP 0.010 0.001 TRP 3 109 HIS 0.003 0.000 HIS 9 41 Details of bonding type rmsd covalent geometry : bond 0.00277 (17636) covalent geometry : angle 0.51323 (23933) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.21603 ( 2) hydrogen bonds : bond 0.04071 ( 1317) hydrogen bonds : angle 3.77058 ( 3915) metal coordination : bond 0.00093 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 343 time to evaluate : 0.856 Fit side-chains REVERT: 0 40 LYS cc_start: 0.8908 (ttpt) cc_final: 0.7180 (mptt) REVERT: 0 41 GLU cc_start: 0.7684 (mt-10) cc_final: 0.6957 (pm20) REVERT: 1 34 GLU cc_start: 0.5758 (tp30) cc_final: 0.5020 (mm-30) REVERT: 1 194 LYS cc_start: 0.7838 (ttmt) cc_final: 0.7627 (ttmm) REVERT: 1 456 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8001 (mtmt) REVERT: 3 271 PHE cc_start: 0.8739 (m-80) cc_final: 0.8295 (m-80) REVERT: 5 74 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8677 (t0) REVERT: 5 94 LYS cc_start: 0.8676 (mtpt) cc_final: 0.7474 (pttt) REVERT: 9 92 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: C 61 MET cc_start: 0.8284 (mmm) cc_final: 0.7969 (mmm) REVERT: C 97 LYS cc_start: 0.8201 (tptt) cc_final: 0.7256 (tptt) REVERT: E 122 PHE cc_start: 0.8211 (t80) cc_final: 0.7991 (t80) REVERT: F 91 ARG cc_start: 0.8171 (mmm160) cc_final: 0.6178 (tpt90) REVERT: F 92 ASN cc_start: 0.8393 (p0) cc_final: 0.8152 (p0) REVERT: F 123 LEU cc_start: 0.8294 (mt) cc_final: 0.8045 (mp) REVERT: G 102 TYR cc_start: 0.7791 (m-10) cc_final: 0.7536 (m-80) REVERT: I 61 MET cc_start: 0.7605 (mmt) cc_final: 0.7078 (mmt) REVERT: M 321 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7847 (pttt) outliers start: 55 outliers final: 46 residues processed: 375 average time/residue: 0.1361 time to fit residues: 77.9660 Evaluate side-chains 383 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 335 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 350 GLU Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 519 GLU Chi-restraints excluded: chain 1 residue 605 LYS Chi-restraints excluded: chain 3 residue 101 ILE Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 122 LEU Chi-restraints excluded: chain 6 residue 71 TYR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 105 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 8 residue 78 HIS Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 26 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 271 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 183 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 423 ASN I 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.092839 restraints weight = 26322.622| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.57 r_work: 0.2923 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17639 Z= 0.149 Angle : 0.526 9.166 23935 Z= 0.265 Chirality : 0.038 0.320 2829 Planarity : 0.004 0.055 3017 Dihedral : 4.060 54.684 2412 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.11 % Favored : 97.84 % Rotamer: Outliers : 3.03 % Allowed : 17.97 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: 2.39 (0.17), residues: 2271 helix: 2.12 (0.12), residues: 1734 sheet: None (None), residues: 0 loop : -0.15 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 91 TYR 0.015 0.001 TYR 9 14 PHE 0.025 0.001 PHE D 122 TRP 0.011 0.001 TRP 3 109 HIS 0.004 0.001 HIS 9 41 Details of bonding type rmsd covalent geometry : bond 0.00335 (17636) covalent geometry : angle 0.52618 (23933) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.19614 ( 2) hydrogen bonds : bond 0.04181 ( 1317) hydrogen bonds : angle 3.80351 ( 3915) metal coordination : bond 0.00143 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 335 time to evaluate : 0.686 Fit side-chains REVERT: 0 40 LYS cc_start: 0.8920 (ttpt) cc_final: 0.7185 (mptt) REVERT: 0 41 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7003 (pm20) REVERT: 1 34 GLU cc_start: 0.5799 (tp30) cc_final: 0.5022 (mm-30) REVERT: 1 456 LYS cc_start: 0.8785 (tmtt) cc_final: 0.8035 (mtmt) REVERT: 3 271 PHE cc_start: 0.8787 (m-80) cc_final: 0.8260 (m-80) REVERT: 5 74 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8676 (t0) REVERT: 5 94 LYS cc_start: 0.8696 (mtpt) cc_final: 0.7482 (pttt) REVERT: 9 92 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: C 97 LYS cc_start: 0.8335 (tptt) cc_final: 0.7331 (tptt) REVERT: F 91 ARG cc_start: 0.8183 (mmm160) cc_final: 0.6179 (tpt90) REVERT: F 92 ASN cc_start: 0.8409 (p0) cc_final: 0.8156 (p0) REVERT: F 123 LEU cc_start: 0.8305 (mt) cc_final: 0.8057 (mp) REVERT: G 102 TYR cc_start: 0.7889 (m-10) cc_final: 0.7671 (m-80) REVERT: I 61 MET cc_start: 0.7652 (mmt) cc_final: 0.7140 (mmt) REVERT: J 115 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8526 (mt) REVERT: M 321 LYS cc_start: 0.8287 (ptmt) cc_final: 0.7878 (pttt) outliers start: 54 outliers final: 47 residues processed: 365 average time/residue: 0.1361 time to fit residues: 75.6320 Evaluate side-chains 377 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 327 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 350 GLU Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 519 GLU