Starting phenix.real_space_refine on Sat Aug 8 23:20:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rg0_19128/08_2026/8rg0_19128.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rg0_19128/08_2026/8rg0_19128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rg0_19128/08_2026/8rg0_19128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rg0_19128/08_2026/8rg0_19128.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rg0_19128/08_2026/8rg0_19128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rg0_19128/08_2026/8rg0_19128.map" } resolution = 3.4 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 152 5.49 5 Mg 1 5.21 5 S 130 5.16 5 C 19040 2.51 5 N 5722 2.21 5 O 6302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31348 Number of models: 1 Model: "" Number of chains: 21 Chain: "3" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1057 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 704 Unresolved non-hydrogen angles: 904 Unresolved non-hydrogen dihedrals: 590 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'PHE:plan': 11, 'GLU:plan': 17, 'GLN:plan1': 14, 'ARG:plan': 7, 'ASN:plan1': 9, 'ASP:plan': 14, 'TYR:plan': 7, 'HIS:plan': 5, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 404 Chain: "4" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1272 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 767 Unresolved non-hydrogen angles: 993 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'ARG:plan': 11, 'HIS:plan': 8, 'ASP:plan': 14, 'TYR:plan': 11, 'GLU:plan': 15, 'ASN:plan1': 16, 'PHE:plan': 6, 'TRP:plan': 1, 'GLN:plan1': 8} Unresolved non-hydrogen planarities: 399 Chain: "5" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4347 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 499} Chain: "6" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2196 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 212} Link IDs: {'PTRANS': 6, 'TRANS': 355} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 725 Unresolved non-hydrogen angles: 923 Unresolved non-hydrogen dihedrals: 589 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLU:plan': 23, 'ASP:plan': 17, 'GLN:plan1': 7, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 7, 'HIS:plan': 6, 'PHE:plan': 6, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 368 Chain: "7" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 663 Classifications: {'RNA': 31} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 13, 'rna3p_pyr': 8} Link IDs: {'rna2p': 10, 'rna3p': 20} Chain: "8" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 1574 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 285} Link IDs: {'PTRANS': 12, 'TRANS': 304} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1043 Unresolved non-hydrogen angles: 1328 Unresolved non-hydrogen dihedrals: 866 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'ASP:plan': 16, 'GLN:plan1': 31, 'HIS:plan': 10, 'TYR:plan': 14, 'GLU:plan': 24, 'ARG:plan': 12, 'ASN:plan1': 14, 'PHE:plan': 10, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 596 Chain: "A" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2594 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 60, 'rna3p_pyr': 48} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain breaks: 11 Chain: "H" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 555 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "I" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 753 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "M" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 257 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 3, 'TRANS': 28} Chain breaks: 1 Chain: "N" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "O" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1455 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 2 Chain: "P" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 651 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 767 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "n" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "u" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 603, 4861 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 24, 'TRANS': 578} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 75 Conformer: "B" Number of residues, atoms: 603, 4861 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 24, 'TRANS': 578} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 75 bond proxies already assigned to first conformer: 4941 Chain: "v" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2740 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 12, 'TRANS': 392} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 632 Unresolved non-hydrogen angles: 810 Unresolved non-hydrogen dihedrals: 528 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'PHE:plan': 9, 'GLU:plan': 15, 'TYR:plan': 11, 'ASN:plan1': 8, 'GLN:plan1': 9, 'ASP:plan': 15, 'HIS:plan': 2, 'ARG:plan': 10, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 374 Chain: "x" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 525 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain breaks: 1 Chain: "y" Number of atoms: 4361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4361 Classifications: {'peptide': 543} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 16, 'TRANS': 526} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17782 SG CYS Q 23 24.841 81.048 116.306 1.00129.97 S ATOM 17803 SG CYS Q 26 20.651 81.301 115.406 1.00138.47 S ATOM 18186 SG CYS Q 74 23.130 78.558 114.206 1.00127.65 S ATOM 18205 SG CYS Q 77 23.005 83.117 114.629 1.00133.63 S Time building chain proxies: 6.88, per 1000 atoms: 0.22 Number of scatterers: 31348 At special positions: 0 Unit cell: (209.96, 197.2, 164.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 130 16.00 P 152 15.00 Mg 1 11.99 O 6302 8.00 N 5722 7.00 C 19040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS y 567 " - pdb=" SG CYS y 571 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 23 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 26 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 77 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 74 " Number of angles added : 6 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7568 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 22 sheets defined 63.3% alpha, 5.3% beta 32 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain '3' and resid 2 through 17 removed outlier: 3.920A pdb=" N GLY 3 17 " --> pdb=" O LYS 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 26 through 39 removed outlier: 3.762A pdb=" N GLU 3 39 " --> pdb=" O THR 3 35 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 57 Processing helix chain '3' and resid 62 through 75 Processing helix chain '3' and resid 80 through 88 Processing helix chain '3' and resid 90 through 96 removed outlier: 3.629A pdb=" N GLN 3 94 " --> pdb=" O ASP 3 90 " (cutoff:3.500A) Processing helix chain '3' and resid 96 through 111 Processing helix chain '3' and resid 114 through 121 Processing helix chain '3' and resid 125 through 131 removed outlier: 3.623A pdb=" N GLU 3 129 " --> pdb=" O MET 3 125 " (cutoff:3.500A) Processing helix chain '3' and resid 133 through 150 Processing helix chain '3' and resid 154 through 162 Processing helix chain '3' and resid 166 through 178 Processing helix chain '3' and resid 210 through 216 removed outlier: 3.568A pdb=" N SER 3 216 " --> pdb=" O SER 3 212 " (cutoff:3.500A) Processing helix chain '4' and resid 95 through 109 removed outlier: 3.640A pdb=" N LEU 4 99 " --> pdb=" O HIS 4 95 " (cutoff:3.500A) Processing helix chain '4' and resid 110 through 112 No H-bonds generated for 'chain '4' and resid 110 through 112' Processing helix chain '4' and resid 149 through 164 Processing helix chain '4' and resid 180 through 194 Processing helix chain '4' and resid 244 through 258 removed outlier: 4.310A pdb=" N GLY 4 248 " --> pdb=" O THR 4 244 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER 4 258 " --> pdb=" O LYS 4 254 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 294 Processing helix chain '4' and resid 301 through 315 removed outlier: 3.865A pdb=" N SER 4 310 " --> pdb=" O ARG 4 306 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU 4 311 " --> pdb=" O PHE 4 307 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL 4 315 " --> pdb=" O LEU 4 311 " (cutoff:3.500A) Processing helix chain '4' and resid 319 through 356 Processing helix chain '5' and resid 49 through 77 Processing helix chain '5' and resid 80 through 97 removed outlier: 3.998A pdb=" N ILE 5 84 " --> pdb=" O SER 5 80 " (cutoff:3.500A) Processing helix chain '5' and resid 97 through 107 Processing helix chain '5' and resid 118 through 123 Processing helix chain '5' and resid 125 through 144 Processing helix chain '5' and resid 149 through 169 Processing helix chain '5' and resid 179 through 203 Processing helix chain '5' and resid 204 through 207 removed outlier: 3.639A pdb=" N LYS 5 207 " --> pdb=" O THR 5 204 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 204 through 207' Processing helix chain '5' and resid 208 through 218 Processing helix chain '5' and resid 223 through 239 Processing helix chain '5' and resid 239 through 249 removed outlier: 3.516A pdb=" N GLN 5 243 " --> pdb=" O ASN 5 239 " (cutoff:3.500A) Processing helix chain '5' and resid 252 through 257 removed outlier: 4.204A pdb=" N VAL 5 256 " --> pdb=" O ASP 5 252 " (cutoff:3.500A) Processing helix chain '5' and resid 258 through 263 removed outlier: 3.933A pdb=" N HIS 5 263 " --> pdb=" O GLU 5 259 " (cutoff:3.500A) Processing helix chain '5' and resid 263 through 285 removed outlier: 3.578A pdb=" N LYS 5 267 " --> pdb=" O HIS 5 263 " (cutoff:3.500A) Processing helix chain '5' and resid 286 through 293 Processing helix chain '5' and resid 303 through 307 Processing helix chain '5' and resid 308 through 326 removed outlier: 3.699A pdb=" N GLN 5 312 " --> pdb=" O VAL 5 308 " (cutoff:3.500A) Processing helix chain '5' and resid 328 through 351 removed outlier: 5.031A pdb=" N SER 5 348 " --> pdb=" O GLN 5 344 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N MET 5 349 " --> pdb=" O ARG 5 345 " (cutoff:3.500A) Processing helix chain '5' and resid 353 through 378 Processing helix chain '5' and resid 383 through 403 removed outlier: 6.901A pdb=" N ASP 5 396 " --> pdb=" O GLU 5 392 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS 5 397 " --> pdb=" O LYS 5 393 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS 5 403 " --> pdb=" O LEU 5 399 " (cutoff:3.500A) Processing helix chain '5' and resid 405 through 417 Processing helix chain '5' and resid 437 through 465 removed outlier: 4.321A pdb=" N GLN 5 456 " --> pdb=" O GLN 5 452 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU 5 457 " --> pdb=" O GLN 5 453 " (cutoff:3.500A) Processing helix chain '5' and resid 472 through 479 Processing helix chain '5' and resid 482 through 498 Processing helix chain '5' and resid 539 through 560 removed outlier: 4.220A pdb=" N PHE 5 543 " --> pdb=" O TYR 5 539 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE 5 544 " --> pdb=" O GLY 5 540 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 41 removed outlier: 6.922A pdb=" N ILE 6 29 " --> pdb=" O LYS 6 25 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N SER 6 30 " --> pdb=" O GLY 6 26 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU 6 31 " --> pdb=" O ALA 6 27 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 54 removed outlier: 3.950A pdb=" N GLU 6 47 " --> pdb=" O ALA 6 43 " (cutoff:3.500A) Processing helix chain '6' and resid 59 through 75 Processing helix chain '6' and resid 80 through 93 Processing helix chain '6' and resid 96 through 111 removed outlier: 4.269A pdb=" N HIS 6 111 " --> pdb=" O SER 