Starting phenix.real_space_refine on Wed May 28 19:50:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rg0_19128/05_2025/8rg0_19128.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rg0_19128/05_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_19128/05_2025/8rg0_19128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rg0_19128/05_2025/8rg0_19128.map" model { file = "/net/cci-nas-00/data/ceres_data/8rg0_19128/05_2025/8rg0_19128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rg0_19128/05_2025/8rg0_19128.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 14, 'HIS:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 4, 'ASP:plan': 14, 'PHE:plan': 11, 'GLU:plan': 17, 'ARG:plan': 7} 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: {'GLN:plan1': 8, 'HIS:plan': 8, 'TYR:plan': 11, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 15, 'ARG:plan': 11} 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: {'GLN:plan1': 7, 'HIS:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 6, 'GLU:plan': 23, 'ARG:plan': 10} 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: {'GLN:plan1': 31, 'ASP:plan': 16, 'TYR:plan': 14, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 10, 'PHE:plan': 10, 'GLU:plan': 24, 'ARG:plan': 12} 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: {'GLN:plan1': 3, 'GLU:plan': 10, 'ARG:plan': 4, 'ASN:plan1': 1} 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: {'GLN:plan1': 3, 'GLU:plan': 10, 'ARG:plan': 4, 'ASN:plan1': 1} 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: {'GLN:plan1': 9, 'ARG:plan': 10, 'TYR:plan': 11, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 9, 'GLU:plan': 15, 'HIS: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, 'ASP:plan': 1, 'ARG: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: 20.52, per 1000 atoms: 0.65 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: 8.09 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 23 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 26 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 77 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 74 " Number of angles added : 6 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7568 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 22 sheets defined 63.3% alpha, 5.3% beta 32 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 10.44 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: 12.20 Time building geometry restraints manager: 9.17 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.370 Check model and map are aligned: 0.260 Set scattering table: 0.310 Process input model: 84.810 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.064 0.003 TRP u 393 HIS 0.020 0.002 HIS y 676 PHE 0.049 0.003 PHE 5 550 TYR 0.035 0.003 TYR N 47 ARG 0.028 0.002 ARG y 846 Details of bonding type rmsd hydrogen bonds : bond 0.13642 ( 1892) hydrogen bonds : angle 6.31342 ( 5442) metal coordination : bond 0.03680 ( 4) metal coordination : angle 23.94810 ( 6) SS BOND : bond 0.00536 ( 1) SS BOND : angle 1.46782 ( 2) covalent geometry : bond 0.00590 (32132) covalent geometry : angle 1.15741 (44343) *********************** 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 : 3.282 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: 0.4653 time to fit residues: 570.7007 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 : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 338 optimal weight: 6.9990 chunk 303 optimal weight: 30.0000 chunk 168 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 chunk 314 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 191 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 364 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 60 HIS 5 124 ASN 5 361 ASN 6 273 ASN ** 6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 336 HIS 6 355 ASN H 19 HIS I 36 GLN P 38 ASN u 79 GLN u 187 GLN u 297 HIS ** u 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 373 ASN ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 460 GLN y 584 GLN y 593 HIS y 662 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.161434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.4156 r_free = 0.4156 target = 0.134583 restraints weight = 86831.238| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 3.43 r_work: 0.3719 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 32137 Z= 0.176 Angle : 0.727 28.194 44351 Z= 0.363 Chirality : 0.043 0.203 5300 Planarity : 0.005 0.080 5253 Dihedral : 16.038 177.625 6528 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.81 % Allowed : 13.17 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3878 helix: 1.41 (0.11), residues: 2335 sheet: -1.05 (0.35), residues: 211 loop : -1.61 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP u 43 HIS 0.009 0.002 HIS O 208 PHE 0.017 0.002 PHE u 377 TYR 0.022 0.002 TYR 5 89 ARG 0.008 0.001 ARG P 121 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 1892) hydrogen bonds : angle 4.84288 ( 5442) metal coordination : bond 0.00885 ( 4) metal coordination : angle 17.51640 ( 6) SS BOND : bond 0.02608 ( 1) SS BOND : angle 6.40175 ( 2) covalent geometry : bond 0.00399 (32132) covalent geometry : angle 0.69697 (44343) *********************** 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 564 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 496 time to evaluate : 3.438 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 89 TYR cc_start: 0.4724 (p90) cc_final: 0.3795 (t80) REVERT: 5 90 GLU cc_start: 0.3232 (OUTLIER) cc_final: 0.2110 (mm-30) REVERT: 5 125 ASP cc_start: 0.1322 (t0) cc_final: 0.1059 (t0) REVERT: 5 135 LEU cc_start: 0.2756 (mt) cc_final: 0.2055 (mt) REVERT: 5 166 TYR cc_start: 0.4310 (t80) cc_final: 0.3885 (t80) REVERT: 5 268 MET cc_start: 0.5648 (mpp) cc_final: 0.5199 (mpp) REVERT: 5 355 TYR cc_start: 0.1933 (p90) cc_final: 0.0948 (t80) REVERT: 5 467 TYR cc_start: 0.6523 (m-80) cc_final: 0.6317 (m-80) REVERT: 5 513 PHE cc_start: 0.4966 (m-80) cc_final: 0.4728 (p90) REVERT: 5 560 MET cc_start: 0.8000 (tpt) cc_final: 0.7782 (ttt) REVERT: 6 306 ASP cc_start: 0.7845 (p0) cc_final: 0.7628 (p0) REVERT: H 16 LYS cc_start: 0.9011 (tptp) cc_final: 0.8600 (tptm) REVERT: I 53 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8971 (mp) REVERT: N 34 MET cc_start: 0.7524 (mtt) cc_final: 0.7069 (mtp) REVERT: O 75 GLN cc_start: 0.8406 (mp10) cc_final: 0.8107 (mm110) REVERT: O 88 THR cc_start: 0.8548 (p) cc_final: 0.8248 (p) REVERT: P 25 GLU cc_start: 0.7087 (pm20) cc_final: 0.6885 (pm20) REVERT: Q 96 THR cc_start: 0.8993 (t) cc_final: 0.8495 (t) REVERT: n 33 GLU cc_start: 0.7468 (pp20) cc_final: 0.7263 (pp20) REVERT: n 35 MET cc_start: 0.7326 (pmm) cc_final: 0.7049 (pmm) REVERT: u 29 ASP cc_start: 0.8186 (p0) cc_final: 0.7904 (p0) REVERT: u 231 