Starting phenix.real_space_refine on Mon Aug 25 22:07:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rg0_19128/08_2025/8rg0_19128.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rg0_19128/08_2025/8rg0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rg0_19128/08_2025/8rg0_19128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rg0_19128/08_2025/8rg0_19128.map" model { file = "/net/cci-nas-00/data/ceres_data/8rg0_19128/08_2025/8rg0_19128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rg0_19128/08_2025/8rg0_19128.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 7.67, per 1000 atoms: 0.24 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: 2.85 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 4.16 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: 6.38 Time building geometry restraints manager: 3.68 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 -34 " pdb=" N1 C 7 -34 " ideal model delta sigma weight residual 1.480 1.573 -0.093 1.50e-02 4.44e+03 3.83e+01 bond pdb=" C1' C 7 -25 " pdb=" N1 C 7 -25 " ideal model delta sigma weight residual 1.480 1.572 -0.092 1.50e-02 4.44e+03 3.73e+01 ... (remaining 32127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 43895 4.66 - 9.32: 386 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: 4485 0.081 - 0.162: 713 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: 1.240 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: 0.040 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 35.230 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5617 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= 0.303 Angle : 1.190 38.761 44351 Z= 0.625 Chirality : 0.060 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 aren 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 covalent geometry : bond 0.00590 (32132) covalent geometry : angle 1.15741 (44343) SS BOND : bond 0.00536 ( 1) SS BOND : angle 1.46782 ( 2) hydrogen bonds : bond 0.13642 ( 1892) hydrogen bonds : angle 6.31342 ( 5442) metal coordination : bond 0.03680 ( 4) metal coordination : angle 23.94810 ( 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 : 1.130 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: 0.4912 (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: 0.0798 (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 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: 0.6037 (tp) REVERT: O 73 ASP cc_start: 0.6567 (m-30) cc_final: 0.6312 (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: 0.5127 (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: 0.6087 (m-80) REVERT: O 155 TYR cc_start: 0.7014 (m-80) cc_final: 0.6032 (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: 0.5727 (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: 0.5031 (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: 0.2042 time to fit residues: 252.1909 Evaluate side-chains 454 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 5 60 HIS 5 86 GLN 5 124 ASN 6 273 ASN 6 355 ASN H 19 HIS P 38 ASN u 79 GLN u 187 GLN ** u 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 216 HIS v 373 ASN ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 584 GLN y 593 HIS y 662 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.163771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.145107 restraints weight = 72475.027| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.67 r_work: 0.3797 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 32137 Z= 0.162 Angle : 0.704 27.627 44351 Z= 0.351 Chirality : 0.042 0.247 5300 Planarity : 0.005 0.078 5253 Dihedral : 16.084 177.387 6528 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.60 % Allowed : 13.34 % Favored : 84.06 % 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 aren not related in a simple way. whole: 0.40 (0.14), residues: 3878 helix: 1.41 (0.11), residues: 2335 sheet: -1.01 (0.35), residues: 201 loop : -1.60 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 121 TYR 0.022 0.002 TYR 5 89 PHE 0.014 0.002 PHE u 377 TRP 0.034 0.002 TRP u 43 HIS 0.008 0.001 HIS y 676 Details of bonding type rmsd covalent geometry : bond 0.00334 (32132) covalent geometry : angle 0.67286 (44343) SS BOND : bond 0.01932 ( 1) SS BOND : angle 5.51166 ( 2) hydrogen bonds : bond 0.04153 ( 1892) hydrogen bonds : angle 4.86359 ( 5442) metal coordination : bond 0.00820 ( 4) metal coordination : angle 17.41620 ( 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 562 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 499 time to evaluate : 0.954 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: 5 89 TYR cc_start: 0.4675 (p90) cc_final: 0.3724 (t80) REVERT: 5 90 GLU cc_start: 0.3147 (OUTLIER) cc_final: 0.2103 (mm-30) REVERT: 5 135 LEU cc_start: 0.2715 (mt) cc_final: 0.2073 (mt) REVERT: 5 166 TYR cc_start: 0.4320 (t80) cc_final: 0.3856 (t80) REVERT: 5 268 MET cc_start: 0.5691 (mpp) cc_final: 0.5245 (mpp) REVERT: 5 355 TYR cc_start: 0.1949 (p90) cc_final: 0.0972 (t80) REVERT: H 16 LYS cc_start: 0.8903 (tptp) cc_final: 0.8561 (tptm) REVERT: I 53 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8876 (mp) REVERT: N 34 MET cc_start: 0.7273 (mtt) cc_final: 0.6859 (mtp) REVERT: O 103 MET cc_start: 0.8274 (tmm) cc_final: 0.7908 (ttt) REVERT: P 113 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6260 (mm110) REVERT: Q 85 ARG cc_start: 0.7760 (mtm110) cc_final: 0.7518 (mtm110) REVERT: Q 96 THR cc_start: 0.8901 (t) cc_final: 0.8360 (t) REVERT: n 33 GLU cc_start: 0.7625 (pp20) cc_final: 0.7424 (pp20) REVERT: n 35 MET cc_start: 0.7342 (pmm) cc_final: 0.7115 (pmm) REVERT: u 16 ASN cc_start: 0.8360 (m-40) cc_final: 0.8125 (m-40) REVERT: u 29 ASP cc_start: 0.8044 (p0) cc_final: 0.7793 (p0) REVERT: u 315 MET cc_start: 0.8669 (tmm) cc_final: 0.8291 (tmm) REVERT: u 497 LEU cc_start: 0.7548 (tt) cc_final: 0.7311 (mm) REVERT: u 518 GLN cc_start: 0.7493 (tp40) cc_final: 0.7249 (tp40) REVERT: u 532 LYS cc_start: 0.7998 (tptm) cc_final: 0.7625 (mmtm) REVERT: u 535 GLU cc_start: 0.3195 (tt0) cc_final: 0.2543 (tt0) REVERT: u 559 LYS cc_start: 0.6589 (mmtm) cc_final: 0.6194 (ptpp) REVERT: v 275 LYS cc_start: 0.7743 (mttt) cc_final: 0.7517 (mtmt) REVERT: v 325 LEU cc_start: 0.7635 (mm) cc_final: 0.7376 (mt) REVERT: x 53 LYS cc_start: 0.5459 (mmmt) cc_final: 0.5170 (tppp) outliers start: 63 outliers final: 39 residues processed: 535 average time/residue: 0.1819 time to fit residues: 153.9168 Evaluate side-chains 418 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 377 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 90 GLU Chi-restraints excluded: chain 6 residue 249 LEU Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 337 SER Chi-restraints excluded: chain H residue 40 CYS 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 53 ILE Chi-restraints excluded: chain I residue 80 LEU 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 174 ARG Chi-restraints excluded: chain O residue 179 ASN