6 107 " (cutoff:3.500A) Processing helix chain '6' and resid 115 through 130 Processing helix chain '6' and resid 133 through 145 Proline residue: 6 141 - end of helix Processing helix chain '6' and resid 155 through 172 Processing helix chain '6' and resid 174 through 192 Processing helix chain '6' and resid 193 through 199 removed outlier: 4.999A pdb=" N ALA 6 197 " --> pdb=" O GLU 6 194 " (cutoff:3.500A) Processing helix chain '6' and resid 200 through 213 Processing helix chain '6' and resid 221 through 227 Processing helix chain '6' and resid 237 through 245 removed outlier: 3.761A pdb=" N LEU 6 241 " --> pdb=" O ILE 6 237 " (cutoff:3.500A) Processing helix chain '6' and resid 249 through 259 Processing helix chain '6' and resid 269 through 288 removed outlier: 3.910A pdb=" N GLU 6 288 " --> pdb=" O GLY 6 284 " (cutoff:3.500A) Processing helix chain '6' and resid 294 through 301 Processing helix chain '6' and resid 304 through 306 No H-bonds generated for 'chain '6' and resid 304 through 306' Processing helix chain '6' and resid 307 through 318 removed outlier: 3.695A pdb=" N THR 6 318 " --> pdb=" O ASP 6 314 " (cutoff:3.500A) Processing helix chain '6' and resid 342 through 369 removed outlier: 4.018A pdb=" N TRP 6 347 " --> pdb=" O GLY 6 343 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN 6 348 " --> pdb=" O LYS 6 344 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN 6 349 " --> pdb=" O GLN 6 345 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU 6 369 " --> pdb=" O LYS 6 365 " (cutoff:3.500A) Processing helix chain '8' and resid 42 through 55 removed outlier: 3.781A pdb=" N VAL 8 46 " --> pdb=" O ASP 8 42 " (cutoff:3.500A) Processing helix chain '8' and resid 83 through 87 Processing helix chain '8' and resid 92 through 107 Processing helix chain '8' and resid 130 through 144 Processing helix chain '8' and resid 170 through 178 Processing helix chain '8' and resid 211 through 225 Processing helix chain '8' and resid 228 through 237 Processing helix chain '8' and resid 247 through 287 Processing helix chain '8' and resid 294 through 304 Processing helix chain '8' and resid 308 through 350 removed outlier: 3.868A pdb=" N ALA 8 312 " --> pdb=" O PRO 8 308 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE 8 323 " --> pdb=" O ILE 8 319 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR 8 350 " --> pdb=" O ALA 8 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 18 removed outlier: 3.752A pdb=" N LYS H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 42 Processing helix chain 'I' and resid 46 through 57 removed outlier: 3.628A pdb=" N ILE I 50 " --> pdb=" O THR I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 68 Processing helix chain 'I' and resid 70 through 78 Processing helix chain 'I' and resid 85 through 104 removed outlier: 3.547A pdb=" N ARG I 104 " --> pdb=" O LYS I 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 106 Processing helix chain 'N' and resid 31 through 36 removed outlier: 4.191A pdb=" N GLN N 36 " --> pdb=" O PHE N 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 76 Processing helix chain 'O' and resid 106 through 114 removed outlier: 3.672A pdb=" N MET O 110 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 175 Processing helix chain 'O' and resid 180 through 189 removed outlier: 3.665A pdb=" N VAL O 184 " --> pdb=" O ASP O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 201 Processing helix chain 'O' and resid 224 through 232 removed outlier: 4.468A pdb=" N LEU O 228 " --> pdb=" O GLU O 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 69 removed outlier: 3.955A pdb=" N SER P 69 " --> pdb=" O ARG P 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 66 through 69' Processing helix chain 'P' and resid 70 through 79 removed outlier: 4.134A pdb=" N GLN P 79 " --> pdb=" O MET P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 122 removed outlier: 4.509A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 48 No H-bonds generated for 'chain 'Q' and resid 46 through 48' Processing helix chain 'Q' and resid 49 through 55 Processing helix chain 'Q' and resid 74 through 81 Processing helix chain 'Q' and resid 89 through 93 Processing helix chain 'u' and resid 7 through 22 removed outlier: 3.724A pdb=" N ALA u 11 " --> pdb=" O ARG u 7 " (cutoff:3.500A) Processing helix chain 'u' and resid 23 through 37 removed outlier: 4.198A pdb=" N ALA u 27 " --> pdb=" O LYS u 23 " (cutoff:3.500A) Processing helix chain 'u' and resid 46 through 61 removed outlier: 3.707A pdb=" N ILE u 50 " --> pdb=" O ILE u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 63 through 78 Processing helix chain 'u' and resid 82 through 116 removed outlier: 3.833A pdb=" N LEU u 86 " --> pdb=" O ASN u 82 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU u 106 " --> pdb=" O GLU u 102 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU u 107 " --> pdb=" O ALA u 103 " (cutoff:3.500A) Processing helix chain 'u' and resid 123 through 133 removed outlier: 3.602A pdb=" N VAL u 132 " --> pdb=" O LEU u 128 " (cutoff:3.500A) Processing helix chain 'u' and resid 136 through 164 removed outlier: 4.451A pdb=" N THR u 147 " --> pdb=" O ARG u 143 " (cutoff:3.500A) Proline residue: u 148 - end of helix Processing helix chain 'u' and resid 170 through 188 removed outlier: 3.536A pdb=" N ASP u 176 " --> pdb=" O ARG u 172 " (cutoff:3.500A) Processing helix chain 'u' and resid 190 through 212 removed outlier: 4.178A pdb=" N GLN u 209 " --> pdb=" O LEU u 205 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG u 210 " --> pdb=" O SER u 206 " (cutoff:3.500A) Processing helix chain 'u' and resid 222 through 243 Processing helix chain 'u' and resid 246 through 261 Processing helix chain 'u' and resid 271 through 286 Processing helix chain 'u' and resid 288 through 307 removed outlier: 3.517A pdb=" N HIS u 292 " --> pdb=" O ASN u 288 " (cutoff:3.500A) Processing helix chain 'u' and resid 311 through 329 Processing helix chain 'u' and resid 346 through 359 removed outlier: 3.997A pdb=" N GLU u 350 " --> pdb=" O GLY u 346 " (cutoff:3.500A) Processing helix chain 'u' and resid 368 through 376 removed outlier: 3.634A pdb=" N MET u 374 " --> pdb=" O LEU u 370 " (cutoff:3.500A) Processing helix chain 'u' and resid 378 through 382 Processing helix chain 'u' and resid 384 through 389 Processing helix chain 'u' and resid 389 through 396 Processing helix chain 'u' and resid 399 through 416 removed outlier: 4.533A pdb=" N CYS u 404 " --> pdb=" O PRO u 400 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLU u 405 " --> pdb=" O LEU u 401 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL u 410 " --> pdb=" O ARG u 406 " (cutoff:3.500A) Processing helix chain 'u' and resid 421 through 426 removed outlier: 3.685A pdb=" N GLN u 425 " --> pdb=" O GLU u 421 " (cutoff:3.500A) Processing helix chain 'u' and resid 427 through 447 removed outlier: 3.937A pdb=" N GLN u 445 " --> pdb=" O GLN u 441 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE u 446 " --> pdb=" O GLN u 442 " (cutoff:3.500A) Processing helix chain 'u' and resid 451 through 459 removed outlier: 3.517A pdb=" N VAL u 459 " --> pdb=" O LEU u 455 " (cutoff:3.500A) Processing helix chain 'u' and resid 463 through 478 Processing helix chain 'u' and resid 486 through 489 Processing helix chain 'u' and resid 516 through 536 removed outlier: 3.522A pdb=" N ARG u 520 " --> pdb=" O SER u 516 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ALA u 525 " --> pdb=" O ASN u 521 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N MET u 526 " --> pdb=" O GLN u 522 " (cutoff:3.500A) Processing helix chain 'u' and resid 539 through 561 removed outlier: 4.734A pdb=" N GLN u 549 " --> pdb=" O GLU u 545 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS u 550 " --> pdb=" O LYS u 546 " (cutoff:3.500A) Processing helix chain 'u' and resid 565 through 569 removed outlier: 3.583A pdb=" N ILE u 568 " --> pdb=" O HIS u 565 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU u 569 " --> pdb=" O GLN u 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 565 through 569' Processing helix chain 'u' and resid 582 through 603 Processing helix chain 'v' and resid 21 through 28 removed outlier: 4.370A pdb=" N GLU v 24 " --> pdb=" O PRO v 21 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL v 28 " --> pdb=" O PHE v 25 " (cutoff:3.500A) Processing helix chain 'v' and resid 36 through 41 Processing helix chain 'v' and resid 48 through 55 Processing helix chain 'v' and resid 61 through 71 Proline residue: v 67 - end of helix removed outlier: 3.592A pdb=" N ARG v 71 " --> pdb=" O PRO v 67 " (cutoff:3.500A) Processing helix chain 'v' and resid 76 through 87 Processing helix chain 'v' and resid 91 through 112 Proline residue: v 98 - end of helix Processing helix chain 'v' and resid 112 through 117 removed outlier: 3.951A pdb=" N LEU v 117 " --> pdb=" O LEU v 113 " (cutoff:3.500A) Processing helix chain 'v' and resid 128 through 143 Processing helix chain 'v' and resid 145 through 158 Processing helix chain 'v' and resid 164 through 180 Processing helix chain 'v' and resid 181 through 199 Processing helix chain 'v' and resid 203 through 217 Processing helix chain 'v' and resid 224 through 234 removed outlier: 3.783A pdb=" N GLY v 228 " --> pdb=" O ASN v 224 " (cutoff:3.500A) Processing helix chain 'v' and resid 238 through 247 removed outlier: 3.680A pdb=" N ILE v 246 " --> pdb=" O TYR v 242 " (cutoff:3.500A) Processing helix chain 'v' and resid 253 through 263 Processing helix chain 'v' and resid 270 through 282 removed outlier: 4.488A pdb=" N ASP v 276 " --> pdb=" O GLN v 272 " (cutoff:3.500A) Processing helix chain 'v' and resid 291 through 302 removed outlier: 4.173A pdb=" N LEU v 299 " --> pdb=" O PHE v 295 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR v 300 " --> pdb=" O VAL v 296 " (cutoff:3.500A) Processing helix chain 'v' and resid 305 through 320 Processing helix chain 'v' and resid 329 through 348 Processing helix chain 'v' and resid 353 through 358 Processing helix chain 'v' and resid 363 through 377 removed outlier: 3.792A pdb=" N ASN v 373 " --> pdb=" O ARG v 369 " (cutoff:3.500A) Processing helix chain 'v' and resid 402 through 421 Processing helix chain 'y' and resid 328 through 340 Processing helix chain 'y' and resid 346 through 364 Processing helix chain 'y' and resid 367 through 384 removed outlier: 4.122A pdb=" N ILE y 371 " --> pdb=" O GLY y 367 " (cutoff:3.500A) Processing helix chain 'y' and resid 394 through 415 removed outlier: 3.508A pdb=" N ASN y 415 " --> pdb=" O ILE y 411 " (cutoff:3.500A) Processing helix chain 'y' and resid 443 through 462 Processing helix chain 'y' and resid 466 through 474 removed outlier: 4.071A pdb=" N VAL y 470 " --> pdb=" O SER y 466 " (cutoff:3.500A) Processing helix chain 'y' and resid 475 through 493 Processing helix chain 'y' and resid 495 through 513 removed outlier: 3.862A pdb=" N HIS y 509 " --> pdb=" O LEU y 505 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR y 512 " --> pdb=" O LEU y 508 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS y 513 " --> pdb=" O HIS y 509 " (cutoff:3.500A) Processing helix chain 'y' and resid 515 through 520 removed outlier: 3.891A pdb=" N HIS y 519 " --> pdb=" O ASP y 515 " (cutoff:3.500A) Processing helix chain 'y' and resid 543 through 558 Processing helix chain 'y' and resid 561 through 579 removed outlier: 3.954A pdb=" N ARG y 565 " --> pdb=" O THR y 561 " (cutoff:3.500A) Processing helix chain 'y' and resid 581 through 593 removed outlier: 4.243A pdb=" N LEU y 588 " --> pdb=" O GLN y 584 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS y 593 " --> pdb=" O MET y 589 " (cutoff:3.500A) Processing helix chain 'y' and resid 594 through 601 removed outlier: 5.312A pdb=" N ILE y 