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7815 (tm-30) REVERT: u 315 MET cc_start: 0.8651 (tmm) cc_final: 0.8283 (tmm) REVERT: u 317 ARG cc_start: 0.7139 (mmp80) cc_final: 0.6684 (mmp-170) REVERT: u 497 LEU cc_start: 0.7646 (tt) cc_final: 0.7408 (mm) REVERT: u 518 GLN cc_start: 0.7550 (tp40) cc_final: 0.7260 (tp-100) REVERT: u 532 LYS cc_start: 0.7967 (tptm) cc_final: 0.7589 (mmtm) REVERT: u 535 GLU cc_start: 0.3283 (tt0) cc_final: 0.2778 (tt0) REVERT: u 559 LYS cc_start: 0.6821 (mmtm) cc_final: 0.6490 (mtmm) REVERT: v 325 LEU cc_start: 0.7670 (mm) cc_final: 0.7407 (mt) REVERT: x 53 LYS cc_start: 0.5683 (mmmt) cc_final: 0.5481 (tppp) REVERT: y 392 TYR cc_start: 0.8426 (p90) cc_final: 0.8205 (p90) outliers start: 68 outliers final: 45 residues processed: 536 average time/residue: 0.4464 time to fit residues: 377.1886 Evaluate side-chains 435 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 388 time to evaluate : 3.654 ------------------------------------------------------------------------------- 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 6 residue 339 HIS 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 122 GLU Chi-restraints excluded: chain O residue 174 ARG 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 349 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 299 LEU Chi-restraints excluded: chain v residue 317 SER Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain y residue 358 VAL Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 451 MET Chi-restraints excluded: chain y residue 711 SER Chi-restraints excluded: chain y residue 741 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 22 optimal weight: 30.0000 chunk 96 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 353 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 290 optimal weight: 0.8980 chunk 387 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 P 38 ASN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 390 HIS ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 472 HIS ** y 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.160553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.136067 restraints weight = 88946.451| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.81 r_work: 0.3781 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 32137 Z= 0.144 Angle : 0.650 21.101 44351 Z= 0.327 Chirality : 0.041 0.215 5300 Planarity : 0.004 0.060 5253 Dihedral : 15.804 179.927 6528 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.39 % Allowed : 16.35 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3878 helix: 1.55 (0.11), residues: 2338 sheet: -1.01 (0.37), residues: 194 loop : -1.62 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP v 370 HIS 0.007 0.001 HIS P 43 PHE 0.017 0.001 PHE 5 350 TYR 0.027 0.002 TYR N 37 ARG 0.012 0.001 ARG P 121 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 1892) hydrogen bonds : angle 4.52122 ( 5442) metal coordination : bond 0.00493 ( 4) metal coordination : angle 14.48354 ( 6) SS BOND : bond 0.02133 ( 1) SS BOND : angle 5.10285 ( 2) covalent geometry : bond 0.00323 (32132) covalent geometry : angle 0.62648 (44343) *********************** 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 504 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 422 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 89 TYR cc_start: 0.4763 (p90) cc_final: 0.3901 (t80) REVERT: 5 90 GLU cc_start: 0.3179 (OUTLIER) cc_final: 0.2168 (mm-30) REVERT: 5 125 ASP cc_start: 0.0918 (t0) cc_final: 0.0678 (t0) REVERT: 5 166 TYR cc_start: 0.4259 (t80) cc_final: 0.3801 (t80) REVERT: 5 349 MET cc_start: 0.3573 (tmm) cc_final: 0.1390 (tpp) REVERT: 5 350 PHE cc_start: 0.1246 (m-10) cc_final: 0.0626 (m-80) REVERT: 5 355 TYR cc_start: 0.1891 (p90) cc_final: 0.0934 (t80) REVERT: 5 497 MET cc_start: 0.5332 (tpp) cc_final: 0.4981 (mtp) REVERT: 5 560 MET cc_start: 0.7929 (tpt) cc_final: 0.7520 (tpp) REVERT: 6 306 ASP cc_start: 0.7905 (p0) cc_final: 0.7587 (p0) REVERT: 6 326 ASP cc_start: 0.7518 (t0) cc_final: 0.7279 (t70) REVERT: H 16 LYS cc_start: 0.8940 (tptp) cc_final: 0.8664 (tptm) REVERT: O 75 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8140 (mm110) REVERT: O 88 THR cc_start: 0.8508 (p) cc_final: 0.8286 (p) REVERT: O 103 MET cc_start: 0.8156 (tmm) cc_final: 0.7745 (ttt) REVERT: u 231 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7617 (tm-30) REVERT: u 316 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6321 (mp10) REVERT: u 340 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6948 (tpt170) REVERT: u 479 ASP cc_start: 0.7415 (m-30) cc_final: 0.7107 (m-30) REVERT: u 532 LYS cc_start: 0.8159 (tptm) cc_final: 0.7876 (mptt) REVERT: u 559 LYS cc_start: 0.6952 (mmtm) cc_final: 0.6503 (mtmm) REVERT: v 275 LYS cc_start: 0.7530 (mttt) cc_final: 0.7075 (mtpt) REVERT: y 392 TYR cc_start: 0.8511 (p90) cc_final: 0.8240 (p90) outliers start: 82 outliers final: 52 residues processed: 471 average time/residue: 0.4123 time to fit residues: 312.1242 Evaluate side-chains 436 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 380 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 90 GLU Chi-restraints excluded: chain 5 residue 375 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 339 HIS Chi-restraints excluded: chain H residue 43 ILE 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 40 LEU 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 75 GLN Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 122 GLU 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 P residue 40 THR 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 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 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 316 GLN Chi-restraints excluded: chain u residue 324 LEU Chi-restraints excluded: chain u residue 340 ARG Chi-restraints excluded: chain u residue 487 THR Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 233 ILE Chi-restraints excluded: chain v residue 299 LEU Chi-restraints excluded: chain v residue 317 SER 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 y residue 350 GLN Chi-restraints excluded: chain y residue 354 LEU Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 424 ILE Chi-restraints excluded: chain y residue 452 ASP Chi-restraints excluded: chain y residue 569 ILE Chi-restraints excluded: chain y residue 720 VAL Chi-restraints excluded: chain y residue 746 MET 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 85 optimal weight: 4.9990 chunk 152 optimal weight: 20.0000 chunk 337 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 30.0000 chunk 381 optimal weight: 0.7980 chunk 304 optimal weight: 30.0000 chunk 290 optimal weight: 7.9990 chunk 371 optimal weight: 0.8980 chunk 157 optimal weight: 40.