Chi-restraints excluded: chain O residue 210 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 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 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 220 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 480 LEU Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 317 SER Chi-restraints excluded: chain v residue 413 PHE Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain y residue 358 VAL Chi-restraints excluded: chain y residue 451 MET 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: 0.7980 chunk 263 optimal weight: 4.9990 chunk 354 optimal weight: 1.9990 chunk 305 optimal weight: 0.1980 chunk 319 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 165 optimal weight: 30.0000 chunk 238 optimal weight: 4.9990 chunk 15 optimal weight: 40.0000 chunk 73 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 86 GLN ** 5 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 124 ASN 5 312 GLN 5 361 ASN P 38 ASN ** u 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 297 HIS u 442 GLN ** u 522 GLN ** 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 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.161877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.144416 restraints weight = 90210.008| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 2.70 r_work: 0.3821 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 32137 Z= 0.143 Angle : 0.651 21.080 44351 Z= 0.327 Chirality : 0.041 0.242 5300 Planarity : 0.004 0.057 5253 Dihedral : 15.820 179.438 6528 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.39 % Allowed : 15.57 % Favored : 81.05 % 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 aren not related in a simple way. whole: 0.54 (0.14), residues: 3878 helix: 1.51 (0.11), residues: 2343 sheet: -0.92 (0.37), residues: 188 loop : -1.54 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG P 121 TYR 0.026 0.002 TYR u 391 PHE 0.029 0.002 PHE 5 513 TRP 0.030 0.002 TRP v 370 HIS 0.008 0.001 HIS P 43 Details of bonding type rmsd covalent geometry : bond 0.00322 (32132) covalent geometry : angle 0.62802 (44343) SS BOND : bond 0.02086 ( 1) SS BOND : angle 4.97464 ( 2) hydrogen bonds : bond 0.03853 ( 1892) hydrogen bonds : angle 4.55507 ( 5442) metal coordination : bond 0.00544 ( 4) metal coordination : angle 14.43999 ( 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 506 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 424 time to evaluate : 1.129 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: 0.4734 (p90) cc_final: 0.3829 (t80) REVERT: 5 90 GLU cc_start: 0.3131 (OUTLIER) cc_final: 0.2098 (mm-30) REVERT: 5 166 TYR cc_start: 0.4213 (t80) cc_final: 0.3748 (t80) REVERT: 5 304 MET cc_start: 0.1576 (ppp) cc_final: 0.0606 (mtp) REVERT: 5 324 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.6215 (mt) REVERT: 5 349 MET cc_start: 0.3572 (tmm) cc_final: 0.2111 (tpp) REVERT: 5 350 PHE cc_start: 0.1171 (m-10) cc_final: 0.0627 (m-80) REVERT: 5 355 TYR cc_start: 0.1916 (p90) cc_final: 0.0973 (t80) REVERT: 5 497 MET cc_start: 0.5243 (tpp) cc_final: 0.4857 (ttm) REVERT: 6 271 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7658 (mp0) REVERT: 6 306 ASP cc_start: 0.7985 (p0) cc_final: 0.7699 (p0) REVERT: 6 307 ASP cc_start: 0.7641 (t0) cc_final: 0.7438 (t0) REVERT: H 16 LYS cc_start: 0.8894 (tptp) cc_final: 0.8630 (tptm) REVERT: N 30 LEU cc_start: 0.8864 (tp) cc_final: 0.8661 (tp) REVERT: O 32 ASP cc_start: 0.7060 (p0) cc_final: 0.6804 (p0) REVERT: O 103 MET cc_start: 0.8280 (tmm) cc_final: 0.7783 (ttt) REVERT: O 228 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8091 (tt) REVERT: u 231 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7719 (tm-30) REVERT: u 316 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.6212 (mp10) REVERT: u 532 LYS cc_start: 0.8205 (tptm) cc_final: 0.7915 (mmtm) REVERT: u 535 GLU cc_start: 0.3129 (tt0) cc_final: 0.2779 (tt0) REVERT: u 559 LYS cc_start: 0.6745 (mmtm) cc_final: 0.6461 (ptpp) REVERT: v 282 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: y 392 TYR cc_start: 0.8429 (p90) cc_final: 0.7950 (p90) outliers start: 82 outliers final: 48 residues processed: 474 average time/residue: 0.1904 time to fit residues: 146.8353 Evaluate side-chains 431 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 378 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 324 LEU 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 269 LEU Chi-restraints excluded: chain 6 residue 339 HIS 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 37 ILE Chi-restraints excluded: chain I residue 92 ILE 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 174 ARG 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 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 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 435 THR 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 233 ILE Chi-restraints excluded: chain v residue 282 GLN 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 350 GLN 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 451 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 353 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 344 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 106 optimal weight: 50.0000 chunk 100 optimal weight: 50.0000 chunk 288 optimal weight: 0.9990 chunk 0 optimal weight: 60.0000 chunk 174 optimal weight: 4.9990 chunk 146 optimal weight: 50.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 86 GLN 5 124 ASN 6 336 HIS ** I 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 ASN ** u 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 522 GLN ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 239 GLN ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 406 ASN y 819 HIS ** y 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 845 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.155285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.129118 restraints weight = 74607.806| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.38 r_work: 0.3686 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 32137 Z= 0.222 Angle : 0.698 21.768 44351 Z= 0.355 Chirality : 0.042 0.196 5300 Planarity : 0.005 0.085 5253 Dihedral : 15.731 178.594 6528 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.46 % Allowed : 16.80 % Favored : 78.74 % 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 aren not related in a simple way. whole: 0.44 (0.14), residues: 3878 helix: 1.45 (0.11), residues: 2335 sheet: -0.87 (0.38), residues: 193 loop : -1.63 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG y 439 TYR 0.031 0.002 TYR N 37 PHE 0.025 0.002 PHE 5 542 TRP 0.030 0.002 TRP u 43 HIS 0.034 0.002 HIS v 390 Details of bonding type rmsd covalent geometry : bond 0.00509 (32132) covalent geometry : angle 0.67350 (44343) SS BOND : bond 0.02667 ( 1) SS BOND : angle 6.84659 ( 2) hydrogen bonds : bond 0.04075 ( 1892) hydrogen bonds : angle 4.53671 ( 5442) metal coordination : bond 0.00357 ( 4) metal coordination : angle 15.14139 ( 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 513 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 405 time to evaluate : 1.110 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: 0.4788 (p90) cc_final: 0.3997 (t80) REVERT: 5 90 GLU cc_start: 0.2986 (OUTLIER) cc_final: 0.2110 (mm-30) REVERT: 5 304 MET cc_start: 0.1464 (ppp) cc_final: 0.0918 (ppp) REVERT: 5 349 MET cc_start: 0.3209 (tmm) cc_final: 0.1246 (tpp) REVERT: 5 355 TYR cc_start: 0.1725 (p90) cc_final: 0.0777 (t80) REVERT: 5 497 MET cc_start: 0.5359 (tpp) cc_final: 0.4820 (ttm) REVERT: 6 271 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7613 (mp0) REVERT: 6 277 MET cc_start: 0.7474 (tpt) cc_final: 0.7012 (tpt) REVERT: 6 280 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8789 (mm) REVERT: 6 306 ASP cc_start: 0.7961 (p0) cc_final: 0.7455 (p0) REVERT: H 16 LYS cc_start: 0.8946 (tptp) cc_final: 0.8601 (tptm) REVERT: I 49 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8108 (mt0) REVERT: I 69 ASN cc_start: 0.7216 (p0) cc_final: 0.6627 (p0) REVERT: O 103 MET cc_start: 0.8165 (tmm) cc_final: 0.7801 (ttt) REVERT: O 171 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7132 (mt) REVERT: P 113 GLN cc_start: 0.7821 (mm-40) cc_final: 0.6487 (mm110) REVERT: u 231 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7754 (tm-30) REVERT: u 316 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.6037 (mp10) REVERT: u 340 ARG cc_start: 0.7209 (mtt90) cc_final: 0.6958 (mtt90) REVERT: u 532 LYS cc_start: 0.8069 (tptm) cc_final: 0.7736 (mptt) REVERT: v 275 LYS cc_start: 0.7493 (mttt) cc_final: 0.6948 (mtpt) REVERT: v 282 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7490 (tt0) REVERT: x 55 TYR cc_start: 0.6534 (m-80) cc_final: 0.6238 (m-80) REVERT: y 392 TYR cc_start: 0.8592 (p90) cc_final: 0.8093 (p90) REVERT: y 471 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: y 667 ARG cc_start: 0.6968 (tmm160) cc_final: 0.6288 (tmm160) outliers start: 108 outliers final: 73 residues processed: 475 average time/residue: 0.1985 time to fit residues: 153.4244 Evaluate side-chains 444 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 364 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 5 residue 550 PHE Chi-restraints excluded: chain 6 residue 261 ASP Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 269 LEU Chi-restraints excluded: chain 6 residue 280 LEU 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 H residue 44 THR Chi-restraints excluded: chain H residue 45 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 40 LEU Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 102 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 88 THR 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 174 ARG 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 116 LEU Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 135 ILE 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 15 THR Chi-restraints excluded: chain n residue 32 VAL 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 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 357 THR 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 550 HIS Chi-restraints excluded: chain v residue 233 ILE Chi-restraints excluded: chain v residue 249 MET Chi-restraints excluded: chain v residue 261 VAL 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 317 SER 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 354 LEU Chi-restraints excluded: chain y residue 406 ASN 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 473 LEU 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: 8.9990 chunk 138 optimal weight: 40.0000 chunk 338 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 39 optimal weight: 30.0000 chunk 150 optimal weight: 40.0000 chunk 199 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 350 optimal weight: 0.3980 chunk 149 optimal weight: 6.9990 chunk 396 optimal weight: 4.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 86 GLN ** 5 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 124 ASN H 51 GLN I 90 HIS O 95 ASN O 124 HIS ** 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 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 512 GLN u 521 ASN u 522 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** v 373 ASN v 421 ASN y 631 ASN y 837 GLN y 845 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.150697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.132235 restraints weight = 84531.140| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.59 r_work: 0.3577 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 32137 Z= 0.309 Angle : 0.790 24.194 44351 Z= 0.401 Chirality : 0.046 0.223 5300 Planarity : 0.005 0.069 5253 Dihedral : 15.835 175.015 6528 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.12 % Allowed : 19.08 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.04 (0.14), residues: 3878 helix: 1.08 (0.11), residues: 2336 sheet: -1.05 (0.36), residues: 218 loop : -1.68 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG y 668 TYR 0.034 0.003 TYR x 69 PHE 0.023 0.002 PHE u 398 TRP 0.038 0.003 TRP u 43 HIS 0.013 0.002 HIS y 572 Details of bonding type rmsd covalent geometry : bond 0.00707 (32132) covalent geometry : angle 0.76336 (44343) SS BOND : bond 0.02962 ( 1) SS BOND : angle 7.47834 ( 2) hydrogen bonds : bond 0.04602 ( 1892) hydrogen bonds : angle 4.76907 ( 5442) metal coordination : bond 0.00735 ( 4) metal coordination : angle 16.94846 ( 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 532 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 408 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 89 TYR cc_start: 0.4619 (p90) cc_final: 0.3827 (t80) REVERT: 5 349 MET cc_start: 0.2986 (tmm) cc_final: 0.2007 (ttp) REVERT: 5 350 PHE cc_start: 0.0985 (m-10) cc_final: 0.0367 (m-80) REVERT: 5 351 GLN cc_start: 0.1337 (OUTLIER) cc_final: 0.1017 (mm-40) REVERT: 5 355 TYR cc_start: 0.1886 (p90) cc_final: 0.0795 (t80) REVERT: 5 497 MET cc_start: 0.5668 (tpp) cc_final: 0.5090 (ttm) REVERT: 6 273 ASN cc_start: 0.8987 (t0) cc_final: 0.8724 (t0) REVERT: 6 280 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8931 (mm) REVERT: 6 306 ASP cc_start: 0.8125 (p0) cc_final: 0.7722 (p0) REVERT: I 49 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8443 (mt0) REVERT: M 127 ASN cc_start: 0.8096 (p0) cc_final: 0.7775 (p0) REVERT: N 32 PHE cc_start: 0.7431 (p90) cc_final: 0.7212 (p90) REVERT: N 35 GLU cc_start: 0.8338 (pt0) cc_final: 0.8015 (pt0) REVERT: O 171 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7834 (mt) REVERT: O 228 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8091 (tt) REVERT: Q 52 ASP cc_start: 0.8046 (t0) cc_final: 0.7788 (t0) REVERT: u 105 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.5847 (mmtt) REVERT: u 