598 " --> pdb=" O GLN y 595 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN y 599 " --> pdb=" O ASP y 596 " (cutoff:3.500A) Processing helix chain 'y' and resid 602 through 623 Processing helix chain 'y' and resid 626 through 639 removed outlier: 4.670A pdb=" N ASP y 635 " --> pdb=" O ASN y 631 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE y 636 " --> pdb=" O ALA y 632 " (cutoff:3.500A) Processing helix chain 'y' and resid 660 through 667 Processing helix chain 'y' and resid 672 through 676 Processing helix chain 'y' and resid 678 through 701 Proline residue: y 696 - end of helix Processing helix chain 'y' and resid 702 through 704 No H-bonds generated for 'chain 'y' and resid 702 through 704' Processing helix chain 'y' and resid 711 through 724 Processing helix chain 'y' and resid 732 through 746 Processing helix chain 'y' and resid 749 through 757 Processing helix chain 'y' and resid 758 through 765 Processing helix chain 'y' and resid 766 through 769 Processing helix chain 'y' and resid 771 through 795 removed outlier: 3.502A pdb=" N VAL y 775 " --> pdb=" O GLU y 771 " (cutoff:3.500A) Processing helix chain 'y' and resid 804 through 812 Processing helix chain 'y' and resid 814 through 827 Processing helix chain 'y' and resid 856 through 875 Processing sheet with id=AA1, first strand: chain '4' and resid 91 through 94 Processing sheet with id=AA2, first strand: chain '4' and resid 128 through 135 removed outlier: 5.061A pdb=" N VAL 4 129 " --> pdb=" O ASP 4 125 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP 4 125 " --> pdb=" O VAL 4 129 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL 4 131 " --> pdb=" O THR 4 123 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR 4 123 " --> pdb=" O VAL 4 131 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY 4 118 " --> pdb=" O TRP 4 172 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TRP 4 172 " --> pdb=" O GLY 4 118 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU 4 120 " --> pdb=" O LEU 4 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '5' and resid 469 through 471 Processing sheet with id=AA4, first strand: chain '5' and resid 499 through 501 removed outlier: 3.607A pdb=" N ASN 5 499 " --> pdb=" O GLN 5 514 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '6' and resid 292 through 293 Processing sheet with id=AA6, first strand: chain '8' and resid 80 through 82 Processing sheet with id=AA7, first strand: chain '8' and resid 168 through 169 Processing sheet with id=AA8, first strand: chain 'H' and resid 44 through 47 removed outlier: 3.735A pdb=" N THR H 44 " --> pdb=" O VAL H 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 64 through 65 Processing sheet with id=AB1, first strand: chain 'M' and resid 96 through 98 Processing sheet with id=AB2, first strand: chain 'O' and resid 33 through 34 removed outlier: 6.030A pdb=" N LYS O 85 " --> pdb=" O HIS O 101 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET O 103 " --> pdb=" O LYS O 83 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS O 83 " --> pdb=" O MET O 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 33 through 34 removed outlier: 13.103A pdb=" N ASN O 99 " --> pdb=" O LYS O 219 " (cutoff:3.500A) removed outlier: 13.299A pdb=" N LYS O 219 " --> pdb=" O ASN O 99 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N HIS O 101 " --> pdb=" O MET O 217 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N MET O 217 " --> pdb=" O HIS O 101 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ARG O 213 " --> pdb=" O LEU O 105 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL O 210 " --> pdb=" O PHE O 142 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N PHE O 142 " --> pdb=" O VAL O 210 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL O 212 " --> pdb=" O VAL O 140 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL O 140 " --> pdb=" O VAL O 212 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU O 134 " --> pdb=" O LEU O 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 29 through 31 Processing sheet with id=AB5, first strand: chain 'P' and resid 34 through 35 Processing sheet with id=AB6, first strand: chain 'P' and resid 92 through 93 Processing sheet with id=AB7, first strand: chain 'P' and resid 96 through 97 removed outlier: 3.546A pdb=" N LEU P 97 " --> pdb=" O GLU P 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'Q' and resid 20 through 22 Processing sheet with id=AB9, first strand: chain 'Q' and resid 36 through 43 Processing sheet with id=AC1, first strand: chain 'n' and resid 39 through 47 removed outlier: 4.967A pdb=" N ARG n 40 " --> pdb=" O PHE n 34 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N CYS n 27 " --> pdb=" O ARG n 20 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG n 20 " --> pdb=" O CYS n 27 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN n 29 " --> pdb=" O LEU n 18 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS n 16 " --> pdb=" O ARG n 31 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU n 33 " --> pdb=" O VAL n 14 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL n 14 " --> pdb=" O GLU n 33 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'u' and resid 482 through 485 Processing sheet with id=AC3, first strand: chain 'v' and resid 351 through 352 Processing sheet with id=AC4, first strand: chain 'y' and resid 801 through 803 1809 hydrogen bonds defined for protein. 5300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 85 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 6.66 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5792 1.33 - 1.45: 8501 1.45 - 1.58: 17335 1.58 - 1.70: 291 1.70 - 1.83: 213 Bond restraints: 32132 Sorted by residual: bond pdb=" C GLU u 350 " pdb=" N LYS u 351 " ideal model delta sigma weight residual 1.335 1.473 -0.138 1.31e-02 5.83e+03 1.11e+02 bond pdb=" C ILE u 347 " pdb=" N ILE u 348 " ideal model delta sigma weight residual 1.335 1.221 0.114 1.23e-02 6.61e+03 8.54e+01 bond pdb=" C THR u 366 " pdb=" N ARG u 367 " ideal model delta sigma weight residual 1.332 1.219 0.114 1.40e-02 5.10e+03 6.57e+01 bond pdb=" C1' C 7 -28 " pdb=" N1 C 7 -28 " ideal model delta sigma weight residual 1.464 1.555 -0.091 1.40e-02 5.10e+03 4.22e+01 bond pdb=" C1' C 7 -34 " pdb=" N1 C 7 -34 " ideal model delta sigma weight residual 1.483 1.573 -0.090 1.50e-02 4.44e+03 3.59e+01 ... (remaining 32127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 43894 4.66 - 9.32: 387 9.32 - 13.98: 53 13.98 - 18.64: 7 18.64 - 23.30: 2 Bond angle restraints: 44343 Sorted by residual: angle pdb=" N LEU u 342 " pdb=" CA LEU u 342 " pdb=" C LEU u 342 " ideal model delta sigma weight residual 108.76 85.46 23.30 1.69e+00 3.50e-01 1.90e+02 angle pdb=" N GLY u 369 " pdb=" CA GLY u 369 " pdb=" C GLY u 369 " ideal model delta sigma weight residual 112.49 98.53 13.96 1.21e+00 6.83e-01 1.33e+02 angle pdb=" O THR u 366 " pdb=" C THR u 366 " pdb=" N ARG u 367 " ideal model delta sigma weight residual 123.29 112.75 10.54 1.00e+00 1.00e+00 1.11e+02 angle pdb=" CA THR u 366 " pdb=" C THR u 366 " pdb=" N ARG u 367 " ideal model delta sigma weight residual 115.38 127.82 -12.44 1.33e+00 5.65e-01 8.75e+01 angle pdb=" N LEU u 341 " pdb=" CA LEU u 341 " pdb=" C LEU u 341 " ideal model delta sigma weight residual 113.72 100.59 13.13 1.52e+00 4.33e-01 7.46e+01 ... (remaining 44338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 19017 35.57 - 71.13: 594 71.13 - 106.70: 81 106.70 - 142.26: 1 142.26 - 177.83: 1 Dihedral angle restraints: 19694 sinusoidal: 8111 harmonic: 11583 Sorted by residual: dihedral pdb=" O4' C 7 -22 " pdb=" C1' C 7 -22 " pdb=" N1 C 7 -22 " pdb=" C2 C 7 -22 " ideal model delta sinusoidal sigma weight residual -160.00 -59.96 -100.04 1 1.50e+01 4.44e-03 5.01e+01 dihedral pdb=" O4' C 7 -34 " pdb=" C1' C 7 -34 " pdb=" N1 C 7 -34 " pdb=" C2 C 7 -34 " ideal model delta sinusoidal sigma weight residual -160.00 -67.80 -92.20 1 1.50e+01 4.44e-03 4.43e+01 dihedral pdb=" O4' C 7 -31 " pdb=" C1' C 7 -31 " pdb=" N1 C 7 -31 " pdb=" C2 C 7 -31 " ideal model delta sinusoidal sigma weight residual -160.00 -69.05 -90.95 1 1.50e+01 4.44e-03 4.34e+01 ... (remaining 19691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4340 0.081 - 0.162: 858 0.162 - 0.243: 82 0.243 - 0.324: 17 0.324 - 0.405: 3 Chirality restraints: 5300 Sorted by residual: chirality pdb=" CB ILE u 446 " pdb=" CA ILE u 446 " pdb=" CG1 ILE u 446 " pdb=" CG2 ILE u 446 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA PHE N 32 " pdb=" N PHE N 32 " pdb=" C PHE N 32 " pdb=" CB PHE N 32 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CG LEU y 857 " pdb=" CB LEU y 857 " pdb=" CD1 LEU y 857 " pdb=" CD2 LEU y 857 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 5297 not shown) Planarity restraints: 5253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA u 505 " -0.091 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO u 506 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO u 506 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO u 506 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA y 568 " 0.023 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C ALA y 568 " -0.081 2.00e-02 2.50e+03 pdb=" O ALA y 568 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE y 569 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS H 37 " -0.066 5.00e-02 4.00e+02 9.83e-02 1.54e+01 pdb=" N PRO H 38 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO H 38 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 38 " -0.055 5.00e-02 4.00e+02 ... (remaining 5250 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 209 2.53 - 3.12: 24952 3.12 - 3.72: 55809 3.72 - 4.31: 69331 4.31 - 4.90: 107565 Nonbonded interactions: 257866 Sorted by model distance: nonbonded pdb=" CG ARG u 340 " pdb=" OE2 GLU y 722 " model vdw 1.939 3.440 nonbonded pdb=" NH2 ARG u 340 " pdb=" O ASP u 345 " model vdw 1.963 3.120 nonbonded pdb=" NH1 ARG u 340 " pdb=" CG1 ILE u 348 " model vdw 2.149 3.520 nonbonded pdb=" OG1 THR O 129 " pdb=" O ASN O 179 " model vdw 2.178 3.040 nonbonded pdb=" O VAL y 738 " pdb=" OG SER y 741 " model vdw 2.198 3.040 ... (remaining 257861 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 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: 0.990 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: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.500 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 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 : 0.006 0.138 32137 Z= 0.329 Angle : 1.214 38.761 44351 Z= 0.708 Chirality : 0.064 0.405 5300 Planarity : 0.007 0.133 5253 Dihedral : 17.281 177.827 12123 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.14 % Favored : 93.84 % Rotamer: Outliers : 0.08 % Allowed : 1.11 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3878 helix: 1.24 (0.11), residues: 2276 sheet: -1.25 (0.34), residues: 206 loop : -1.65 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG y 846 TYR 0.035 0.003 TYR N 47 PHE 0.049 0.003 PHE 5 550 TRP 0.064 0.003 TRP u 393 HIS 0.020 0.002 HIS y 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.33 (32132) covalent geometry : angle 1.18209 / 0.71 (44343) SS BOND : bond 0.00536 / 0.28 ( 1) SS BOND : angle 1.46782 / 0.98 ( 2) hydrogen bonds : bond 0.13642 / 10.39 ( 1892) hydrogen bonds : angle 6.31342 / 4.74 ( 5442) metal coordination : bond 0.03680 / 1.40 ( 4) metal coordination : angle 23.94810 / 12.