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- 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 I 90 HIS P 38 ASN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 16 ASN ** u 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 239 GLN ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 373 ASN ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 819 HIS ** 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 = 0.4388 r_free = 0.4388 target = 0.154185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.135173 restraints weight = 98644.390| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.86 r_work: 0.3572 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 32137 Z= 0.263 Angle : 0.747 24.057 44351 Z= 0.378 Chirality : 0.044 0.195 5300 Planarity : 0.005 0.066 5253 Dihedral : 15.811 177.502 6528 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.71 % Allowed : 17.05 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3878 helix: 1.31 (0.11), residues: 2335 sheet: -0.95 (0.37), residues: 203 loop : -1.69 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP u 149 HIS 0.043 0.002 HIS v 390 PHE 0.038 0.002 PHE 5 513 TYR 0.032 0.002 TYR N 37 ARG 0.013 0.001 ARG y 563 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 1892) hydrogen bonds : angle 4.63684 ( 5442) metal coordination : bond 0.00466 ( 4) metal coordination : angle 16.36090 ( 6) SS BOND : bond 0.02937 ( 1) SS BOND : angle 7.74597 ( 2) covalent geometry : bond 0.00603 (32132) covalent geometry : angle 0.72049 (44343) *********************** 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 527 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 413 time to evaluate : 3.801 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: 0.4725 (p90) cc_final: 0.3924 (t80) REVERT: 5 125 ASP cc_start: 0.1153 (t0) cc_final: 0.0889 (t0) REVERT: 5 349 MET cc_start: 0.3345 (tmm) cc_final: 0.1974 (tpp) REVERT: 5 350 PHE cc_start: 0.1146 (m-10) cc_final: 0.0517 (m-80) REVERT: 5 355 TYR cc_start: 0.1772 (p90) cc_final: 0.0772 (t80) REVERT: 5 497 MET cc_start: 0.5394 (tpp) cc_final: 0.4710 (ttm) REVERT: 6 280 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8955 (mm) REVERT: 6 292 ILE cc_start: 0.7893 (tp) cc_final: 0.7666 (pt) REVERT: 6 306 ASP cc_start: 0.8279 (p0) cc_final: 0.8005 (p0) REVERT: H 16 LYS cc_start: 0.8914 (tptp) cc_final: 0.8606 (tptm) REVERT: I 49 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8342 (mt0) REVERT: I 69 ASN cc_start: 0.7872 (p0) cc_final: 0.7283 (p0) REVERT: M 127 ASN cc_start: 0.7938 (p0) cc_final: 0.7676 (p0) REVERT: N 35 GLU cc_start: 0.8382 (pt0) cc_final: 0.8179 (pt0) REVERT: O 75 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8314 (mm110) REVERT: O 103 MET cc_start: 0.8245 (tmm) cc_final: 0.7933 (ttt) REVERT: O 171 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7574 (mt) REVERT: O 228 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8034 (tt) REVERT: P 75 MET cc_start: 0.8652 (tmm) cc_final: 0.8396 (tmm) REVERT: Q 52 ASP cc_start: 0.8063 (t0) cc_final: 0.7819 (t0) REVERT: u 231 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7995 (tm-30) REVERT: u 316 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6563 (mp10) REVERT: u 485 ASP cc_start: 0.7657 (t0) cc_final: 0.7354 (t0) REVERT: u 532 LYS cc_start: 0.8195 (tptm) cc_final: 0.7971 (mmtm) REVERT: u 535 GLU cc_start: 0.4505 (tt0) cc_final: 0.4184 (tt0) REVERT: u 559 LYS cc_start: 0.7246 (mmtm) cc_final: 0.6867 (mtmm) REVERT: v 275 LYS cc_start: 0.7703 (mttt) cc_final: 0.7017 (mtpt) REVERT: x 28 MET cc_start: 0.7836 (mmp) cc_final: 0.7563 (mmt) REVERT: x 55 TYR cc_start: 0.6978 (m-80) cc_final: 0.6579 (m-80) REVERT: x 82 LEU cc_start: 0.7309 (tp) cc_final: 0.6891 (tp) REVERT: y 471 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: y 666 GLU cc_start: 0.8170 (pp20) cc_final: 0.7878 (pt0) REVERT: y 667 ARG cc_start: 0.7543 (tmm160) cc_final: 0.7006 (tmm160) REVERT: y 804 MET cc_start: 0.7888 (mmm) cc_final: 0.7676 (mtt) outliers start: 114 outliers final: 70 residues processed: 486 average time/residue: 0.4297 time to fit residues: 339.0248 Evaluate side-chains 442 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 365 time to evaluate : 3.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 94 ILE Chi-restraints excluded: chain 5 residue 247 TYR Chi-restraints excluded: chain 5 residue 550 PHE Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 280 LEU Chi-restraints excluded: chain 6 residue 325 ILE Chi-restraints excluded: chain 6 residue 337 SER Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain 6 residue 369 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 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 39 LYS 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 75 GLN Chi-restraints excluded: chain O residue 96 CYS 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 210 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 122 SER 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 507 ILE Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 233 ILE Chi-restraints excluded: chain v residue 261 VAL Chi-restraints excluded: chain v residue 299 LEU Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 318 VAL Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain y residue 353 LEU Chi-restraints excluded: chain y residue 354 LEU Chi-restraints excluded: chain y residue 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 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 7 optimal weight: 0.3980 chunk 196 optimal weight: 0.6980 chunk 287 optimal weight: 0.9980 chunk 330 optimal weight: 0.6980 chunk 139 optimal weight: 20.0000 chunk 112 optimal weight: 50.0000 chunk 183 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 302 optimal weight: 30.0000 chunk 362 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 5 124 ASN O 124 HIS ** u 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 209 GLN u 212 HIS u 226 GLN u 236 GLN ** u 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 521 ASN ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 225 HIS ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 282 GLN v 373 ASN ** y 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 837 GLN y 845 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.158160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.140024 restraints weight = 73812.258| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 3.71 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4218 r_free = 0.4218 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4218 r_free = 0.4218 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 32137 Z= 0.126 Angle : 0.617 18.701 44351 Z= 0.313 Chirality : 0.039 0.192 5300 Planarity : 0.004 0.063 5253 Dihedral : 15.650 178.327 6528 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.72 % Allowed : 19.24 