296 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8739 (mm) REVERT: u 316 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6102 (mp10) REVERT: u 340 ARG cc_start: 0.7588 (mtt90) cc_final: 0.7323 (mtt90) REVERT: u 404 CYS cc_start: 0.7859 (t) cc_final: 0.7642 (t) REVERT: u 415 ARG cc_start: 0.8428 (mtm110) cc_final: 0.7905 (mtm110) REVERT: u 485 ASP cc_start: 0.7607 (t0) cc_final: 0.7346 (t0) REVERT: u 514 MET cc_start: 0.9132 (pmm) cc_final: 0.8570 (ptp) REVERT: u 519 ILE cc_start: 0.8633 (mm) cc_final: 0.8401 (mt) REVERT: u 532 LYS cc_start: 0.8319 (tptm) cc_final: 0.8095 (mptt) REVERT: u 559 LYS cc_start: 0.7150 (mmtm) cc_final: 0.6840 (mtmm) REVERT: v 275 LYS cc_start: 0.7820 (mttt) cc_final: 0.7558 (mttp) REVERT: x 55 TYR cc_start: 0.6857 (m-80) cc_final: 0.6515 (m-80) REVERT: x 82 LEU cc_start: 0.7438 (tp) cc_final: 0.7086 (tp) REVERT: y 471 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: y 666 GLU cc_start: 0.8305 (pp20) cc_final: 0.7967 (pt0) outliers start: 124 outliers final: 83 residues processed: 483 average time/residue: 0.2034 time to fit residues: 159.8547 Evaluate side-chains 456 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 364 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 351 GLN 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 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 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 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 40 LEU Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 72 LEU 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 88 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 147 ASN Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 171 ILE Chi-restraints excluded: chain O residue 174 ARG 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 40 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 135 ILE 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 15 THR Chi-restraints excluded: chain n residue 32 VAL Chi-restraints excluded: chain n residue 42 ILE 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 105 LYS 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 320 THR Chi-restraints excluded: chain u residue 324 LEU Chi-restraints excluded: chain u residue 357 THR Chi-restraints excluded: chain u residue 435 THR 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 237 LEU Chi-restraints excluded: chain v residue 243 LEU Chi-restraints excluded: chain v residue 249 MET Chi-restraints excluded: chain v residue 261 VAL 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 317 SER Chi-restraints excluded: chain v residue 318 VAL Chi-restraints excluded: chain v residue 384 ILE 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 412 LEU Chi-restraints excluded: chain y residue 424 ILE Chi-restraints excluded: chain y residue 452 ASP Chi-restraints excluded: chain y residue 471 GLU Chi-restraints excluded: chain y residue 473 LEU Chi-restraints excluded: chain y residue 547 LEU Chi-restraints excluded: chain y residue 633 LEU Chi-restraints excluded: chain y residue 732 SER Chi-restraints excluded: chain y residue 802 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 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: 20.0000 chunk 140 optimal weight: 50.0000 chunk 351 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 321 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 245 optimal weight: 0.0070 chunk 329 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 190 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** u 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 209 GLN ** u 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 226 GLN ** u 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 481 GLN u 521 ASN ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 225 HIS ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 377 ASN ** 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 = 0.4404 r_free = 0.4404 target = 0.155535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.126969 restraints weight = 74375.899| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.30 r_work: 0.3648 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.182 32137 Z= 0.155 Angle : 0.666 20.131 44351 Z= 0.338 Chirality : 0.041 0.431 5300 Planarity : 0.004 0.066 5253 Dihedral : 15.671 178.000 6528 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.00 % Allowed : 21.39 % Favored : 74.61 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: 0.42 (0.14), residues: 3878 helix: 1.43 (0.11), residues: 2337 sheet: -0.73 (0.38), residues: 199 loop : -1.65 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 5 545 TYR 0.024 0.002 TYR 5 89 PHE 0.015 0.001 PHE 6 311 TRP 0.025 0.002 TRP u 393 HIS 0.008 0.001 HIS P 43 Details of bonding type rmsd covalent geometry : bond 0.00359 (32132) covalent geometry : angle 0.64185 (44343) SS BOND : bond 0.03770 ( 1) SS BOND : angle 11.24082 ( 2) hydrogen bonds : bond 0.03712 ( 1892) hydrogen bonds : angle 4.47703 ( 5442) metal coordination : bond 0.00449 ( 4) metal coordination : angle 13.92447 ( 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 512 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 415 time to evaluate : 1.216 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: 0.4824 (p90) cc_final: 0.4115 (t80) REVERT: 5 268 MET cc_start: 0.5502 (mpp) cc_final: 0.5113 (mpp) REVERT: 5 349 MET cc_start: 0.2883 (tmm) cc_final: 0.2010 (ttp) REVERT: 5 350 PHE cc_start: 0.1176 (m-10) cc_final: 0.0551 (m-80) REVERT: 5 355 TYR cc_start: 0.1728 (p90) cc_final: 0.0914 (t80) REVERT: 5 497 MET cc_start: 0.5845 (tpp) cc_final: 0.5243 (ttm) REVERT: 6 273 ASN cc_start: 0.9024 (t0) cc_final: 0.8800 (t0) REVERT: 6 280 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8672 (mm) REVERT: 6 306 ASP cc_start: 0.8030 (p0) cc_final: 0.7801 (p0) REVERT: 6 309 GLU cc_start: 0.7902 (pm20) cc_final: 0.7552 (mp0) REVERT: 6 362 ASN cc_start: 0.8060 (m-40) cc_final: 0.7384 (p0) REVERT: I 69 ASN cc_start: 0.7447 (p0) cc_final: 0.6822 (p0) REVERT: M 127 ASN cc_start: 0.7743 (p0) cc_final: 0.7368 (p0) REVERT: O 175 GLU cc_start: 0.8106 (pp20) cc_final: 0.7300 (pt0) REVERT: O 228 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7880 (tt) REVERT: Q 52 ASP cc_start: 0.8007 (t0) cc_final: 0.7772 (t0) REVERT: u 231 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7671 (tm-30) REVERT: u 260 PHE cc_start: 0.8329 (m-10) cc_final: 0.7892 (m-10) REVERT: u 316 GLN cc_start: 0.6643 (OUTLIER) cc_final: 0.5798 (mp10) REVERT: u 404 CYS cc_start: 0.7794 (t) cc_final: 0.7586 (t) REVERT: u 485 ASP cc_start: 0.7349 (t0) cc_final: 0.7044 (t70) REVERT: u 532 LYS cc_start: 0.8204 (tptm) cc_final: 0.7843 (mptt) REVERT: u 559 LYS cc_start: 0.7174 (mmtm) cc_final: 0.6781 (mtmm) REVERT: v 282 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7532 (tp40) REVERT: x 55 TYR cc_start: 0.6484 (m-80) cc_final: 0.6113 (m-80) REVERT: x 82 LEU cc_start: 0.6651 (tp) cc_final: 0.6301 (tp) REVERT: y 468 GLU cc_start: 0.7834 (tt0) cc_final: 0.7613 (tt0) REVERT: y 471 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7325 (mm-30) REVERT: y 644 GLU cc_start: 0.7976 (pm20) cc_final: 0.7656 (mm-30) REVERT: y 666 GLU cc_start: 0.8232 (pp20) cc_final: 0.7933 (pt0) REVERT: y 830 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.5303 (tp30) outliers start: 97 outliers final: 64 residues processed: 477 average time/residue: 0.2056 time to fit residues: 158.8628 Evaluate side-chains 443 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 373 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 94 ILE 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 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 78 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 42 LYS Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 174 ARG 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 129 ILE Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 100 ARG 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 324 LEU Chi-restraints excluded: chain u residue 486 HIS Chi-restraints excluded: chain u residue 507 ILE Chi-restraints excluded: chain u residue 530 LEU Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 237 LEU Chi-restraints excluded: chain v residue 249 MET Chi-restraints excluded: chain v residue 261 VAL Chi-restraints excluded: chain v residue 282 GLN Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 318 VAL Chi-restraints excluded: chain v residue 384 ILE Chi-restraints excluded: chain v residue 415 SER Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain x residue 27 ASP Chi-restraints excluded: chain y residue 353 LEU Chi-restraints excluded: chain y residue 354 LEU Chi-restraints excluded: chain y residue 366 LEU Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 424 ILE Chi-restraints excluded: chain y residue 452 ASP Chi-restraints excluded: chain y residue 471 GLU Chi-restraints excluded: chain y residue 576 HIS Chi-restraints excluded: chain y residue 633 LEU Chi-restraints excluded: chain y residue 732 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 388 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 138 optimal weight: 40.0000 chunk 183 optimal weight: 0.7980 chunk 390 optimal weight: 0.9990 chunk 369 optimal weight: 0.0000 chunk 151 optimal weight: 9.9990 chunk 318 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 392 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 86 GLN 5 121 GLN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 47 HIS u 209 GLN ** u 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 241 GLN ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 715 HIS y 724 GLN y 845 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.155530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.129773 restraints weight = 77719.283| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.47 r_work: 0.3716 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.159 32137 Z= 0.133 Angle : 0.648 17.896 44351 Z= 0.326 Chirality : 0.040 0.489 5300 Planarity : 0.004 0.065 5253 Dihedral : 15.504 179.769 6528 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.47 % Allowed : 22.83 % Favored : 73.70 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: 0.64 (0.14), residues: 3878 helix: 1.58 (0.11), residues: 2356 sheet: -0.47 (0.39), residues: 190 loop : -1.60 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG u 7 TYR 0.025 0.001 TYR 5 89 PHE 0.027 0.001 PHE P 41 TRP 0.026 0.002 TRP u 149 HIS 0.009 0.001 HIS P 43 Details of bonding type rmsd covalent geometry : bond 0.00302 (32132) covalent geometry : angle 0.62762 (44343) SS BOND : bond 0.06085 ( 1) SS BOND : angle 10.44714 ( 2) hydrogen bonds : bond 0.03460 ( 1892) hydrogen bonds : angle 4.36585 ( 5442) metal coordination : bond 0.00450 ( 4) metal coordination : angle 12.57145 ( 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 482 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 398 time to evaluate : 1.239 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: 0.4675 (p90) cc_final: 0.3996 (t80) REVERT: 5 268 MET cc_start: 0.5500 (mpp) cc_final: 0.5140 (mpp) REVERT: 5 349 MET cc_start: 0.3063 (tmm) cc_final: 0.2270 (ttp) REVERT: 5 350 PHE cc_start: 0.1156 (m-10) cc_final: 0.0553 (m-80) REVERT: 5 351 GLN cc_start: 0.1257 (OUTLIER) cc_final: 0.1024 (mm-40) REVERT: 5 355 TYR cc_start: 0.1711 (p90) cc_final: 0.0909 (t80) REVERT: 5 497 MET cc_start: 0.5896 (tpp) cc_final: 0.5436 (mtp) REVERT: 6 274 MET cc_start: 0.9092 (tpp) cc_final: 0.8884 (tpt) REVERT: 6 280 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8550 (mm) REVERT: 6 306 ASP cc_start: 0.7989 (p0) cc_final: 0.7774 (p0) REVERT: 6 309 GLU cc_start: 0.8002 (pm20) cc_final: 0.7644 (mp0) REVERT: 6 362 ASN cc_start: 0.8028 (m-40) cc_final: 0.7364 (p0) REVERT: O 110 MET cc_start: 0.7684 (mmm) cc_final: 0.7362 (mtt) REVERT: O 228 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7825 (tt) REVERT: Q 52 ASP cc_start: 0.7975 (t0) cc_final: 0.7706 (t0) REVERT: n 33 GLU cc_start: 0.7407 (pp20) cc_final: 0.7165 (pp20) REVERT: u 260 PHE cc_start: 0.8276 (m-10) cc_final: 0.7835 (m-10) REVERT: u 316 GLN cc_start: 0.6397 (OUTLIER) cc_final: 0.6061 (mp10) REVERT: u 485 ASP cc_start: 0.7264 (t0) cc_final: 0.6995 (t70) REVERT: u 532 LYS cc_start: 0.8175 (tptm) cc_final: 0.7918 (mptt) REVERT: u 559 LYS cc_start: 0.7105 (mmtm) cc_final: 0.6708 (mtmm) REVERT: v 282 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7544 (tp40) REVERT: v 292 ILE cc_start: 0.7778 (mt) cc_final: 0.7552 (mt) REVERT: v 362 MET cc_start: 0.6514 (ppp) cc_final: 0.5028 (ptt) REVERT: y 468 GLU cc_start: 0.7697 (tt0) cc_final: 0.7480 (tt0) REVERT: y 471 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7465 (mm-30) REVERT: y 646 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9099 (mp) REVERT: y 666 GLU cc_start: 0.8238 (pp20) cc_final: 0.7976 (pt0) outliers start: 84 outliers final: 59 residues processed: 454 average time/residue: 0.2011 time to fit residues: 148.7998 Evaluate side-chains 439 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 373 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 94 ILE Chi-restraints excluded: chain 5 residue 255 SER 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 269 LEU Chi-restraints excluded: chain 6 residue 280 LEU Chi-restraints excluded: chain H residue 25 VAL 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 71 ILE Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 42 LYS 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 129 ILE Chi-restraints excluded: chain P residue 135 ILE 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 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 443 VAL Chi-restraints excluded: chain u residue 486 HIS Chi-restraints excluded: chain u residue 507 ILE Chi-restraints