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 806 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 53 LYS cc_start: 0.5934 (mttt) cc_final: 0.5568 (mmmt) REVERT: 5 58 TYR cc_start: 0.6589 (t80) cc_final: 0.6342 (t80) REVERT: 5 89 TYR cc_start: 0.4765 (p90) cc_final: 0.4037 (t80) REVERT: 5 114 GLU cc_start: 0.5561 (mp0) cc_final: 0.4911 (tp30) REVERT: 5 125 ASP cc_start: 0.1891 (t0) cc_final: 0.1562 (m-30) REVERT: 5 135 LEU cc_start: 0.3199 (mt) cc_final: 0.2838 (mt) REVERT: 5 166 TYR cc_start: 0.4494 (t80) cc_final: 0.3882 (t80) REVERT: 5 304 MET cc_start: 0.1838 (mpp) cc_final: 0.1259 (ppp) REVERT: 5 345 ARG cc_start: 0.6549 (ppt170) cc_final: 0.6308 (mpp80) REVERT: 5 355 TYR cc_start: 0.1397 (p90) cc_final: 0.0797 (t80) REVERT: 5 359 MET cc_start: 0.4112 (ppp) cc_final: 0.3751 (ppp) REVERT: 5 513 PHE cc_start: 0.5376 (m-80) cc_final: 0.5019 (p90) REVERT: 5 560 MET cc_start: 0.7949 (tpt) cc_final: 0.7703 (ttt) REVERT: 6 255 PHE cc_start: 0.5949 (m-80) cc_final: 0.5462 (m-80) REVERT: 6 309 GLU cc_start: 0.7398 (pm20) cc_final: 0.7157 (pm20) REVERT: 6 327 GLN cc_start: 0.7259 (pt0) cc_final: 0.7038 (tt0) REVERT: I 78 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7738 (mmtt) REVERT: M 121 GLN cc_start: 0.7011 (pm20) cc_final: 0.6760 (tp-100) REVERT: N 32 PHE cc_start: 0.7187 (p90) cc_final: 0.6979 (p90) REVERT: N 34 MET cc_start: 0.7720 (mtt) cc_final: 0.7005 (mtp) REVERT: N 37 TYR cc_start: 0.6492 (m-80) cc_final: 0.6219 (m-80) REVERT: O 71 LEU cc_start: 0.6399 (tp) cc_final: 0.6038 (tp) REVERT: O 73 ASP cc_start: 0.6567 (m-30) cc_final: 0.6313 (m-30) REVERT: O 88 THR cc_start: 0.8255 (p) cc_final: 0.7959 (p) REVERT: O 110 MET cc_start: 0.5583 (pmm) cc_final: 0.5128 (mmm) REVERT: O 131 ASP cc_start: 0.8814 (m-30) cc_final: 0.8556 (m-30) REVERT: O 138 PHE cc_start: 0.6337 (m-80) cc_final: 0.6094 (m-80) REVERT: O 155 TYR cc_start: 0.7014 (m-80) cc_final: 0.6033 (m-80) REVERT: O 170 GLU cc_start: 0.6612 (tm-30) cc_final: 0.6239 (mm-30) REVERT: P 91 THR cc_start: 0.6910 (p) cc_final: 0.6701 (p) REVERT: P 95 ILE cc_start: 0.8180 (mp) cc_final: 0.7956 (mm) REVERT: P 130 GLU cc_start: 0.6922 (pm20) cc_final: 0.6604 (pm20) REVERT: Q 52 ASP cc_start: 0.7671 (p0) cc_final: 0.7155 (t0) REVERT: Q 67 LEU cc_start: 0.6238 (tt) cc_final: 0.5856 (tt) REVERT: Q 68 TYR cc_start: 0.6067 (m-80) cc_final: 0.5728 (m-80) REVERT: Q 94 ASP cc_start: 0.6450 (m-30) cc_final: 0.6086 (t0) REVERT: n 33 GLU cc_start: 0.6872 (pp20) cc_final: 0.6473 (tm-30) REVERT: n 35 MET cc_start: 0.7240 (pmm) cc_final: 0.6894 (pmm) REVERT: n 54 ASP cc_start: 0.7784 (m-30) cc_final: 0.7214 (t0) REVERT: u 17 GLU cc_start: 0.7006 (pp20) cc_final: 0.6611 (pp20) REVERT: u 82 ASN cc_start: 0.7058 (m110) cc_final: 0.6742 (t0) REVERT: u 109 GLN cc_start: 0.5768 (pp30) cc_final: 0.4961 (pp30) REVERT: u 138 GLN cc_start: 0.5462 (tp40) cc_final: 0.3969 (tp40) REVERT: u 199 ASP cc_start: 0.8134 (p0) cc_final: 0.7907 (m-30) REVERT: u 228 MET cc_start: 0.6473 (ttp) cc_final: 0.6244 (ttp) REVERT: u 245 LEU cc_start: 0.6995 (tp) cc_final: 0.6615 (tp) REVERT: u 304 ARG cc_start: 0.7150 (mmm-85) cc_final: 0.6172 (ptm-80) REVERT: u 337 ASP cc_start: 0.7951 (p0) cc_final: 0.7282 (t70) REVERT: u 343 ASP cc_start: 0.5381 (m-30) cc_final: 0.5030 (m-30) REVERT: u 344 MET cc_start: 0.6849 (mtp) cc_final: 0.6643 (pmm) REVERT: u 368 ILE cc_start: 0.5312 (mm) cc_final: 0.5100 (mm) REVERT: u 389 ASP cc_start: 0.6840 (p0) cc_final: 0.6535 (t0) REVERT: u 450 ILE cc_start: 0.6763 (mt) cc_final: 0.6495 (mt) REVERT: u 497 LEU cc_start: 0.8012 (tt) cc_final: 0.7587 (mm) REVERT: u 518 GLN cc_start: 0.6415 (tp40) cc_final: 0.6213 (tp40) REVERT: u 523 LEU cc_start: 0.7158 (tp) cc_final: 0.6828 (tp) REVERT: u 530 LEU cc_start: 0.7292 (mm) cc_final: 0.6524 (mm) REVERT: u 545 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6746 (mm-30) REVERT: v 249 MET cc_start: 0.5242 (pmm) cc_final: 0.4657 (ppp) REVERT: v 282 GLN cc_start: 0.7426 (tp40) cc_final: 0.6568 (pp30) REVERT: v 286 TYR cc_start: 0.5767 (t80) cc_final: 0.5020 (t80) REVERT: v 313 ARG cc_start: 0.7526 (ttp80) cc_final: 0.7154 (mpt90) REVERT: v 325 LEU cc_start: 0.7481 (mm) cc_final: 0.7270 (mt) REVERT: v 362 MET cc_start: 0.7523 (ppp) cc_final: 0.7179 (ppp) REVERT: v 406 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6365 (mm-30) REVERT: x 55 TYR cc_start: 0.2509 (m-10) cc_final: 0.1827 (m-80) REVERT: y 392 TYR cc_start: 0.7083 (p90) cc_final: 0.6445 (p90) REVERT: y 517 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7509 (mmtm) REVERT: y 596 ASP cc_start: 0.7371 (p0) cc_final: 0.6750 (m-30) REVERT: y 641 ARG cc_start: 0.7584 (mtp-110) cc_final: 0.7334 (ptm160) REVERT: y 680 GLU cc_start: 0.6706 (tp30) cc_final: 0.6382 (mt-10) REVERT: y 693 LEU cc_start: 0.6606 (mp) cc_final: 0.6360 (mp) REVERT: y 712 LYS cc_start: 0.6858 (tptt) cc_final: 0.6568 (mmtm) REVERT: y 720 VAL cc_start: 0.5769 (m) cc_final: 0.5565 (p) REVERT: y 733 MET cc_start: 0.6406 (ppp) cc_final: 0.6147 (ptp) REVERT: y 831 LEU cc_start: 0.6879 (pt) cc_final: 0.6570 (pp) outliers start: 2 outliers final: 0 residues processed: 808 average time/residue: 0.2029 time to fit residues: 253.4407 Evaluate side-chains 455 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 197 optimal weight: 0.0870 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 60 HIS 5 86 GLN 5 124 ASN 6 273 ASN H 19 HIS P 38 ASN u 79 GLN u 187 GLN ** u 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 430 GLN v 216 HIS ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 584 GLN y 662 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.164357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.139058 restraints weight = 72687.676| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.67 r_work: 0.3835 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3840 r_free = 0.3840 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3840 r_free = 0.3840 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32137 Z= 0.159 Angle : 0.737 28.324 44351 Z= 0.371 Chirality : 0.043 0.341 5300 Planarity : 0.005 0.100 5253 Dihedral : 16.201 178.697 6528 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.35 % Allowed : 13.21 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3878 helix: 1.22 (0.11), residues: 2320 sheet: -1.13 (0.35), residues: 203 loop : -1.57 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG y 668 TYR 0.023 0.002 TYR 5 89 PHE 0.020 0.002 PHE 5 420 TRP 0.035 0.002 TRP u 43 HIS 0.008 0.001 HIS y 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (32132) covalent geometry : angle 0.70248 / 0.37 (44343) SS BOND : bond 0.00174 / 0.09 ( 1) SS BOND : angle 5.21744 / 3.48 ( 2) hydrogen bonds : bond 0.04751 / 3.61 ( 1892) hydrogen bonds : angle 5.13341 / 3.89 ( 5442) metal coordination : bond 0.00879 / 0.33 ( 4) metal coordination : angle 18.93201 / 10.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 496 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 89 TYR cc_start: 0.4749 (p90) cc_final: 0.3801 (t80) REVERT: 5 135 LEU cc_start: 0.2687 (mt) cc_final: 0.2070 (mt) REVERT: 5 166 TYR cc_start: 0.4302 (t80) cc_final: 0.3312 (t80) REVERT: 5 349 MET cc_start: 0.1793 (ttp) cc_final: 0.1515 (tmm) REVERT: 5 355 TYR cc_start: 0.2055 (p90) cc_final: 0.1093 (t80) REVERT: 5 497 MET cc_start: 0.5088 (mmt) cc_final: 0.4751 (ttm) REVERT: H 16 LYS cc_start: 0.9030 (tptp) cc_final: 0.8784 (tptm) REVERT: H 33 MET cc_start: 0.8250 (pmm) cc_final: 0.8006 (ptt) REVERT: I 53 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8813 (mt) REVERT: N 34 MET cc_start: 0.7200 (mtt) cc_final: 0.6868 (mtp) REVERT: O 32 ASP cc_start: 0.7123 (p0) cc_final: 0.6920 (p0) REVERT: O 88 THR cc_start: 0.8441 (p) cc_final: 0.8185 (p) REVERT: O 217 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.7066 (mtm) REVERT: P 25 GLU cc_start: 0.6868 (pm20) cc_final: 0.6659 (pm20) REVERT: Q 96 THR cc_start: 0.8822 (t) cc_final: 0.8309 (t) REVERT: n 54 ASP cc_start: 0.7630 (m-30) cc_final: 0.7060 (t0) REVERT: u 16 ASN cc_start: 0.8241 (m-40) cc_final: 0.8026 (m-40) REVERT: u 29 ASP cc_start: 0.7890 (p0) cc_final: 0.7622 (p0) REVERT: u 109 GLN cc_start: 0.6491 (pp30) cc_final: 0.6186 (pp30) REVERT: u 138 GLN cc_start: 0.8028 (tp40) cc_final: 0.6974 (tp-100) REVERT: u 228 MET cc_start: 0.7633 (ttp) cc_final: 0.7380 (ttm) REVERT: u 374 MET cc_start: 0.7146 (mmm) cc_final: 0.6925 (mmp) REVERT: u 479 ASP cc_start: 0.7368 (m-30) cc_final: 0.7162 (m-30) REVERT: u 497 LEU cc_start: 0.7514 (tt) cc_final: 0.7192 (mm) REVERT: u 518 GLN cc_start: 0.7414 (tp40) cc_final: 0.7164 (tp40) REVERT: u 532 LYS cc_start: 0.7920 (tptm) cc_final: 0.7500 (mmtm) REVERT: u 535 GLU cc_start: 0.2800 (tt0) cc_final: 0.2055 (tt0) REVERT: u 559 LYS cc_start: 0.6245 (mmtm) cc_final: 0.5912 (ptpp) REVERT: v 325 LEU cc_start: 0.7607 (mm) cc_final: 0.7382 (mt) REVERT: x 53 LYS cc_start: 0.5752 (mmmt) cc_final: 0.5250 (tppp) outliers start: 57 outliers final: 38 residues processed: 530 average time/residue: 0.2060 time to fit residues: 173.7075 Evaluate side-chains 420 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 380 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 90 GLU Chi-restraints excluded: chain 5 residue 380 MET Chi-restraints excluded: chain 6 residue 249 LEU Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 269 LEU Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 179 ASN Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 217 MET Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 126 ILE Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 32 VAL Chi-restraints excluded: chain u residue 98 GLU Chi-restraints excluded: chain u residue 171 GLU Chi-restraints excluded: chain u residue 220 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 320 THR Chi-restraints excluded: chain u residue 347 ILE Chi-restraints excluded: chain u residue 435 THR Chi-restraints excluded: chain u residue 446 ILE Chi-restraints excluded: chain v residue 413 PHE Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain y residue 328 VAL Chi-restraints excluded: chain y residue 358 VAL Chi-restraints excluded: chain y residue 711 SER Chi-restraints excluded: chain y residue 810 MET Chi-restraints excluded: chain y residue 827 ILE Chi-restraints excluded: chain y residue 835 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 232 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 354 optimal weight: 6.9990 chunk 305 optimal weight: 0.9990 chunk 319 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 165 optimal weight: 30.0000 chunk 238 optimal weight: 0.0570 chunk 15 optimal weight: 40.0000 chunk 73 optimal weight: 20.0000 chunk 327 optimal weight: 2.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 86 GLN ** 5 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 124 ASN 5 361 ASN 6 355 ASN P 38 ASN P 113 GLN ** u 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 297 HIS ** u 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 390 HIS ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 460 GLN y 593 HIS y 758 ASN ** y 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.159129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.142009 restraints weight = 90165.442| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.57 r_work: 0.3754 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 32137 Z= 0.182 Angle : 0.701 23.861 44351 Z= 0.357 Chirality : 0.043 0.342 5300 Planarity : 0.005 0.059 5253 Dihedral : 15.937 178.066 6528 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.69 % Rotamer: Outliers : 3.55 % Allowed : 15.81 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3878 helix: 1.26 (0.11), residues: 2329 sheet: -1.09 (0.36), residues: 199 loop : -1.62 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG u 317 TYR 0.040 0.002 TYR N 37 PHE 0.036 0.002 PHE 5 542 TRP 0.026 0.002 TRP u 43 HIS 0.015 0.002 HIS u 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (32132) covalent geometry : angle 0.67385 / 0.36 (44343) SS BOND : bond 0.02002 / 1.05 ( 1) SS BOND : angle 5.56607 / 3.71 ( 2) hydrogen bonds : bond 0.04387 / 3.34 ( 1892) hydrogen bonds : angle 4.79366 / 3.65 ( 5442) metal coordination : bond 0.00482 / 0.24 ( 4) metal coordination : angle 16.41724 / 9.