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 3878 helix: 1.58 (0.11), residues: 2344 sheet: -0.46 (0.39), residues: 191 loop : -1.59 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP u 393 HIS 0.008 0.001 HIS P 43 PHE 0.018 0.001 PHE 5 513 TYR 0.025 0.001 TYR 5 89 ARG 0.008 0.001 ARG v 211 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 1892) hydrogen bonds : angle 4.36545 ( 5442) metal coordination : bond 0.00557 ( 4) metal coordination : angle 13.08312 ( 6) SS BOND : bond 0.02274 ( 1) SS BOND : angle 4.63380 ( 2) covalent geometry : bond 0.00277 (32132) covalent geometry : angle 0.59736 (44343) *********************** 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 513 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 423 time to evaluate : 3.503 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: 5 89 TYR cc_start: 0.3819 (p90) cc_final: 0.3247 (t80) REVERT: 5 294 LEU cc_start: 0.4754 (OUTLIER) cc_final: 0.4442 (pp) REVERT: 5 349 MET cc_start: 0.3189 (tmm) cc_final: 0.2060 (tpp) REVERT: 5 355 TYR cc_start: 0.1470 (p90) cc_final: 0.0825 (t80) REVERT: 6 280 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8559 (mm) REVERT: I 49 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8152 (mt0) REVERT: I 69 ASN cc_start: 0.7161 (p0) cc_final: 0.6568 (p0) REVERT: N 42 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7528 (tttp) REVERT: O 228 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7714 (tt) REVERT: u 231 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7419 (tm-30) REVERT: u 316 GLN cc_start: 0.5568 (OUTLIER) cc_final: 0.5146 (mp10) REVERT: u 485 ASP cc_start: 0.6568 (t0) cc_final: 0.6344 (t0) REVERT: x 55 TYR cc_start: 0.6398 (m-80) cc_final: 0.6103 (m-80) REVERT: x 82 LEU cc_start: 0.6643 (tp) cc_final: 0.6400 (tp) REVERT: y 471 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7350 (mm-30) REVERT: y 744 MET cc_start: 0.7322 (ptm) cc_final: 0.7021 (ptm) REVERT: y 804 MET cc_start: 0.7341 (mmm) cc_final: 0.7134 (mtt) REVERT: y 830 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.5332 (tp30) outliers start: 90 outliers final: 48 residues processed: 484 average time/residue: 0.4120 time to fit residues: 321.5783 Evaluate side-chains 433 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 377 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 294 LEU 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 6 residue 339 HIS Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain N residue 42 LYS 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 210 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 116 LEU 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 56 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain u residue 98 GLU Chi-restraints excluded: chain u residue 171 GLU Chi-restraints excluded: chain u residue 205 LEU Chi-restraints excluded: chain u residue 220 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 316 GLN Chi-restraints excluded: chain u residue 340 ARG Chi-restraints excluded: chain u residue 507 ILE Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 261 VAL Chi-restraints excluded: chain v residue 282 GLN Chi-restraints excluded: chain v residue 293 THR Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 318 VAL Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain y residue 354 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 628 ASP Chi-restraints excluded: chain y residue 746 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 297 optimal weight: 20.0000 chunk 277 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 365 optimal weight: 0.7980 chunk 294 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 268 optimal weight: 0.8980 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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** 5 312 GLN ** 6 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 421 ASN y 377 ASN y 724 GLN y 758 ASN y 819 HIS y 845 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.152574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.126685 restraints weight = 73260.211| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.39 r_work: 0.3628 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 32137 Z= 0.231 Angle : 0.713 21.433 44351 Z= 0.360 Chirality : 0.043 0.245 5300 Planarity : 0.005 0.067 5253 Dihedral : 15.639 177.864 6528 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.17 % Allowed : 20.44 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3878 helix: 1.46 (0.11), residues: 2338 sheet: -0.76 (0.37), residues: 209 loop : -1.66 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP u 149 HIS 0.008 0.002 HIS y 572 PHE 0.018 0.002 PHE 6 311 TYR 0.027 0.002 TYR x 59 ARG 0.013 0.001 ARG u 415 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 1892) hydrogen bonds : angle 4.48587 ( 5442) metal coordination : bond 0.00487 ( 4) metal coordination : angle 15.12931 ( 6) SS BOND : bond 0.02758 ( 1) SS BOND : angle 6.88114 ( 2) covalent geometry : bond 0.00530 (32132) covalent geometry : angle 0.68911 (44343) *********************** 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 475 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 374 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 89 TYR cc_start: 0.4553 (p90) cc_final: 0.4016 (t80) REVERT: 5 349 MET cc_start: 0.3057 (tmm) cc_final: 0.1785 (tpp) REVERT: 5 351 GLN cc_start: 0.1229 (OUTLIER) cc_final: 0.0962 (mm-40) REVERT: 5 355 TYR cc_start: 0.1711 (p90) cc_final: 0.0715 (t80) REVERT: 6 280 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8810 (mm) REVERT: I 46 THR cc_start: 0.8307 (p) cc_final: 0.7957 (p) REVERT: I 49 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8161 (mt0) REVERT: I 69 ASN cc_start: 0.7811 (p0) cc_final: 0.7164 (p0) REVERT: M 127 ASN cc_start: 0.7759 (p0) cc_final: 0.7455 (p0) REVERT: O 171 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8028 (mt) REVERT: O 175 GLU cc_start: 0.8224 (pp20) cc_final: 0.7393 (pt0) REVERT: O 228 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8017 (tt) REVERT: u 33 ASP cc_start: 0.8473 (p0) cc_final: 0.8169 (p0) REVERT: u 105 LYS cc_start: 0.7531 (mmtt) cc_final: 0.7275 (mmtt) REVERT: u 231 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7603 (tm-30) REVERT: u 245 LEU cc_start: 0.6948 (tp) cc_final: 0.6530 (tp) REVERT: u 296 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8563 (mm) REVERT: u 316 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6268 (mp10) REVERT: u 485 ASP cc_start: 0.7398 (t0) cc_final: 0.7189 (t0) REVERT: x 28 MET cc_start: 0.7817 (mmp) cc_final: 0.7547 (mmt) REVERT: x 55 TYR cc_start: 0.6740 (m-80) cc_final: 0.6372 (m-80) REVERT: x 82 LEU cc_start: 0.6772 (tp) cc_final: 0.6473 (tp) REVERT: y 471 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7537 (mm-30) REVERT: y 644 GLU cc_start: 0.8046 (pm20) cc_final: 0.7830 (mm-30) REVERT: y 666 GLU cc_start: 0.8212 (pp20) cc_final: 0.7944 (pt0) REVERT: y 667 ARG cc_start: 0.7542 (tmm160) cc_final: 0.7121 (tmm160) REVERT: y 804 MET cc_start: 0.7748 (mmm) cc_final: 0.7430 (mtt) outliers start: 101 outliers final: 70 residues processed: 440 average time/residue: 0.3881 time to fit residues: 279.9190 Evaluate side-chains 435 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 357 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 94 ILE 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 45 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 72 LEU 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 44 ASP Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 96 CYS 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 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 135 ILE Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 14 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 28 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 115 ILE 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 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 343 ASP Chi-restraints excluded: chain u residue 357 THR 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 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 261 VAL Chi-restraints excluded: chain v residue 293 THR Chi-restraints excluded: chain v residue 299 LEU Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 318 VAL Chi-restraints excluded: chain v residue 384 ILE Chi-restraints excluded: chain v residue 417 MET Chi-restraints excluded: chain y residue 354 LEU Chi-restraints excluded: chain y residue 412 LEU Chi-restraints excluded: chain y residue 452 ASP Chi-restraints excluded: chain y residue 471 GLU Chi-restraints excluded: chain y residue 547 LEU Chi-restraints excluded: chain y residue 628 ASP Chi-restraints excluded: chain y residue 633 LEU Chi-restraints excluded: chain y residue 634 LEU Chi-restraints excluded: chain y residue 732 SER Chi-restraints excluded: chain y residue 746 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 50 optimal weight: 6.9990 chunk 141 optimal weight: 50.0000 chunk 257 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 120 optimal weight: 30.0000 chunk 360 optimal weight: 0.8980 chunk 19 optimal weight: 50.0000 chunk 75 optimal weight: 6.9990 chunk 315 optimal weight: 3.9990 chunk 335 optimal weight: 20.0000 chunk 204 optimal weight: 0.4980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 442 GLN u 512 GLN ** v 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 239 GLN ** v 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 373 ASN x 81 GLN y 845 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.153644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.124835 restraints weight = 78120.985| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.42 r_work: 0.3614 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 32137 Z= 0.203 Angle : 0.687 21.127 44351 Z= 0.346 Chirality : 0.042 0.198 5300 Planarity : 0.004 0.067 5253 Dihedral : 15.609 178.842 6528 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.54 % Allowed : 21.06 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3878 helix: 1.44 (0.11), residues: 2354 sheet: -0.78 (0.38), residues: 199 loop : -1.60 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP u 43 HIS 0.009 0.001 HIS u 510 PHE 0.020 0.002 PHE u 398 TYR 0.023 0.002 TYR 5 89 ARG 0.010 0.001 ARG u 415 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 1892) hydrogen bonds : angle 4.41961 ( 5442) metal coordination : bond 0.00389 ( 4) metal coordination : angle 14.73621 ( 6) SS BOND : bond 0.02572 ( 1) SS BOND : angle 5.94123 ( 2) covalent geometry : bond 0.00465 (32132) covalent geometry : angle 0.66407 (44343) *********************** 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 488 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 378 time to evaluate : 3.539 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: 0.4584 (p90) cc_final: 0.4132 (t80) REVERT: 5 349 MET cc_start: 0.3007 (tmm) cc_final: 0.2523 (ttt) REVERT: 5 351 GLN cc_start: 0.1270 (OUTLIER) cc_final: 0.1006 (mm-40) REVERT: 5 355 TYR cc_start: 0.1699 (p90) cc_final: 0.0873 (t80) REVERT: 5 380 MET cc_start: 0.7770 (ttm) cc_final: 0.7453 (ttm) REVERT: 5 545 ARG cc_start: 0.7398 (mmm160) cc_final: 0.7101 (mmm160) REVERT: 6 280 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8725 (mm) REVERT: 6 309 GLU cc_start: 0.7830 (pm20) cc_final: 0.7422 (mp0) REVERT: I 46 THR cc_start: 0.8404 (p) cc_final: 0.8060 (p) REVERT: I 49 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8286 (mt0) REVERT: I 69 ASN cc_start: 0.7939 (p0) cc_final: 0.7506 (p0) REVERT: M 127 ASN cc_start: 0.7871 (p0) cc_final: 0.7527 (p0) REVERT: O 171 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7934 (mt) REVERT: O 175 GLU cc_start: 0.8360 (pp20) cc_final: 0.7492 (pt0) REVERT: O 228 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7984 (tt) REVERT: Q 46 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6716 (mm-30) REVERT: u 33 ASP cc_start: 0.8590 (p0) cc_final: 0.8339 (p0) REVERT: u 296 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8542 (mm) REVERT: u 316 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.5911 (mp10) REVERT: u 317 ARG cc_start: 0.7161 (mmp80) cc_final: 0.6945 (mmp-170) REVERT: u 452 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7270 (m-80) REVERT: u 485 ASP cc_start: 0.7489 (t0) cc_final: 0.7198 (t70) REVERT: v 275 LYS cc_start: 0.7383 (mttp) cc_final: 0.7027 (mppt) REVERT: x 28 MET cc_start: 0.7839 (mmp) cc_final: 0.7596 (mmt) REVERT: x 55 TYR cc_start: 0.6563 (m-80) cc_final: 0.6184 (m-80) REVERT: y 471 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7583 (mm-30) REVERT: y 644 GLU cc_start: 0.8044 (pm20) cc_final: 0.7767 (mm-30) REVERT: y 666 GLU cc_start: 0.8356 (pp20) cc_final: 0.8003 (pt0) REVERT: y 830 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6121 (tm-30) outliers start: 110 outliers final: 78 residues processed: 450 average time/residue: 0.3921 time to fit residues: 291.5627 Evaluate side-chains 444 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 356 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 94 ILE Chi-restraints excluded: chain 5 residue 247 TYR Chi-restraints excluded: chain 5 residue 351 GLN Chi-restraints excluded: chain 5 residue 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 337 SER Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 72 LEU 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 44 ASP Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain O residue 96 CYS 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 210 VAL Chi-restraints excluded: chain O