Chi-restraints excluded: chain 1 residue 578 ASP Chi-restraints excluded: chain 1 residue 605 LYS Chi-restraints excluded: chain 3 residue 101 ILE Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 122 LEU Chi-restraints excluded: chain 6 residue 71 TYR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 105 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 8 residue 78 HIS Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 26 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 264 SER Chi-restraints excluded: chain M residue 271 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 8 optimal weight: 0.0470 chunk 208 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.091720 restraints weight = 26214.327| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.63 r_work: 0.2929 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17639 Z= 0.136 Angle : 0.525 10.413 23935 Z= 0.266 Chirality : 0.038 0.344 2829 Planarity : 0.004 0.056 3017 Dihedral : 4.037 54.517 2412 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.11 % Favored : 97.84 % Rotamer: Outliers : 2.86 % Allowed : 18.42 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: 2271 helix: 2.15 (0.12), residues: 1735 sheet: None (None), residues: 0 loop : -0.10 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 0 34 TYR 0.017 0.001 TYR D 102 PHE 0.024 0.001 PHE B 122 TRP 0.010 0.001 TRP 3 109 HIS 0.004 0.001 HIS 9 41 Details of bonding type rmsd covalent geometry : bond 0.00303 (17636) covalent geometry : angle 0.52493 (23933) SS BOND : bond 0.00080 ( 1) SS BOND : angle 0.28166 ( 2) hydrogen bonds : bond 0.04099 ( 1317) hydrogen bonds : angle 3.78507 ( 3915) metal coordination : bond 0.00096 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 326 time to evaluate : 0.602 Fit side-chains REVERT: 0 40 LYS cc_start: 0.8924 (ttpt) cc_final: 0.7184 (mptt) REVERT: 0 41 GLU cc_start: 0.7667 (mt-10) cc_final: 0.6998 (pm20) REVERT: 1 34 GLU cc_start: 0.5786 (tp30) cc_final: 0.5031 (mm-30) REVERT: 1 456 LYS cc_start: 0.8802 (tmtt) cc_final: 0.8065 (mtmt) REVERT: 3 271 PHE cc_start: 0.8781 (m-80) cc_final: 0.8271 (m-80) REVERT: 5 74 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8680 (t0) REVERT: 5 94 LYS cc_start: 0.8677 (mtpt) cc_final: 0.7464 (pttt) REVERT: 9 12 GLU cc_start: 0.8493 (tt0) cc_final: 0.8038 (tm-30) REVERT: 9 92 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: C 97 LYS cc_start: 0.8352 (tptt) cc_final: 0.7286 (tptt) REVERT: F 91 ARG cc_start: 0.8165 (mmm160) cc_final: 0.6175 (tpt90) REVERT: F 92 ASN cc_start: 0.8337 (p0) cc_final: 0.8132 (p0) REVERT: F 123 LEU cc_start: 0.8273 (mt) cc_final: 0.8034 (mp) REVERT: I 61 MET cc_start: 0.7640 (mmt) cc_final: 0.7124 (mmt) REVERT: J 115 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8516 (mt) REVERT: M 321 LYS cc_start: 0.8266 (ptmt) cc_final: 0.7853 (pttt) outliers start: 51 outliers final: 45 residues processed: 356 average time/residue: 0.1292 time to fit residues: 69.9151 Evaluate side-chains 371 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 323 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 49 GLU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 350 GLU Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 519 GLU Chi-restraints excluded: chain 1 residue 605 LYS Chi-restraints excluded: chain 3 residue 101 ILE Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 103 VAL Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 122 LEU Chi-restraints excluded: chain 6 residue 71 TYR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 105 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 8 residue 78 HIS Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 26 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 271 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 39 optimal weight: 0.9990 chunk 131 optimal weight: 0.0270 chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 202 optimal weight: 0.0170 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.092245 restraints weight = 26285.512| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.64 r_work: 0.2944 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17639 Z= 0.127 Angle : 0.522 11.306 23935 Z= 0.264 Chirality : 0.038 0.365 2829 Planarity : 0.004 0.056 3017 Dihedral : 4.012 53.993 2412 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.86 % Allowed : 18.64 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: 2.48 (0.18), residues: 2271 helix: 2.16 (0.12), residues: 1741 sheet: None (None), residues: 0 loop : -0.05 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 0 34 TYR 0.017 0.001 TYR F 102 PHE 0.026 0.001 PHE B 122 TRP 0.009 0.001 TRP 3 109 HIS 0.004 0.000 HIS 9 41 Details of bonding type rmsd covalent geometry : bond 0.00276 (17636) covalent geometry : angle 0.52202 (23933) SS BOND : bond 0.00052 ( 1) SS BOND : angle 0.24883 ( 2) hydrogen bonds : bond 0.04018 ( 1317) hydrogen bonds : angle 3.76061 ( 3915) metal coordination : bond 0.00072 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5679.92 seconds wall clock time: 97 minutes 49.85 seconds (5869.85 seconds total)