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 408 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 89 TYR cc_start: 0.4647 (p90) cc_final: 0.3638 (t80) REVERT: 5 90 GLU cc_start: 0.2694 (OUTLIER) cc_final: 0.1796 (mm-30) REVERT: 5 166 TYR cc_start: 0.4219 (t80) cc_final: 0.3756 (t80) REVERT: 5 304 MET cc_start: 0.1906 (ppp) cc_final: 0.0819 (mtp) REVERT: 5 349 MET cc_start: 0.1694 (ttp) cc_final: 0.1387 (tmm) REVERT: 5 355 TYR cc_start: 0.1974 (p90) cc_final: 0.1002 (t80) REVERT: 5 398 MET cc_start: 0.5237 (ttm) cc_final: 0.5012 (ttm) REVERT: 6 277 MET cc_start: 0.7183 (tpt) cc_final: 0.6900 (tpt) REVERT: 6 280 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8943 (mm) REVERT: 6 306 ASP cc_start: 0.7981 (p0) cc_final: 0.7698 (p0) REVERT: I 53 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8942 (mp) REVERT: O 88 THR cc_start: 0.8522 (p) cc_final: 0.8288 (p) REVERT: n 54 ASP cc_start: 0.7843 (m-30) cc_final: 0.7120 (t0) REVERT: u 316 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6247 (mp10) REVERT: u 497 LEU cc_start: 0.7611 (tt) cc_final: 0.7389 (mm) REVERT: u 526 MET cc_start: 0.5209 (mmt) cc_final: 0.4893 (mmt) REVERT: u 532 LYS cc_start: 0.8195 (tptm) cc_final: 0.7856 (mptt) REVERT: u 535 GLU cc_start: 0.3371 (tt0) cc_final: 0.3154 (tt0) REVERT: u 559 LYS cc_start: 0.6641 (mmtm) cc_final: 0.6247 (mtmm) REVERT: v 275 LYS cc_start: 0.7584 (mttt) cc_final: 0.7353 (mtpt) REVERT: x 53 LYS cc_start: 0.5780 (mmmt) cc_final: 0.5332 (tppp) REVERT: x 55 TYR cc_start: 0.5620 (m-80) cc_final: 0.5418 (m-80) REVERT: y 392 TYR cc_start: 0.8418 (p90) cc_final: 0.8168 (p90) REVERT: y 731 GLU cc_start: 0.6988 (pm20) cc_final: 0.6725 (pt0) REVERT: y 778 MET cc_start: 0.8905 (tmm) cc_final: 0.8694 (tmm) outliers start: 86 outliers final: 52 residues processed: 456 average time/residue: 0.1806 time to fit residues: 134.7620 Evaluate side-chains 418 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 362 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 90 GLU Chi-restraints excluded: chain 5 residue 247 TYR Chi-restraints excluded: chain 5 residue 375 LEU Chi-restraints excluded: chain 6 residue 249 LEU Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 280 LEU Chi-restraints excluded: chain 6 residue 337 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 126 ILE Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain u residue 98 GLU Chi-restraints excluded: chain u residue 171 GLU Chi-restraints excluded: chain u residue 220 LEU Chi-restraints excluded: chain u residue 221 ASN Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 316 GLN Chi-restraints excluded: chain u residue 320 THR Chi-restraints excluded: chain u residue 324 LEU Chi-restraints excluded: chain u residue 340 ARG Chi-restraints excluded: chain u residue 435 THR Chi-restraints excluded: chain u residue 450 ILE Chi-restraints excluded: chain u residue 480 LEU Chi-restraints excluded: chain u residue 487 THR Chi-restraints excluded: chain u residue 507 ILE Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 233 ILE Chi-restraints excluded: chain v residue 299 LEU Chi-restraints excluded: chain v residue 318 VAL Chi-restraints excluded: chain v residue 390 HIS Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain y residue 328 VAL Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 569 ILE Chi-restraints excluded: chain y residue 810 MET Chi-restraints excluded: chain y residue 827 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 353 optimal weight: 0.6980 chunk 203 optimal weight: 7.9990 chunk 344 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 286 optimal weight: 0.9980 chunk 106 optimal weight: 40.0000 chunk 100 optimal weight: 7.9990 chunk 288 optimal weight: 0.7980 chunk 0 optimal weight: 60.0000 chunk 174 optimal weight: 9.9990 chunk 146 optimal weight: 40.0000 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 86 GLN 5 124 ASN 5 312 GLN I 36 GLN P 38 ASN P 113 GLN ** u 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 209 GLN ** u 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 442 GLN ** u 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 631 ASN y 758 ASN ** y 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 845 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.157646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.130533 restraints weight = 75251.982| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.55 r_work: 0.3679 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 32137 Z= 0.201 Angle : 0.694 23.096 44351 Z= 0.352 Chirality : 0.043 0.349 5300 Planarity : 0.005 0.064 5253 Dihedral : 15.807 176.531 6528 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.34 % Allowed : 16.68 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3878 helix: 1.28 (0.11), residues: 2330 sheet: -1.07 (0.36), residues: 197 loop : -1.71 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 5 545 TYR 0.024 0.002 TYR u 391 PHE 0.035 0.002 PHE v 295 TRP 0.024 0.002 TRP u 43 HIS 0.040 0.002 HIS v 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (32132) covalent geometry : angle 0.66728 / 0.35 (44343) SS BOND : bond 0.02424 / 1.28 ( 1) SS BOND : angle 6.12887 / 4.09 ( 2) hydrogen bonds : bond 0.04201 / 3.19 ( 1892) hydrogen bonds : angle 4.67198 / 3.56 ( 5442) metal coordination : bond 0.00526 / 0.27 ( 4) metal coordination : angle 15.96980 / 9.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 390 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 89 TYR cc_start: 0.4563 (p90) cc_final: 0.3795 (t80) REVERT: 5 90 GLU cc_start: 0.2860 (OUTLIER) cc_final: 0.1937 (mm-30) REVERT: 5 166 TYR cc_start: 0.4287 (t80) cc_final: 0.3846 (t80) REVERT: 5 349 MET cc_start: 0.1859 (ttp) cc_final: 0.1481 (tmm) REVERT: 5 355 TYR cc_start: 0.1803 (p90) cc_final: 0.0849 (t80) REVERT: 5 497 MET cc_start: 0.4784 (OUTLIER) cc_final: 0.4095 (ttm) REVERT: H 16 LYS cc_start: 0.8981 (tptp) cc_final: 0.8645 (tptm) REVERT: O 32 ASP cc_start: 0.7707 (p0) cc_final: 0.7393 (p0) REVERT: O 75 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: O 88 THR cc_start: 0.8580 (p) cc_final: 0.8330 (p) REVERT: O 188 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8416 (mt) REVERT: P 75 MET cc_start: 0.8319 (tmm) cc_final: 0.8115 (tmm) REVERT: Q 52 ASP cc_start: 0.7994 (t0) cc_final: 0.7739 (t0) REVERT: n 33 GLU cc_start: 0.7349 (pp20) cc_final: 0.7076 (pp20) REVERT: n 54 ASP cc_start: 0.8092 (m-30) cc_final: 0.7219 (t0) REVERT: u 316 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.5941 (mp10) REVERT: u 317 ARG cc_start: 0.7134 (mmp80) cc_final: 0.6680 (mmp-170) REVERT: u 415 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7460 (mtm-85) REVERT: u 532 LYS cc_start: 0.8123 (tptm) cc_final: 0.7722 (mmtm) REVERT: u 559 LYS cc_start: 0.7045 (mmtm) cc_final: 0.6571 (mtmm) REVERT: x 55 TYR cc_start: 0.6368 (m-80) cc_final: 0.6065 (m-80) REVERT: y 392 TYR cc_start: 0.8658 (p90) cc_final: 0.8185 (p90) REVERT: y 431 LEU cc_start: 0.4844 (OUTLIER) cc_final: 0.3667 (mt) REVERT: y 471 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: y 804 MET cc_start: 0.7757 (mmm) cc_final: 0.7499 (mtt) outliers start: 105 outliers final: 65 residues processed: 456 average time/residue: 0.1906 time to fit residues: 142.7824 Evaluate side-chains 426 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 354 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 90 GLU Chi-restraints excluded: chain 5 residue 497 MET Chi-restraints excluded: chain 5 residue 550 PHE Chi-restraints excluded: chain 6 residue 249 LEU Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 292 ILE Chi-restraints excluded: chain 6 residue 325 ILE Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain O residue 75 GLN Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 14 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain u residue 98 GLU Chi-restraints excluded: chain u residue 171 GLU Chi-restraints excluded: chain u residue 205 LEU Chi-restraints excluded: chain u residue 220 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 316 GLN Chi-restraints excluded: chain u residue 320 THR Chi-restraints excluded: chain u residue 324 LEU Chi-restraints excluded: chain u residue 340 ARG Chi-restraints excluded: chain u residue 435 THR Chi-restraints excluded: chain u residue 443 VAL Chi-restraints excluded: chain u residue 480 LEU Chi-restraints excluded: chain u residue 487 THR Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 233 ILE Chi-restraints excluded: chain v residue 293 THR Chi-restraints excluded: chain v residue 299 LEU Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 318 VAL Chi-restraints excluded: chain v residue 390 HIS Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain y residue 354 LEU Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 424 ILE Chi-restraints excluded: chain y residue 431 LEU Chi-restraints excluded: chain y residue 440 VAL Chi-restraints excluded: chain y residue 452 ASP Chi-restraints excluded: chain y residue 471 GLU Chi-restraints excluded: chain y residue 569 ILE Chi-restraints excluded: chain y residue 810 MET Chi-restraints excluded: chain y residue 827 ILE Chi-restraints excluded: chain y residue 835 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 87 optimal weight: 5.9990 chunk 138 optimal weight: 50.0000 chunk 338 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 39 optimal weight: 30.0000 chunk 150 optimal weight: 30.0000 chunk 199 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 350 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 396 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 86 GLN ** 5 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 124 ASN 6 336 HIS H 51 GLN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 442 GLN ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 377 ASN ** y 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 845 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.154653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.135325 restraints weight = 85791.899| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.74 r_work: 0.3605 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 32137 Z= 0.248 Angle : 0.732 23.389 44351 Z= 0.373 Chirality : 0.045 0.334 5300 Planarity : 0.005 0.067 5253 Dihedral : 15.760 174.358 6528 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.67 % Allowed : 17.88 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3878 helix: 1.20 (0.11), residues: 2332 sheet: -1.06 (0.37), residues: 205 loop : -1.72 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG y 563 TYR 0.027 0.002 TYR u 391 PHE 0.026 0.002 PHE v 295 TRP 0.032 0.003 TRP u 43 HIS 0.013 0.002 HIS v 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.25 (32132) covalent geometry : angle 0.70522 / 0.37 (44343) SS BOND : bond 0.02699 / 1.42 ( 1) SS BOND : angle 6.91558 / 4.61 ( 2) hydrogen bonds : bond 0.04408 / 3.35 ( 1892) hydrogen bonds : angle 4.68197 / 3.56 ( 5442) metal coordination : bond 0.00577 / 0.29 ( 4) metal coordination : angle 16.36269 / 9.