residue 217 MET 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 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 14 VAL Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain u residue 98 GLU Chi-restraints excluded: chain u residue 130 SER Chi-restraints excluded: chain u residue 171 GLU Chi-restraints excluded: chain u residue 205 LEU Chi-restraints excluded: chain u residue 220 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 296 LEU Chi-restraints excluded: chain u residue 316 GLN Chi-restraints excluded: chain u residue 324 LEU Chi-restraints excluded: chain u residue 343 ASP Chi-restraints excluded: chain u residue 435 THR Chi-restraints excluded: chain u residue 452 PHE Chi-restraints excluded: chain u residue 486 HIS 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 261 VAL 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 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 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 628 ASP Chi-restraints excluded: chain y residue 633 LEU Chi-restraints excluded: chain y residue 634 LEU Chi-restraints excluded: chain y residue 732 SER Chi-restraints excluded: chain y residue 746 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 315 optimal weight: 30.0000 chunk 136 optimal weight: 30.0000 chunk 391 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 268 optimal weight: 0.8980 chunk 398 optimal weight: 9.9990 chunk 299 optimal weight: 8.9990 overall best weight: 5.4986 ------------------------------------------------------------------------------- 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** ** 6 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 ASN u 229 HIS ** u 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 282 GLN y 572 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 = 0.4331 r_free = 0.4331 target = 0.149698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.130590 restraints weight = 87738.875| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.72 r_work: 0.3504 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 32137 Z= 0.332 Angle : 0.834 24.531 44351 Z= 0.420 Chirality : 0.047 0.243 5300 Planarity : 0.006 0.071 5253 Dihedral : 15.810 177.592 6528 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 5.08 % Allowed : 21.80 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3878 helix: 1.10 (0.11), residues: 2339 sheet: -1.08 (0.34), residues: 243 loop : -1.84 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP u 149 HIS 0.009 0.002 HIS y 572 PHE 0.040 0.002 PHE v 295 TYR 0.027 0.003 TYR 6 252 ARG 0.018 0.001 ARG y 563 Details of bonding type rmsd hydrogen bonds : bond 0.04706 ( 1892) hydrogen bonds : angle 4.80850 ( 5442) metal coordination : bond 0.00817 ( 4) metal coordination : angle 17.46724 ( 6) SS BOND : bond 0.03045 ( 1) SS BOND : angle 7.98580 ( 2) covalent geometry : bond 0.00758 (32132) covalent geometry : angle 0.80707 (44343) *********************** 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 491 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 368 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 349 MET cc_start: 0.3174 (tmm) cc_final: 0.2672 (ttt) REVERT: 5 351 GLN cc_start: 0.1491 (OUTLIER) cc_final: 0.1214 (mm-40) REVERT: 5 355 TYR cc_start: 0.1633 (p90) cc_final: 0.0817 (t80) REVERT: 6 280 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8824 (mm) REVERT: 6 309 GLU cc_start: 0.8154 (pm20) cc_final: 0.7669 (mp0) REVERT: 6 339 HIS cc_start: 0.7478 (OUTLIER) cc_final: 0.7137 (m90) REVERT: I 46 THR cc_start: 0.8556 (p) cc_final: 0.8339 (p) REVERT: I 49 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8593 (mt0) REVERT: I 67 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8066 (m) REVERT: I 69 ASN cc_start: 0.7929 (p0) cc_final: 0.7439 (p0) REVERT: M 127 ASN cc_start: 0.8258 (p0) cc_final: 0.7920 (p0) REVERT: O 171 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8076 (mt) REVERT: O 228 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8199 (tt) REVERT: Q 44 ILE cc_start: 0.8646 (mm) cc_final: 0.8390 (mm) REVERT: Q 46 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7148 (mm-30) REVERT: Q 52 ASP cc_start: 0.8066 (t0) cc_final: 0.7803 (t0) REVERT: n 33 GLU cc_start: 0.7561 (pp20) cc_final: 0.7255 (pp20) REVERT: u 33 ASP cc_start: 0.8642 (p0) cc_final: 0.8374 (p0) REVERT: u 105 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7503 (mmtt) REVERT: u 109 GLN cc_start: 0.7175 (pp30) cc_final: 0.6852 (pp30) REVERT: u 231 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7642 (tm-30) REVERT: u 452 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7243 (m-80) REVERT: u 485 ASP cc_start: 0.7546 (t0) cc_final: 0.7287 (t70) REVERT: u 514 MET cc_start: 0.9083 (pmm) cc_final: 0.8637 (ptp) REVERT: v 275 LYS cc_start: 0.7806 (mttp) cc_final: 0.7535 (mtpt) REVERT: v 282 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: v 362 MET cc_start: 0.6840 (ppp) cc_final: 0.5490 (ptt) REVERT: x 55 TYR cc_start: 0.6959 (m-80) cc_final: 0.6518 (m-80) REVERT: y 471 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: y 644 GLU cc_start: 0.8097 (pm20) cc_final: 0.7888 (mm-30) REVERT: y 662 GLN cc_start: 0.7509 (tm130) cc_final: 0.7192 (tp40) REVERT: y 666 GLU cc_start: 0.8611 (pp20) cc_final: 0.8202 (pt0) REVERT: y 831 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7694 (pp) outliers start: 123 outliers final: 85 residues processed: 445 average time/residue: 0.3903 time to fit residues: 285.1837 Evaluate side-chains 446 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 350 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 94 ILE Chi-restraints excluded: chain 5 residue 247 TYR Chi-restraints excluded: chain 5 residue 351 GLN Chi-restraints excluded: chain 5 residue 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 325 ILE Chi-restraints excluded: chain 6 residue 337 SER Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 71 ILE 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 34 MET Chi-restraints excluded: chain N residue 42 LYS Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 88 THR 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 210 VAL Chi-restraints excluded: chain O residue 217 MET Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 41 PHE Chi-restraints excluded: chain P residue 116 LEU 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 28 THR Chi-restraints excluded: chain n residue 32 VAL Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain u residue 98 GLU Chi-restraints excluded: chain u residue 115 ILE Chi-restraints excluded: chain u residue 130 SER Chi-restraints excluded: chain u residue 171 GLU Chi-restraints excluded: chain u residue 205 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 316 GLN Chi-restraints excluded: chain u residue 318 MET