excluded: chain u residue 530 LEU Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 237 LEU Chi-restraints excluded: chain v residue 261 VAL Chi-restraints excluded: chain v residue 282 GLN 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 27 ASP Chi-restraints excluded: chain y residue 353 LEU Chi-restraints excluded: chain y residue 354 LEU Chi-restraints excluded: chain y residue 366 LEU 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 591 MET Chi-restraints excluded: chain y residue 633 LEU Chi-restraints excluded: chain y residue 646 LEU Chi-restraints excluded: chain y residue 732 SER Chi-restraints excluded: chain y residue 827 ILE 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: 7.9990 chunk 141 optimal weight: 50.0000 chunk 286 optimal weight: 0.5980 chunk 18 optimal weight: 50.0000 chunk 66 optimal weight: 40.0000 chunk 69 optimal weight: 20.0000 chunk 320 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 346 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 101 HIS ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 82 ASN u 209 GLN ** u 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 226 GLN u 442 GLN ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 241 GLN ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 758 ASN y 819 HIS y 845 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.152824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.133654 restraints weight = 72981.300| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.36 r_work: 0.3640 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 32137 Z= 0.202 Angle : 0.690 20.100 44351 Z= 0.349 Chirality : 0.042 0.426 5300 Planarity : 0.004 0.067 5253 Dihedral : 15.479 179.693 6528 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.92 % Allowed : 23.00 % Favored : 73.08 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: 0.51 (0.14), residues: 3878 helix: 1.47 (0.11), residues: 2363 sheet: -0.50 (0.37), residues: 198 loop : -1.66 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG y 563 TYR 0.024 0.002 TYR 5 89 PHE 0.020 0.002 PHE P 41 TRP 0.031 0.002 TRP u 43 HIS 0.008 0.001 HIS P 43 Details of bonding type rmsd covalent geometry : bond 0.00465 (32132) covalent geometry : angle 0.66844 (44343) SS BOND : bond 0.05359 ( 1) SS BOND : angle 9.37959 ( 2) hydrogen bonds : bond 0.03781 ( 1892) hydrogen bonds : angle 4.39069 ( 5442) metal coordination : bond 0.00386 ( 4) metal coordination : angle 13.85252 ( 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 470 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 375 time to evaluate : 1.222 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: 0.4401 (p90) cc_final: 0.3929 (t80) REVERT: 5 268 MET cc_start: 0.5692 (mpp) cc_final: 0.5351 (mpp) REVERT: 5 349 MET cc_start: 0.3121 (tmm) cc_final: 0.2387 (ttp) REVERT: 5 351 GLN cc_start: 0.1346 (OUTLIER) cc_final: 0.1132 (mm-40) REVERT: 5 355 TYR cc_start: 0.1769 (p90) cc_final: 0.0911 (t80) REVERT: 6 280 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8698 (mm) REVERT: 6 306 ASP cc_start: 0.7916 (p0) cc_final: 0.7704 (p0) REVERT: 6 309 GLU cc_start: 0.8081 (pm20) cc_final: 0.7704 (mp0) REVERT: O 110 MET cc_start: 0.7852 (mmm) cc_final: 0.7557 (mtt) REVERT: O 171 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7730 (mt) REVERT: O 188 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8559 (mt) REVERT: O 228 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7994 (tt) REVERT: Q 46 GLU cc_start: 0.8081 (pm20) cc_final: 0.7600 (mm-30) REVERT: Q 52 ASP cc_start: 0.7999 (t0) cc_final: 0.7723 (t0) REVERT: n 33 GLU cc_start: 0.7440 (pp20) cc_final: 0.7160 (pp20) REVERT: n 63 ARG cc_start: 0.4772 (ttp-170) cc_final: 0.4556 (ttm110) REVERT: u 105 LYS cc_start: 0.6205 (mtpp) cc_final: 0.5471 (mmtm) REVERT: u 231 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7742 (tm-30) REVERT: u 316 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.6030 (mp10) REVERT: u 485 ASP cc_start: 0.7411 (t0) cc_final: 0.7153 (t70) REVERT: u 514 MET cc_start: 0.9006 (pmm) cc_final: 0.8334 (ptp) REVERT: u 559 LYS cc_start: 0.7157 (mmtm) cc_final: 0.6831 (mtmm) REVERT: v 282 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7580 (tp40) REVERT: x 55 TYR cc_start: 0.6657 (m-80) cc_final: 0.6189 (m-80) REVERT: x 82 LEU cc_start: 0.6673 (tp) cc_final: 0.6435 (tp) REVERT: y 454 GLU cc_start: 0.8070 (tp30) cc_final: 0.7848 (tt0) REVERT: y 468 GLU cc_start: 0.7776 (tt0) cc_final: 0.7571 (tt0) REVERT: y 471 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: y 666 GLU cc_start: 0.8265 (pp20) cc_final: 0.8009 (pt0) REVERT: y 830 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.5519 (tp30) outliers start: 95 outliers final: 74 residues processed: 437 average time/residue: 0.1983 time to fit residues: 141.4989 Evaluate side-chains 444 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 361 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 94 ILE Chi-restraints excluded: chain 5 residue 255 SER 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 325 ILE Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain H residue 25 VAL 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 40 LEU Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 42 LYS Chi-restraints excluded: chain O residue 147 ASN Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 171 ILE Chi-restraints excluded: chain O residue 188 LEU 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 P residue 129 ILE Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 100 ARG 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 17 VAL Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain n residue 46 VAL 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 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 343 ASP Chi-restraints excluded: chain u residue 443 VAL Chi-restraints excluded: chain u residue 480 LEU Chi-restraints excluded: chain u residue 486 HIS Chi-restraints excluded: chain u residue 507 ILE Chi-restraints excluded: chain u residue 530 LEU Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 233 ILE Chi-restraints excluded: chain v residue 237 LEU Chi-restraints excluded: chain v residue 249 MET Chi-restraints excluded: chain v residue 261 VAL 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 384 ILE Chi-restraints excluded: chain v residue 415 SER Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain x residue 81 GLN Chi-restraints excluded: chain y residue 353 LEU Chi-restraints excluded: chain y residue 354 LEU Chi-restraints excluded: chain y residue 366 LEU Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 424 ILE 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 566 THR Chi-restraints excluded: chain y residue 576 HIS Chi-restraints excluded: chain y residue 591 MET Chi-restraints excluded: chain y residue 633 LEU Chi-restraints excluded: chain y residue 634 LEU Chi-restraints