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 392 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 89 TYR cc_start: 0.4551 (p90) cc_final: 0.3768 (t80) REVERT: 5 351 GLN cc_start: 0.1403 (OUTLIER) cc_final: 0.1063 (mm-40) REVERT: 5 355 TYR cc_start: 0.1809 (p90) cc_final: 0.0792 (t80) REVERT: 6 277 MET cc_start: 0.7377 (tpt) cc_final: 0.6990 (tpt) REVERT: 6 280 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9062 (mm) REVERT: 6 362 ASN cc_start: 0.7892 (m-40) cc_final: 0.7112 (p0) REVERT: H 16 LYS cc_start: 0.8913 (tptp) cc_final: 0.8654 (tptm) REVERT: H 51 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8086 (mt0) REVERT: I 49 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8401 (mt0) REVERT: I 69 ASN cc_start: 0.7431 (p0) cc_final: 0.6790 (p0) REVERT: O 228 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8053 (tt) REVERT: P 113 GLN cc_start: 0.8156 (mm110) cc_final: 0.7894 (mm110) REVERT: Q 52 ASP cc_start: 0.8046 (t0) cc_final: 0.7711 (t0) REVERT: n 33 GLU cc_start: 0.7440 (pp20) cc_final: 0.7154 (pp20) REVERT: n 54 ASP cc_start: 0.8401 (m-30) cc_final: 0.7307 (t0) REVERT: n 63 ARG cc_start: 0.5145 (ttp-170) cc_final: 0.4695 (ttp-170) REVERT: u 169 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7895 (mmm-85) REVERT: u 314 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7913 (mm-30) REVERT: u 316 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6562 (mp10) REVERT: u 532 LYS cc_start: 0.8196 (tptm) cc_final: 0.7872 (mmtm) REVERT: u 559 LYS cc_start: 0.7072 (mmtm) cc_final: 0.6646 (mtmm) REVERT: v 275 LYS cc_start: 0.7683 (mttp) cc_final: 0.7141 (mtpt) REVERT: x 55 TYR cc_start: 0.6576 (m-80) cc_final: 0.6163 (m-80) REVERT: y 392 TYR cc_start: 0.8843 (p90) cc_final: 0.8333 (p90) REVERT: y 471 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: y 666 GLU cc_start: 0.8105 (pp20) cc_final: 0.7862 (pt0) REVERT: y 742 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8207 (mptt) REVERT: y 804 MET cc_start: 0.7896 (mmm) cc_final: 0.7638 (mtt) outliers start: 113 outliers final: 73 residues processed: 469 average time/residue: 0.1819 time to fit residues: 140.4220 Evaluate side-chains 433 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 352 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 94 ILE Chi-restraints excluded: chain 5 residue 247 TYR Chi-restraints excluded: chain 5 residue 351 GLN Chi-restraints excluded: chain 5 residue 375 LEU Chi-restraints excluded: chain 5 residue 385 SER Chi-restraints excluded: chain 5 residue 550 PHE Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 280 LEU Chi-restraints excluded: chain 6 residue 325 ILE Chi-restraints excluded: chain 6 residue 337 SER Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain 6 residue 369 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 191 ASP Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 14 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain u residue 98 GLU Chi-restraints excluded: chain u residue 115 ILE Chi-restraints excluded: chain u residue 171 GLU Chi-restraints excluded: chain u residue 205 LEU Chi-restraints excluded: chain u residue 220 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 316 GLN Chi-restraints excluded: chain u residue 318 MET Chi-restraints excluded: chain u residue 320 THR Chi-restraints excluded: chain u residue 324 LEU Chi-restraints excluded: chain u residue 340 ARG Chi-restraints excluded: chain u residue 396 VAL Chi-restraints excluded: chain u residue 435 THR Chi-restraints excluded: chain u residue 443 VAL Chi-restraints excluded: chain u residue 480 LEU Chi-restraints excluded: chain u residue 507 ILE Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 233 ILE Chi-restraints excluded: chain v residue 243 LEU Chi-restraints excluded: chain v residue 293 THR Chi-restraints excluded: chain v residue 299 LEU Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 318 VAL Chi-restraints excluded: chain v residue 415 SER Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain y residue 354 LEU Chi-restraints excluded: chain y residue 397 MET Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 452 ASP Chi-restraints excluded: chain y residue 471 GLU Chi-restraints excluded: chain y residue 742 LYS Chi-restraints excluded: chain y residue 810 MET Chi-restraints excluded: chain y residue 827 ILE Chi-restraints excluded: chain y residue 835 LEU Chi-restraints excluded: chain y residue 841 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 26 optimal weight: 0.1980 chunk 140 optimal weight: 50.0000 chunk 351 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 321 optimal weight: 3.9990 chunk 284 optimal weight: 0.7980 chunk 245 optimal weight: 2.9990 chunk 329 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 190 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.4943 > 50:) chunk 177 optimal weight: 40.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 5 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 124 ASN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 82 ASN u 209 GLN ** u 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 236 GLN u 442 GLN ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 225 HIS ** v 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 432 HIS ** y 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 837 GLN y 845 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.155544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.129522 restraints weight = 74198.822| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.58 r_work: 0.3670 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 32137 Z= 0.143 Angle : 0.648 20.657 44351 Z= 0.331 Chirality : 0.041 0.335 5300 Planarity : 0.004 0.064 5253 Dihedral : 15.696 174.195 6528 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.88 % Allowed : 19.57 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3878 helix: 1.38 (0.11), residues: 2334 sheet: -0.84 (0.38), residues: 190 loop : -1.67 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 5 545 TYR 0.025 0.002 TYR 5 89 PHE 0.022 0.001 PHE u 398 TRP 0.031 0.002 TRP u 393 HIS 0.010 0.001 HIS y 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (32132) covalent geometry : angle 0.62529 / 0.33 (44343) SS BOND : bond 0.02322 / 1.22 ( 1) SS BOND : angle 5.10596 / 3.40 ( 2) hydrogen bonds : bond 0.03882 / 2.94 ( 1892) hydrogen bonds : angle 4.53916 / 3.45 ( 5442) metal coordination : bond 0.00596 / 0.30 ( 4) metal coordination : angle 14.20696 / 8.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 396 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 89 TYR cc_start: 0.4691 (p90) cc_final: 0.4072 (t80) REVERT: 5 349 MET cc_start: 0.2085 (ttp) cc_final: 0.0671 (tpp) REVERT: 5 351 GLN cc_start: 0.1220 (OUTLIER) cc_final: 0.0979 (mm-40) REVERT: 5 355 TYR cc_start: 0.1663 (p90) cc_final: 0.0732 (t80) REVERT: 6 277 MET cc_start: 0.7385 (tpt) cc_final: 0.7059 (tpt) REVERT: 6 309 GLU cc_start: 0.7735 (pm20) cc_final: 0.7474 (mp0) REVERT: H 16 LYS cc_start: 0.8918 (tptp) cc_final: 0.8718 (tptm) REVERT: I 49 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: I 69 ASN cc_start: 0.7319 (p0) cc_final: 0.6709 (p0) REVERT: N 35 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: O 171 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7337 (mt) REVERT: O 228 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7950 (tt) REVERT: Q 52 ASP cc_start: 0.7924 (t0) cc_final: 0.7673 (t0) REVERT: n 33 GLU cc_start: 0.7263 (pp20) cc_final: 0.6978 (pp20) REVERT: n 54 ASP cc_start: 0.8364 (m-30) cc_final: 0.7875 (p0) REVERT: u 316 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6214 (mp10) REVERT: u 532 LYS cc_start: 0.8064 (tptm) cc_final: 0.7808 (mptt) REVERT: u 559 LYS cc_start: 0.7185 (mmtm) cc_final: 0.6849 (mtmm) REVERT: x 55 TYR cc_start: 0.6456 (m-80) cc_final: 0.6109 (m-80) REVERT: y 471 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7488 (mm-30) REVERT: y 666 GLU cc_start: 0.7997 (pp20) cc_final: 0.7767 (pt0) REVERT: y 742 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8051 (mptt) outliers start: 94 outliers final: 56 residues processed: 455 average time/residue: 0.1847 time to fit residues: 139.7226 Evaluate side-chains 428 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 364 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 351 GLN Chi-restraints excluded: chain 5 residue 385 SER Chi-restraints excluded: chain 5 residue 470 MET Chi-restraints excluded: chain 5 residue 550 PHE Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 308 VAL Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 171 ILE Chi-restraints excluded: chain O residue 182 LYS Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 14 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain u residue 98 GLU Chi-restraints excluded: chain u residue 130 SER Chi-restraints excluded: chain u residue 171 GLU Chi-restraints excluded: chain u residue 205 LEU Chi-restraints excluded: chain u residue 220 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 316 GLN Chi-restraints excluded: chain u residue 324 LEU Chi-restraints excluded: chain u residue 340 ARG Chi-restraints excluded: chain u residue 450 ILE Chi-restraints excluded: chain u residue 452 PHE Chi-restraints excluded: chain u residue 487 THR Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 249 MET Chi-restraints excluded: chain v residue 282 GLN Chi-restraints excluded: chain v residue 299 LEU Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 318 VAL Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain y residue 353 LEU Chi-restraints excluded: chain y residue 354 LEU Chi-restraints excluded: chain y residue 397 MET Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 432 HIS Chi-restraints excluded: chain y residue 440 VAL Chi-restraints excluded: chain y residue 471 GLU Chi-restraints excluded: chain y residue 547 LEU Chi-restraints excluded: chain y residue 742 LYS Chi-restraints excluded: chain y residue 827 ILE Chi-restraints excluded: chain y residue 835 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 388 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 138 optimal weight: 50.0000 chunk 183 optimal weight: 5.9990 chunk 390 optimal weight: 0.7980 chunk 369 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 318 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 392 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 5 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 86 GLN ** 5 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 124 ASN H 51 GLN O 124 HIS ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 47 HIS u 82 ASN u 226 GLN ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 239 GLN ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 283 GLN ** y 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 845 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.155853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.130732 restraints weight = 77971.475| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.37 r_work: 0.3695 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 32137 Z= 0.136 Angle : 0.651 19.013 44351 Z= 0.328 Chirality : 0.041 0.336 5300 Planarity : 0.004 0.062 5253 Dihedral : 15.597 174.572 6528 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.63 % Allowed : 20.44 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3878 helix: 1.46 (0.11), residues: 2336 sheet: -0.71 (0.38), residues: 193 loop : -1.62 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 5 545 TYR 0.025 0.001 TYR 5 89 PHE 0.021 0.001 PHE 6 311 TRP 0.026 0.002 TRP u 393 HIS 0.040 0.001 HIS y 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (32132) covalent geometry : angle 0.63123 / 0.33 (44343) SS BOND : bond 0.02342 / 1.23 ( 1) SS BOND : angle 4.94857 / 3.30 ( 2) hydrogen bonds : bond 0.03683 / 2.80 ( 1892) hydrogen bonds : angle 4.45390 / 3.38 ( 5442) metal coordination : bond 0.00564 / 0.28 ( 4) metal coordination : angle 13.35757 / 7.