Chi-restraints excluded: chain u residue 320 THR Chi-restraints excluded: chain u residue 324 LEU Chi-restraints excluded: chain u residue 340 ARG Chi-restraints excluded: chain u residue 343 ASP 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 452 PHE 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 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 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 384 ILE 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 412 LEU 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 591 MET Chi-restraints excluded: chain y residue 628 ASP Chi-restraints excluded: chain y residue 633 LEU Chi-restraints excluded: chain y residue 634 LEU Chi-restraints excluded: chain y residue 727 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 831 LEU Chi-restraints excluded: chain y residue 835 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 30 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 299 optimal weight: 9.9990 chunk 293 optimal weight: 0.9980 chunk 323 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 chunk 22 optimal weight: 30.0000 chunk 79 optimal weight: 8.9990 chunk 281 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 121 GLN ** 6 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 241 GLN ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 472 HIS y 519 HIS ** y 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 845 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.152506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.133707 restraints weight = 96516.098| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.68 r_work: 0.3592 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 32137 Z= 0.160 Angle : 0.699 20.345 44351 Z= 0.350 Chirality : 0.041 0.278 5300 Planarity : 0.004 0.068 5253 Dihedral : 15.638 178.285 6528 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.63 % Allowed : 23.29 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3878 helix: 1.37 (0.11), residues: 2375 sheet: -0.87 (0.36), residues: 215 loop : -1.79 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP u 43 HIS 0.010 0.001 HIS v 216 PHE 0.028 0.001 PHE v 295 TYR 0.039 0.002 TYR 5 158 ARG 0.012 0.001 ARG y 667 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 1892) hydrogen bonds : angle 4.48307 ( 5442) metal coordination : bond 0.00164 ( 4) metal coordination : angle 14.34588 ( 6) SS BOND : bond 0.02432 ( 1) SS BOND : angle 5.02542 ( 2) covalent geometry : bond 0.00368 (32132) covalent geometry : angle 0.67826 (44343) *********************** 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 459 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 371 time to evaluate : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 349 MET cc_start: 0.3013 (tmm) cc_final: 0.2424 (ttp) REVERT: 5 351 GLN cc_start: 0.1146 (OUTLIER) cc_final: 0.0942 (mm-40) REVERT: 5 355 TYR cc_start: 0.1995 (p90) cc_final: 0.1066 (t80) REVERT: 5 545 ARG cc_start: 0.7102 (mmm160) cc_final: 0.6863 (mmm160) REVERT: 6 273 ASN cc_start: 0.8685 (t0) cc_final: 0.8446 (t0) REVERT: 6 280 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8660 (mm) REVERT: 6 309 GLU cc_start: 0.8178 (pm20) cc_final: 0.7837 (mp0) REVERT: I 46 THR cc_start: 0.8259 (p) cc_final: 0.7944 (p) REVERT: I 49 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8381 (mt0) REVERT: I 69 ASN cc_start: 0.7515 (p0) cc_final: 0.7148 (p0) REVERT: M 127 ASN cc_start: 0.8005 (p0) cc_final: 0.7667 (p0) REVERT: N 34 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7424 (tpp) REVERT: O 175 GLU cc_start: 0.8256 (pp20) cc_final: 0.7519 (pt0) REVERT: O 228 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8046 (tt) REVERT: P 39 ASP cc_start: 0.8298 (p0) cc_final: 0.8040 (p0) REVERT: P 75 MET cc_start: 0.8691 (tmm) cc_final: 0.8477 (tmm) REVERT: Q 44 ILE cc_start: 0.8427 (mm) cc_final: 0.8223 (mm) REVERT: Q 52 ASP cc_start: 0.7992 (t0) cc_final: 0.7787 (t0) REVERT: n 33 GLU cc_start: 0.7523 (pp20) cc_final: 0.7233 (pp20) REVERT: u 33 ASP cc_start: 0.8584 (p0) cc_final: 0.8289 (p0) REVERT: u 260 PHE cc_start: 0.8236 (m-10) cc_final: 0.7800 (m-10) REVERT: u 316 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6270 (mp10) REVERT: u 452 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.7152 (m-80) REVERT: u 485 ASP cc_start: 0.7436 (t0) cc_final: 0.7172 (t70) REVERT: u 514 MET cc_start: 0.8989 (pmm) cc_final: 0.8530 (ptp) REVERT: v 242 TYR cc_start: 0.6880 (m-80) cc_final: 0.6307 (m-80) REVERT: v 275 LYS cc_start: 0.7728 (mttp) cc_final: 0.7469 (mppt) REVERT: v 362 MET cc_start: 0.6580 (ppp) cc_final: 0.5250 (ptt) REVERT: y 471 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7500 (mm-30) REVERT: y 644 GLU cc_start: 0.7964 (pm20) cc_final: 0.7672 (mm-30) REVERT: y 662 GLN cc_start: 0.7346 (tm130) cc_final: 0.7052 (tp40) REVERT: y 666 GLU cc_start: 0.8450 (pp20) cc_final: 0.7989 (pt0) REVERT: y 744 MET cc_start: 0.7803 (ptm) cc_final: 0.7546 (ptm) REVERT: y 830 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.5657 (tp30) outliers start: 88 outliers final: 62 residues processed: 426 average time/residue: 0.3914 time to fit residues: 273.9092 Evaluate side-chains 426 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 355 time to evaluate : 3.304 ------------------------------------------------------------------------------- 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 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 45 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 33 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 49 GLN 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 M residue 126 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 88 THR 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 217 MET 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 135 ILE 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 28 THR Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain u residue 98 GLU Chi-restraints excluded: chain u residue 115 ILE Chi-restraints excluded: chain u residue 205 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 316 GLN Chi-restraints excluded: chain u residue 318 MET Chi-restraints excluded: chain u residue 343 ASP Chi-restraints excluded: chain u residue 357 THR Chi-restraints excluded: chain u residue 452 PHE 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 243 LEU Chi-restraints excluded: chain v residue 261 VAL 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 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 628 ASP Chi-restraints excluded: chain y residue 633 LEU Chi-restraints excluded: chain y residue 634 LEU Chi-restraints excluded: chain y residue 732 SER Chi-restraints excluded: chain y residue 810 MET Chi-restraints excluded: chain y residue 827 ILE Chi-restraints