excluded: chain y residue 827 ILE Chi-restraints excluded: chain y residue 830 GLU Chi-restraints excluded: chain y residue 835 LEU Chi-restraints excluded: chain y residue 845 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 45 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 346 optimal weight: 2.9990 chunk 328 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 239 optimal weight: 4.9990 chunk 380 optimal weight: 4.9990 chunk 256 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 86 GLN H 51 GLN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 209 GLN u 212 HIS u 247 GLN u 521 ASN ** v 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 359 GLN ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.151719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.125933 restraints weight = 73947.638| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.56 r_work: 0.3611 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.176 32137 Z= 0.224 Angle : 0.737 27.170 44351 Z= 0.371 Chirality : 0.043 0.435 5300 Planarity : 0.005 0.068 5253 Dihedral : 15.520 178.738 6528 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.76 % Allowed : 23.29 % Favored : 72.96 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: 0.40 (0.14), residues: 3878 helix: 1.39 (0.11), residues: 2368 sheet: -0.59 (0.37), residues: 204 loop : -1.72 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG y 846 TYR 0.031 0.002 TYR v 286 PHE 0.022 0.002 PHE v 295 TRP 0.033 0.002 TRP u 43 HIS 0.023 0.002 HIS y 845 Details of bonding type rmsd covalent geometry : bond 0.00518 (32132) covalent geometry : angle 0.71433 (44343) SS BOND : bond 0.05902 ( 1) SS BOND : angle 10.57895 ( 2) hydrogen bonds : bond 0.03916 ( 1892) hydrogen bonds : angle 4.49015 ( 5442) metal coordination : bond 0.00376 ( 4) metal coordination : angle 14.41364 ( 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 470 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 379 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 268 MET cc_start: 0.5339 (mpp) cc_final: 0.5031 (mpp) REVERT: 5 349 MET cc_start: 0.3081 (tmm) cc_final: 0.2531 (ttt) REVERT: 5 351 GLN cc_start: 0.1391 (OUTLIER) cc_final: 0.1151 (mm-40) REVERT: 5 355 TYR cc_start: 0.1785 (p90) cc_final: 0.0901 (t80) REVERT: 5 497 MET cc_start: 0.5749 (tpp) cc_final: 0.5099 (ttm) REVERT: 6 280 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8732 (mm) REVERT: 6 306 ASP cc_start: 0.7921 (p0) cc_final: 0.7691 (p0) REVERT: 6 309 GLU cc_start: 0.8056 (pm20) cc_final: 0.7789 (mp0) REVERT: 6 362 ASN cc_start: 0.7992 (m-40) cc_final: 0.7374 (p0) REVERT: N 32 PHE cc_start: 0.7481 (p90) cc_final: 0.7126 (p90) REVERT: O 171 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7880 (mt) REVERT: O 188 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8582 (mt) REVERT: O 228 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8008 (tt) REVERT: Q 46 GLU cc_start: 0.8104 (pm20) cc_final: 0.7524 (mm-30) REVERT: Q 52 ASP cc_start: 0.8129 (t0) cc_final: 0.7836 (t0) REVERT: n 33 GLU cc_start: 0.7412 (pp20) cc_final: 0.7155 (pp20) REVERT: u 105 LYS cc_start: 0.6283 (mtpp) cc_final: 0.5518 (mmtm) REVERT: u 231 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7610 (tm-30) REVERT: u 485 ASP cc_start: 0.7384 (t0) cc_final: 0.7134 (t70) REVERT: u 514 MET cc_start: 0.9036 (pmm) cc_final: 0.8636 (ptp) REVERT: u 559 LYS cc_start: 0.7308 (mmtm) cc_final: 0.6919 (mtmm) REVERT: v 362 MET cc_start: 0.6424 (ppp) cc_final: 0.5182 (ptt) REVERT: x 55 TYR cc_start: 0.6663 (m-80) cc_final: 0.6314 (m-80) REVERT: x 82 LEU cc_start: 0.6681 (tp) cc_final: 0.6463 (tp) REVERT: y 454 GLU cc_start: 0.8109 (tp30) cc_final: 0.7882 (tt0) REVERT: y 468 GLU cc_start: 0.7920 (tt0) cc_final: 0.7719 (tt0) REVERT: y 471 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: y 567 CYS cc_start: 0.5924 (m) cc_final: 0.5521 (m) REVERT: y 666 GLU cc_start: 0.8296 (pp20) cc_final: 0.8032 (pt0) REVERT: y 830 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.5817 (tp30) outliers start: 91 outliers final: 73 residues processed: 437 average time/residue: 0.2040 time to fit residues: 145.3985 Evaluate side-chains 443 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 363 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 94 ILE Chi-restraints excluded: chain 5 residue 255 SER 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 325 ILE Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain H residue 25 VAL 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 33 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 42 LYS Chi-restraints excluded: chain O residue 147 ASN Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 171 ILE Chi-restraints excluded: chain O residue 188 LEU 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 P residue 129 ILE Chi-restraints excluded: chain P residue 135 ILE 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 17 VAL Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain u residue 17 GLU 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 324 LEU Chi-restraints excluded: chain u residue 343 ASP 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 486 HIS Chi-restraints excluded: chain u residue 507 ILE Chi-restraints excluded: chain u residue 530 LEU Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 233 ILE Chi-restraints excluded: chain v residue 237 LEU Chi-restraints excluded: chain v residue 249 MET Chi-restraints excluded: chain v residue 261 VAL Chi-restraints excluded: chain v residue 282 GLN Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 384 ILE Chi-restraints excluded: chain v residue 415 SER Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain x residue 81 GLN Chi-restraints excluded: chain y residue 353 LEU Chi-restraints excluded: chain y residue 354 LEU Chi-restraints excluded: chain y residue 366 LEU Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 424 ILE 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 576 HIS Chi-restraints excluded: chain y residue 591 MET Chi-restraints excluded: chain y residue 633 LEU Chi-restraints excluded: chain y residue 634 LEU 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 Chi-restraints excluded: chain y residue 845 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 294 optimal weight: 1.9990 chunk 161 optimal weight: 30.0000 chunk 40 optimal weight: 0.0770 chunk 81 optimal weight: 4.9990 chunk 266 optimal weight: 4.9990 chunk 112 optimal weight: 50.0000 chunk 88 optimal weight: 9.9990 chunk 381 optimal weight: 0.9980 chunk 22 optimal weight: 30.0000 chunk 201 optimal weight: 3.9990 chunk 322 optimal weight: 0.1980 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 51 GLN P 113 GLN ** u 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 209 GLN u 247 GLN ** u 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 359 GLN ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 662 