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 385 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 89 TYR cc_start: 0.4716 (p90) cc_final: 0.4064 (t80) REVERT: 5 349 MET cc_start: 0.1858 (ttp) cc_final: 0.1561 (tmm) REVERT: 5 351 GLN cc_start: 0.1187 (OUTLIER) cc_final: 0.0957 (mm-40) REVERT: 5 355 TYR cc_start: 0.1658 (p90) cc_final: 0.0923 (t80) REVERT: 6 277 MET cc_start: 0.7369 (tpt) cc_final: 0.7014 (tpt) REVERT: 6 280 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8865 (mm) REVERT: 6 362 ASN cc_start: 0.7838 (m-40) cc_final: 0.7132 (p0) REVERT: H 51 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7870 (mm110) REVERT: I 46 THR cc_start: 0.8162 (p) cc_final: 0.7748 (p) REVERT: I 49 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7957 (mt0) REVERT: I 69 ASN cc_start: 0.7264 (p0) cc_final: 0.6630 (p0) REVERT: O 228 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7948 (tt) REVERT: Q 52 ASP cc_start: 0.7893 (t0) cc_final: 0.7689 (t0) REVERT: n 33 GLU cc_start: 0.7445 (pp20) cc_final: 0.7158 (pp20) REVERT: n 54 ASP cc_start: 0.8271 (m-30) cc_final: 0.7865 (p0) REVERT: u 35 MET cc_start: 0.8589 (mmm) cc_final: 0.8220 (mmm) REVERT: u 231 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7771 (tp30) REVERT: u 316 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.6440 (mp10) REVERT: u 532 LYS cc_start: 0.8146 (tptm) cc_final: 0.7776 (mptt) REVERT: u 559 LYS cc_start: 0.7191 (mmtm) cc_final: 0.6854 (mtmm) REVERT: x 55 TYR cc_start: 0.6507 (m-80) cc_final: 0.6159 (m-80) REVERT: y 471 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: y 666 GLU cc_start: 0.8002 (pp20) cc_final: 0.7760 (pt0) REVERT: y 742 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8053 (mptt) REVERT: y 744 MET cc_start: 0.7586 (ptm) cc_final: 0.7117 (ptm) REVERT: y 830 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.5516 (tp30) outliers start: 88 outliers final: 58 residues processed: 441 average time/residue: 0.1907 time to fit residues: 138.2066 Evaluate side-chains 433 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 366 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 351 GLN Chi-restraints excluded: chain 5 residue 550 PHE Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 280 LEU Chi-restraints excluded: chain 6 residue 308 VAL Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain O residue 38 MET Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 14 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain u residue 98 GLU Chi-restraints excluded: chain u residue 130 SER Chi-restraints excluded: chain u residue 205 LEU Chi-restraints excluded: chain u residue 220 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 316 GLN Chi-restraints excluded: chain u residue 340 ARG Chi-restraints excluded: chain u residue 450 ILE Chi-restraints excluded: chain u residue 452 PHE Chi-restraints excluded: chain u residue 507 ILE Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 243 LEU Chi-restraints excluded: chain v residue 249 MET Chi-restraints excluded: chain v residue 293 THR Chi-restraints excluded: chain v residue 299 LEU Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 318 VAL Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain y residue 353 LEU Chi-restraints excluded: chain y residue 354 LEU Chi-restraints excluded: chain y residue 397 MET Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 424 ILE Chi-restraints excluded: chain y residue 440 VAL Chi-restraints excluded: chain y residue 452 ASP Chi-restraints excluded: chain y residue 471 GLU Chi-restraints excluded: chain y residue 547 LEU Chi-restraints excluded: chain y residue 633 LEU Chi-restraints excluded: chain y residue 634 LEU Chi-restraints excluded: chain y residue 742 LYS Chi-restraints excluded: chain y residue 827 ILE Chi-restraints excluded: chain y residue 830 GLU Chi-restraints excluded: chain y residue 835 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 317 optimal weight: 5.9990 chunk 141 optimal weight: 50.0000 chunk 286 optimal weight: 3.9990 chunk 18 optimal weight: 40.0000 chunk 66 optimal weight: 40.0000 chunk 69 optimal weight: 5.9990 chunk 320 optimal weight: 0.9990 chunk 241 optimal weight: 0.0670 chunk 36 optimal weight: 5.9990 chunk 346 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 5 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 124 ASN H 51 GLN ** I 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 819 HIS y 845 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.154719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.128980 restraints weight = 73571.851| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.31 r_work: 0.3666 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 32137 Z= 0.171 Angle : 0.674 19.847 44351 Z= 0.340 Chirality : 0.042 0.337 5300 Planarity : 0.004 0.080 5253 Dihedral : 15.557 174.598 6528 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.84 % Allowed : 20.60 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3878 helix: 1.46 (0.11), residues: 2341 sheet: -0.60 (0.39), residues: 188 loop : -1.65 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 5 545 TYR 0.029 0.002 TYR 5 72 PHE 0.023 0.001 PHE u 398 TRP 0.029 0.002 TRP u 43 HIS 0.009 0.001 HIS P 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (32132) covalent geometry : angle 0.65440 / 0.34 (44343) SS BOND : bond 0.02465 / 1.30 ( 1) SS BOND : angle 5.66834 / 3.78 ( 2) hydrogen bonds : bond 0.03812 / 2.90 ( 1892) hydrogen bonds : angle 4.43521 / 3.37 ( 5442) metal coordination : bond 0.00418 / 0.21 ( 4) metal coordination : angle 13.61674 / 7.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 372 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 89 TYR cc_start: 0.4713 (p90) cc_final: 0.4046 (t80) REVERT: 5 349 MET cc_start: 0.1757 (ttp) cc_final: 0.0689 (tpp) REVERT: 5 351 GLN cc_start: 0.1198 (OUTLIER) cc_final: 0.0947 (mm-40) REVERT: 5 355 TYR cc_start: 0.1672 (p90) cc_final: 0.0933 (t80) REVERT: 6 274 MET cc_start: 0.9058 (tpp) cc_final: 0.8648 (tpt) REVERT: 6 277 MET cc_start: 0.7370 (tpt) cc_final: 0.7123 (tpt) REVERT: 6 280 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8913 (mm) REVERT: 6 285 MET cc_start: 0.7508 (ttm) cc_final: 0.7257 (ttm) REVERT: 6 309 GLU cc_start: 0.7815 (pm20) cc_final: 0.7387 (mp0) REVERT: 6 362 ASN cc_start: 0.7884 (m-40) cc_final: 0.7118 (p0) REVERT: I 46 THR cc_start: 0.8211 (p) cc_final: 0.7771 (p) REVERT: I 49 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: I 69 ASN cc_start: 0.7572 (p0) cc_final: 0.6952 (p0) REVERT: O 171 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7391 (mt) REVERT: O 228 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7996 (tt) REVERT: Q 52 ASP cc_start: 0.7831 (t0) cc_final: 0.7586 (t0) REVERT: n 33 GLU cc_start: 0.7457 (pp20) cc_final: 0.7173 (pp20) REVERT: n 54 ASP cc_start: 0.8312 (m-30) cc_final: 0.7886 (p0) REVERT: u 296 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8399 (mm) REVERT: u 314 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7820 (mm-30) REVERT: u 316 GLN cc_start: 0.6903 (OUTLIER) cc_final: 0.6199 (mp10) REVERT: u 532 LYS cc_start: 0.8177 (tptm) cc_final: 0.7924 (mptt) REVERT: u 559 LYS cc_start: 0.7161 (mmtm) cc_final: 0.6793 (mtmm) REVERT: x 55 TYR cc_start: 0.6473 (m-80) cc_final: 0.6182 (m-80) REVERT: y 471 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7557 (mm-30) REVERT: y 666 GLU cc_start: 0.8027 (pp20) cc_final: 0.7784 (pt0) REVERT: y 830 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5730 (tp30) outliers start: 93 outliers final: 67 residues processed: 436 average time/residue: 0.1747 time to fit residues: 126.7453 Evaluate side-chains 440 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 364 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 351 GLN Chi-restraints excluded: chain 5 residue 385 SER Chi-restraints excluded: chain 5 residue 550 PHE Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 280 LEU Chi-restraints excluded: chain 6 residue 308 VAL Chi-restraints excluded: chain 6 residue 325 ILE Chi-restraints excluded: chain 6 residue 337 SER Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 38 MET Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 171 ILE Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 14 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain u residue 98 GLU Chi-restraints excluded: chain u residue 130 SER Chi-restraints excluded: chain u residue 171 GLU Chi-restraints excluded: chain u residue 205 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 296 LEU Chi-restraints excluded: chain u residue 316 GLN Chi-restraints excluded: chain u residue 324 LEU Chi-restraints excluded: chain u residue 340 ARG Chi-restraints excluded: chain u residue 343 ASP Chi-restraints excluded: chain u residue 443 VAL Chi-restraints excluded: chain u residue 450 ILE Chi-restraints excluded: chain u residue 452 PHE Chi-restraints excluded: chain u residue 480 LEU Chi-restraints excluded: chain u residue 507 ILE Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 233 ILE Chi-restraints excluded: chain v residue 243 LEU Chi-restraints excluded: chain v residue 249 MET Chi-restraints excluded: chain v residue 293 THR Chi-restraints excluded: chain v residue 299 LEU Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 318 VAL Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain y residue 353 LEU Chi-restraints excluded: chain y residue 354 LEU Chi-restraints excluded: chain y residue 397 MET Chi-restraints excluded: chain y residue 406 ASN Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 452 ASP Chi-restraints excluded: chain y residue 471 GLU Chi-restraints excluded: chain y residue 547 LEU Chi-restraints excluded: chain y residue 633 LEU Chi-restraints excluded: chain y residue 634 LEU Chi-restraints excluded: chain y residue 732 SER Chi-restraints excluded: chain y residue 810 MET Chi-restraints excluded: chain y residue 827 ILE Chi-restraints excluded: chain y residue 830 GLU Chi-restraints excluded: chain y residue 835 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 45 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 346 optimal weight: 0.0570 chunk 328 optimal weight: 0.0980 chunk 83 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 380 optimal weight: 0.9990 chunk 256 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 5 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 86 GLN ** 5 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 124 ASN H 51 GLN I 36 GLN ** u 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 481 GLN ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 819 HIS y 845 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.156799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.129256 restraints weight = 75172.208| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.28 r_work: 0.3681 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 32137 Z= 0.139 Angle : 0.659 18.616 44351 Z= 0.333 Chirality : 0.041 0.370 5300 Planarity : 0.004 0.063 5253 Dihedral : 15.503 175.519 6528 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.01 % Allowed : 21.35 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3878 helix: 1.53 (0.11), residues: 2344 sheet: -0.63 (0.38), residues: 192 loop : -1.59 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 5 545 TYR 0.024 0.001 TYR 5 89 PHE 0.018 0.001 PHE u 398 TRP 0.026 0.002 TRP u 393 HIS 0.010 0.001 HIS P 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (32132) covalent geometry : angle 0.64091 / 0.33 (44343) SS BOND : bond 0.02323 / 1.22 ( 1) SS BOND : angle 4.92442 / 3.28 ( 2) hydrogen bonds : bond 0.03635 / 2.76 ( 1892) hydrogen bonds : angle 4.36711 / 3.31 ( 5442) metal coordination : bond 0.00544 / 0.26 ( 4) metal coordination : angle 12.80157 / 7.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 387 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 89 TYR cc_start: 0.4495 (p90) cc_final: 0.4057 (t80) REVERT: 5 349 MET cc_start: 0.1951 (ttp) cc_final: 0.0700 (tpp) REVERT: 5 351 GLN cc_start: 0.1197 (OUTLIER) cc_final: 0.0956 (mm-40) REVERT: 5 355 TYR cc_start: 0.1656 (p90) cc_final: 0.0923 (t80) REVERT: 6 274 MET cc_start: 0.9028 (tpp) cc_final: 0.8615 (tpt) REVERT: 6 277 MET cc_start: 0.7378 (tpt) cc_final: 0.7029 (tpt) REVERT: 6 280 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8838 (mm) REVERT: 6 309 GLU cc_start: 0.7830 (pm20) cc_final: 0.7559 (mp0) REVERT: 6 362 ASN cc_start: 0.7894 (m-40) cc_final: 0.7163 (p0) REVERT: H 13 GLU cc_start: 0.8152 (pp20) cc_final: 0.7787 (tm-30) REVERT: I 46 THR cc_start: 0.8163 (p) cc_final: 0.7778 (p) REVERT: I 49 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: I 69 ASN cc_start: 0.7602 (p0) cc_final: 0.6974 (p0) REVERT: O 155 TYR cc_start: 0.8871 (m-80) cc_final: 0.8128 (m-80) REVERT: O 171 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7487 (mt) REVERT: O 175 GLU cc_start: 0.8059 (pp20) cc_final: 0.7337 (pt0) REVERT: O 228 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7949 (tt) REVERT: Q 46 GLU cc_start: 0.8216 (pm20) cc_final: 0.7330 (mm-30) REVERT: Q 52 ASP cc_start: 0.7919 (t0) cc_final: 0.7661 (t0) REVERT: n 33 GLU cc_start: 0.7507 (pp20) cc_final: 0.7252 (pp20) REVERT: n 54 ASP cc_start: 0.8262 (m-30) cc_final: 0.7901 (p0) REVERT: u 231 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7739 (tp30) REVERT: u 316 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6472 (mp10) REVERT: u 532 LYS cc_start: 0.8163 (tptm) cc_final: 0.7850 (mptt) REVERT: u 559 LYS cc_start: 0.7147 (mmtm) cc_final: 0.6738 (mtmm) REVERT: v 270 ARG cc_start: 0.5926 (mpt180) cc_final: 0.5385 (mmp-170) REVERT: x 55 TYR cc_start: 0.6490 (m-80) cc_final: 0.6153 (m-80) REVERT: y 471 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: y 830 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.5472 (tp30) REVERT: y 846 ARG cc_start: 0.7071 (tpt170) cc_final: 0.6864 (tpt170) outliers start: 73 outliers final: 55 residues processed: 436 average time/residue: 0.1876 time to fit residues: 135.7602 Evaluate side-chains 427 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 364 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 247 TYR Chi-restraints excluded: chain 5 residue 351 GLN Chi-restraints excluded: chain 5 residue 550 PHE Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 280 LEU Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain O residue 38 MET Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 171 ILE Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 14 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain u residue 98 GLU Chi-restraints excluded: chain u residue 130 SER Chi-restraints excluded: chain u residue 171 GLU Chi-restraints excluded: chain u residue 205 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 316 GLN Chi-restraints excluded: chain u residue 340 ARG Chi-restraints excluded: chain u residue 450 ILE Chi-restraints excluded: chain u residue 487 THR Chi-restraints excluded: chain u residue 507 ILE Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 299 LEU Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 318 VAL Chi-restraints excluded: chain v residue 415 SER Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain y residue 353 LEU Chi-restraints excluded: chain y residue 354 LEU Chi-restraints excluded: chain y residue 397 MET Chi-restraints excluded: chain y residue 406 ASN Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 440 VAL Chi-restraints excluded: chain y residue 452 ASP Chi-restraints excluded: chain y residue 471 GLU Chi-restraints excluded: chain y residue 547 LEU Chi-restraints excluded: chain y residue 633 LEU Chi-restraints excluded: chain y residue 634 LEU Chi-restraints excluded: chain y residue 732 SER Chi-restraints excluded: chain y residue 810 MET Chi-restraints excluded: chain y residue 827 ILE Chi-restraints excluded: chain y residue 830 GLU Chi-restraints excluded: chain y residue 835 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 294 optimal weight: 3.9990 chunk 161 optimal weight: 30.0000 chunk 40 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 112 optimal weight: 50.0000 chunk 88 optimal weight: 5.9990 chunk 381 optimal weight: 0.8980 chunk 22 optimal weight: 30.0000 chunk 201 optimal weight: 1.9990 chunk 322 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 5 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 481 GLN ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 377 ASN ** y 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 724 GLN y 819 HIS ** y 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 845 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.156516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.128729 restraints weight = 79348.211| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.52 r_work: 0.3651 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 32137 Z= 0.152 Angle : 0.673 19.047 44351 Z= 0.338 Chirality : 0.041 0.340 5300 Planarity : 0.004 0.064 5253 Dihedral : 15.431 176.265 6528 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.26 % Allowed : 21.68 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3878 helix: 1.54 (0.11), residues: 2351 sheet: -0.74 (0.38), residues: 197 loop : -1.52 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG v 211 TYR 0.025 0.002 TYR x 59 PHE 0.020 0.001 PHE u 398 TRP 0.029 0.002 TRP u 149 HIS 0.011 0.001 HIS 5 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (32132) covalent geometry : angle 0.65479 / 0.34 (44343) SS BOND : bond 0.02408 / 1.27 ( 1) SS BOND : angle 5.26838 / 3.51 ( 2) hydrogen bonds : bond 0.03661 / 2.78 ( 1892) hydrogen bonds : angle 4.34729 / 3.30 ( 5442) metal coordination : bond 0.00490 / 0.24 ( 4) metal coordination : angle 12.88501 / 7.39 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 377 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 89 TYR cc_start: 0.4581 (p90) cc_final: 0.4102 (t80) REVERT: 5 349 MET cc_start: 0.1940 (ttp) cc_final: 0.0699 (tpp) REVERT: 5 351 GLN cc_start: 0.1198 (OUTLIER) cc_final: 0.0965 (mm-40) REVERT: 5 355 TYR cc_start: 0.1649 (p90) cc_final: 0.0917 (t80) REVERT: 6 277 MET cc_start: 0.7475 (tpt) cc_final: 0.7116 (tpt) REVERT: 6 280 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8848 (mm) REVERT: 6 362 ASN cc_start: 0.7952 (m-40) cc_final: 0.7193 (p0) REVERT: H 13 GLU cc_start: 0.8084 (pp20) cc_final: 0.7744 (tm-30) REVERT: I 46 THR cc_start: 0.8178 (p) cc_final: 0.7688 (p) REVERT: I 49 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: I 69 ASN cc_start: 0.7738 (p0) cc_final: 0.7113 (p0) REVERT: O 171 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7425 (mt) REVERT: O 228 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7973 (tt) REVERT: Q 46 GLU cc_start: 0.8184 (pm20) cc_final: 0.7437 (mm-30) REVERT: Q 52 ASP cc_start: 0.7967 (t0) cc_final: 0.7664 (t0) REVERT: n 33 GLU cc_start: 0.7531 (pp20) cc_final: 0.7259 (pp20) REVERT: n 54 ASP cc_start: 0.8299 (m-30) cc_final: 0.7894 (p0) REVERT: u 105 LYS cc_start: 0.6206 (mtpp) cc_final: 0.5603 (mmtt) REVERT: u 296 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8409 (mm) REVERT: u 314 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7643 (mm-30) REVERT: u 316 GLN cc_start: 0.6897 (OUTLIER) cc_final: 0.6414 (mp10) REVERT: u 532 LYS cc_start: 0.8157 (tptm) cc_final: 0.7858 (mptt) REVERT: u 559 LYS cc_start: 0.7137 (mmtm) cc_final: 0.6775 (mtmm) REVERT: v 282 GLN cc_start: 0.7742 (tp40) cc_final: 0.7484 (tt0) REVERT: x 55 TYR cc_start: 0.6538 (m-80) cc_final: 0.6216 (m-80) REVERT: y 471 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7558 (mm-30) REVERT: y 667 ARG cc_start: 0.7160 (tmm-80) cc_final: 0.6827 (ttp-170) REVERT: y 830 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.5883 (tp30) REVERT: y 832 MET cc_start: 0.6103 (tpt) cc_final: 0.5523 (ttm) outliers start: 79 outliers final: 61 residues processed: 430 average time/residue: 0.1890 time to fit residues: 134.4292 Evaluate side-chains 437 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 367 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 247 TYR Chi-restraints excluded: chain 5 residue 351 GLN Chi-restraints excluded: chain 5 residue 550 PHE Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 280 LEU Chi-restraints excluded: chain 6 residue 292 ILE Chi-restraints excluded: chain 6 residue 325 ILE Chi-restraints excluded: chain 6 residue 337 SER Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain O residue 38 MET Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 171 ILE Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 14 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain u residue 98 GLU Chi-restraints excluded: chain u residue 130 SER Chi-restraints excluded: chain u residue 171 GLU Chi-restraints excluded: chain u residue 205 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 296 LEU Chi-restraints excluded: chain u residue 316 GLN Chi-restraints excluded: chain u residue 340 ARG Chi-restraints excluded: chain u residue 343 ASP Chi-restraints excluded: chain u residue 443 VAL Chi-restraints excluded: chain u residue 450 ILE Chi-restraints excluded: chain u residue 487 THR Chi-restraints excluded: chain u residue 507 ILE Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 237 LEU Chi-restraints excluded: chain v residue 293 THR Chi-restraints excluded: chain v residue 299 LEU Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 318 VAL Chi-restraints excluded: chain v residue 415 SER Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain y residue 353 LEU Chi-restraints excluded: chain y residue 354 LEU Chi-restraints excluded: chain y residue 397 MET Chi-restraints excluded: chain y residue 406 ASN Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 440 VAL Chi-restraints excluded: chain y residue 452 ASP Chi-restraints excluded: chain y residue 471 GLU Chi-restraints excluded: chain y residue 547 LEU Chi-restraints excluded: chain y residue 633 LEU Chi-restraints excluded: chain y residue 634 LEU Chi-restraints excluded: chain y residue 732 SER Chi-restraints excluded: chain y residue 810 MET Chi-restraints excluded: chain y residue 827 ILE Chi-restraints excluded: chain y residue 830 GLU Chi-restraints excluded: chain y residue 835 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 27 optimal weight: 40.0000 chunk 260 optimal weight: 3.9990 chunk 382 optimal weight: 0.7980 chunk 216 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 164 optimal weight: 40.0000 chunk 23 optimal weight: 50.0000 chunk 153 optimal weight: 40.0000 chunk 255 optimal weight: 0.1980 chunk 227 optimal weight: 0.7980 chunk 292 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 86 GLN 5 121 GLN ** I 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 845 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.156050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.130904 restraints weight = 70069.658| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.12 r_work: 0.3713 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 32137 Z= 0.133 Angle : 0.658 17.616 44351 Z= 0.333 Chirality : 0.040 0.340 5300 Planarity : 0.004 0.063 5253 Dihedral : 15.387 177.463 6528 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.97 % Allowed : 22.21 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3878 helix: 1.58 (0.11), residues: 2355 sheet: -0.46 (0.40), residues: 184 loop : -1.55 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG u 317 TYR 0.024 0.001 TYR x 59 PHE 0.017 0.001 PHE v 295 TRP 0.026 0.002 TRP u 393 HIS 0.010 0.001 HIS P 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (32132) covalent geometry : angle 0.64234 / 0.33 (44343) SS BOND : bond 0.02291 / 1.21 ( 1) SS BOND : angle 4.67345 / 3.12 ( 2) hydrogen bonds : bond 0.03518 / 2.67 ( 1892) hydrogen bonds : angle 4.30047 / 3.27 ( 5442) metal coordination : bond 0.00558 / 0.27 ( 4) metal coordination : angle 12.08792 / 6.96 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9487.91 seconds wall clock time: 162 minutes 56.16 seconds (9776.16 seconds total)