GLN ** y 676 HIS ** 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 = 0.4422 r_free = 0.4422 target = 0.155561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.130389 restraints weight = 78273.295| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.11 r_work: 0.3718 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.157 32137 Z= 0.148 Angle : 0.680 21.083 44351 Z= 0.341 Chirality : 0.040 0.415 5300 Planarity : 0.004 0.067 5253 Dihedral : 15.432 176.609 6528 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.06 % Allowed : 23.91 % Favored : 73.04 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: 0.56 (0.14), residues: 3878 helix: 1.51 (0.11), residues: 2374 sheet: -0.52 (0.37), residues: 198 loop : -1.65 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG u 317 TYR 0.023 0.001 TYR v 238 PHE 0.034 0.001 PHE v 295 TRP 0.029 0.002 TRP u 43 HIS 0.009 0.001 HIS P 43 Details of bonding type rmsd covalent geometry : bond 0.00343 (32132) covalent geometry : angle 0.66027 (44343) SS BOND : bond 0.03761 ( 1) SS BOND : angle 10.53848 ( 2) hydrogen bonds : bond 0.03529 ( 1892) hydrogen bonds : angle 4.38021 ( 5442) metal coordination : bond 0.00396 ( 4) metal coordination : angle 12.70445 ( 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 442 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 368 time to evaluate : 1.238 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: 5 268 MET cc_start: 0.5275 (mpp) cc_final: 0.4974 (mpp) REVERT: 5 349 MET cc_start: 0.3047 (tmm) cc_final: 0.2361 (ttp) REVERT: 5 351 GLN cc_start: 0.1097 (OUTLIER) cc_final: 0.0830 (mm-40) REVERT: 5 355 TYR cc_start: 0.1828 (p90) cc_final: 0.0972 (t80) REVERT: 5 497 MET cc_start: 0.5706 (tpp) cc_final: 0.4959 (ttm) REVERT: 6 266 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.5986 (mm) REVERT: 6 274 MET cc_start: 0.9142 (tpp) cc_final: 0.8900 (tpt) REVERT: 6 280 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8533 (mm) REVERT: 6 306 ASP cc_start: 0.7888 (p0) cc_final: 0.7679 (p0) REVERT: 6 309 GLU cc_start: 0.7900 (pm20) cc_final: 0.7626 (mp0) REVERT: 6 362 ASN cc_start: 0.8140 (m-40) cc_final: 0.7505 (p0) REVERT: O 171 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7797 (mt) REVERT: O 228 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7981 (tt) REVERT: P 75 MET cc_start: 0.8583 (tmm) cc_final: 0.8370 (tmm) REVERT: Q 46 GLU cc_start: 0.7847 (pm20) cc_final: 0.7537 (mm-30) REVERT: Q 52 ASP cc_start: 0.8141 (t0) cc_final: 0.7858 (t0) REVERT: n 33 GLU cc_start: 0.7367 (pp20) cc_final: 0.7116 (pp20) REVERT: u 105 LYS cc_start: 0.5945 (mtpp) cc_final: 0.5331 (mmtt) REVERT: u 138 GLN cc_start: 0.8114 (tp40) cc_final: 0.7647 (tp-100) REVERT: u 260 PHE cc_start: 0.8198 (m-10) cc_final: 0.7749 (m-10) REVERT: u 485 ASP cc_start: 0.7277 (t0) cc_final: 0.7028 (t70) REVERT: u 514 MET cc_start: 0.8815 (pmm) cc_final: 0.8393 (ptp) REVERT: u 559 LYS cc_start: 0.7304 (mmtm) cc_final: 0.6932 (mtmm) REVERT: v 282 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7459 (tp40) REVERT: v 362 MET cc_start: 0.6527 (ppp) cc_final: 0.5354 (ptt) REVERT: x 82 LEU cc_start: 0.6569 (tp) cc_final: 0.6348 (tp) REVERT: y 393 MET cc_start: 0.7419 (ptm) cc_final: 0.7185 (mtp) REVERT: y 454 GLU cc_start: 0.7949 (tp30) cc_final: 0.7586 (tt0) REVERT: y 468 GLU cc_start: 0.7694 (tt0) cc_final: 0.7489 (tt0) REVERT: y 471 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7423 (mm-30) REVERT: y 666 GLU cc_start: 0.8210 (pp20) cc_final: 0.7980 (pt0) REVERT: y 830 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.5570 (tp30) outliers start: 74 outliers final: 55 residues processed: 417 average time/residue: 0.1957 time to fit residues: 135.2915 Evaluate side-chains 415 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 352 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 94 ILE Chi-restraints excluded: chain 5 residue 255 SER 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 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 40 LEU Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 102 LEU 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 129 ILE Chi-restraints excluded: chain P residue 135 ILE 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 17 VAL Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain n residue 46 VAL 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 324 LEU Chi-restraints excluded: chain u residue 343 ASP Chi-restraints excluded: chain u residue 486 HIS 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 261 VAL Chi-restraints excluded: chain v residue 282 GLN Chi-restraints excluded: chain v residue 287 THR Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 384 ILE Chi-restraints excluded: chain v residue 390 HIS 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 366 LEU Chi-restraints excluded: chain y residue 424 ILE Chi-restraints excluded: chain y residue 452 ASP Chi-restraints excluded: chain y residue 471 GLU Chi-restraints excluded: chain y residue 576 HIS Chi-restraints excluded: chain y residue 591 MET Chi-restraints excluded: chain y residue 633 LEU 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: 0.9980 chunk 382 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 164 optimal weight: 20.0000 chunk 23 optimal weight: 50.0000 chunk 153 optimal weight: 50.0000 chunk 255 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 292 optimal weight: 0.4980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 273 ASN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 209 GLN u 316 GLN ** v 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 359 GLN ** y 377 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.155285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.129889 restraints weight = 69495.010| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.48 r_work: 0.3689 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 32137 Z= 0.155 Angle : 0.685 20.786 44351 Z= 0.345 Chirality : 0.041 0.407 5300 Planarity : 0.004 0.067 5253 Dihedral : 15.358 176.286 6528 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.06 % Allowed : 23.99 % Favored : 72.96 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: 0.61 (0.14), residues: 3878 helix: 1.55 (0.11), residues: 2379 sheet: -0.59 (0.37), residues: 197 loop : -1.62 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG u 317 TYR 0.033 0.002 TYR v 286 PHE 0.025 0.001 PHE P 41 TRP 0.035 0.002 TRP u 43 HIS 0.010 0.001 HIS P 43 Details of bonding type rmsd covalent geometry : bond 0.00358 (32132) covalent geometry : angle 0.66506 (44343) SS BOND : bond 0.03831 ( 1) SS BOND : angle 10.12877 ( 2) hydrogen bonds : bond 0.03541 ( 1892) hydrogen bonds : angle 4.34442 ( 5442) metal coordination : bond 0.00421 ( 4) metal coordination : angle 12.72025 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9603.36 seconds wall clock time: 165 minutes 0.97 seconds (9900.97 seconds total)