excluded: chain y residue 830 GLU Chi-restraints excluded: chain y residue 835 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 204 optimal weight: 1.9990 chunk 221 optimal weight: 0.0370 chunk 105 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 265 optimal weight: 0.0570 chunk 120 optimal weight: 50.0000 chunk 72 optimal weight: 4.9990 chunk 146 optimal weight: 30.0000 chunk 207 optimal weight: 0.3980 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 GLN ** u 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 845 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.155261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.136718 restraints weight = 84393.885| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.34 r_work: 0.3719 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32137 Z= 0.137 Angle : 0.687 18.424 44351 Z= 0.341 Chirality : 0.040 0.262 5300 Planarity : 0.004 0.077 5253 Dihedral : 15.479 176.678 6528 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.97 % Allowed : 23.74 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3878 helix: 1.52 (0.11), residues: 2383 sheet: -0.71 (0.36), residues: 211 loop : -1.70 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP v 370 HIS 0.010 0.001 HIS P 43 PHE 0.025 0.001 PHE v 295 TYR 0.038 0.002 TYR 5 158 ARG 0.013 0.001 ARG y 667 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 1892) hydrogen bonds : angle 4.34747 ( 5442) metal coordination : bond 0.00543 ( 4) metal coordination : angle 12.83965 ( 6) SS BOND : bond 0.02413 ( 1) SS BOND : angle 4.78646 ( 2) covalent geometry : bond 0.00308 (32132) covalent geometry : angle 0.67020 (44343) ********************** 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 437 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 365 time to evaluate : 3.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 304 MET cc_start: 0.1704 (ppp) cc_final: 0.0751 (mtp) REVERT: 5 349 MET cc_start: 0.3213 (tmm) cc_final: 0.2520 (ttp) REVERT: 5 351 GLN cc_start: 0.1103 (OUTLIER) cc_final: 0.0888 (mm-40) REVERT: 5 355 TYR cc_start: 0.1907 (p90) cc_final: 0.1023 (t80) REVERT: 5 545 ARG cc_start: 0.6864 (mmm160) cc_final: 0.6627 (mmm160) REVERT: 6 273 ASN cc_start: 0.8701 (t0) cc_final: 0.8444 (t0) REVERT: 6 274 MET cc_start: 0.9159 (tpp) cc_final: 0.8956 (tpt) REVERT: 6 280 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8492 (mm) REVERT: 6 309 GLU cc_start: 0.7931 (pm20) cc_final: 0.7730 (mp0) REVERT: I 46 THR cc_start: 0.8057 (p) cc_final: 0.7675 (p) REVERT: I 49 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8249 (mt0) REVERT: M 127 ASN cc_start: 0.7855 (p0) cc_final: 0.7546 (p0) REVERT: O 175 GLU cc_start: 0.8050 (pp20) cc_final: 0.7679 (pt0) REVERT: O 228 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8005 (tt) REVERT: P 39 ASP cc_start: 0.8090 (p0) cc_final: 0.7874 (p0) REVERT: n 33 GLU cc_start: 0.7395 (pp20) cc_final: 0.7190 (pp20) REVERT: u 33 ASP cc_start: 0.8388 (p0) cc_final: 0.8076 (p0) REVERT: u 88 ASP cc_start: 0.7691 (t0) cc_final: 0.7224 (t0) REVERT: u 138 GLN cc_start: 0.8285 (tp40) cc_final: 0.7854 (tp-100) REVERT: u 260 PHE cc_start: 0.8212 (m-10) cc_final: 0.7756 (m-10) REVERT: u 316 GLN cc_start: 0.6521 (OUTLIER) cc_final: 0.5856 (mp10) REVERT: u 452 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.7096 (m-80) REVERT: u 485 ASP cc_start: 0.7498 (t0) cc_final: 0.7273 (t70) REVERT: u 514 MET cc_start: 0.8963 (pmm) cc_final: 0.8604 (ptp) REVERT: v 237 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6715 (tp) REVERT: v 362 MET cc_start: 0.6489 (ppp) cc_final: 0.5240 (ptt) REVERT: x 55 TYR cc_start: 0.6364 (m-80) cc_final: 0.6031 (m-80) REVERT: y 471 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: y 662 GLN cc_start: 0.7354 (tm130) cc_final: 0.7118 (tp40) REVERT: y 666 GLU cc_start: 0.8331 (pp20) cc_final: 0.7844 (pt0) REVERT: y 773 ASP cc_start: 0.7626 (m-30) cc_final: 0.7380 (m-30) REVERT: y 830 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.5550 (tp30) outliers start: 72 outliers final: 53 residues processed: 416 average time/residue: 0.3962 time to fit residues: 272.5773 Evaluate side-chains 408 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 346 time to evaluate : 3.429 ------------------------------------------------------------------------------- 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 249 LEU Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 280 LEU Chi-restraints excluded: chain H residue 45 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 33 VAL Chi-restraints excluded: chain I residue 49 GLN 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 49 ILE Chi-restraints excluded: chain O residue 88 THR 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 217 MET Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain P residue 40 THR 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 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 205 LEU Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 316 GLN Chi-restraints excluded: chain u residue 318 MET Chi-restraints excluded: chain u residue 324 LEU Chi-restraints excluded: chain u residue 343 ASP Chi-restraints excluded: chain u residue 452 PHE Chi-restraints excluded: chain u residue 486 HIS Chi-restraints excluded: chain u residue 507 ILE Chi-restraints excluded: chain u residue 511 LEU Chi-restraints excluded: chain u residue 550 HIS Chi-restraints excluded: chain v residue 237 LEU Chi-restraints excluded: chain v residue 243 LEU Chi-restraints excluded: chain v residue 261 VAL 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 452 ASP Chi-restraints excluded: chain y residue 471 GLU Chi-restraints excluded: chain y residue 547 LEU Chi-restraints excluded: chain y residue 628 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 30 optimal weight: 8.9990 chunk 15 optimal weight: 40.0000 chunk 12 optimal weight: 40.0000 chunk 71 optimal weight: 0.0970 chunk 206 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 139 optimal weight: 30.0000 chunk 63 optimal weight: 6.9990 chunk 160 optimal weight: 30.0000 chunk 231 optimal weight: 8.9990 chunk 301 optimal weight: 40.0000 overall best weight: 6.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 442 GLN ** v 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 283 GLN ** y 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 819 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.147979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.121652 restraints weight = 73098.681| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.34 r_work: 0.3567 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.6460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.141 32137 Z= 0.376 Angle : 0.863 23.619 44351 Z= 0.433 Chirality : 0.049 0.338 5300 Planarity : 0.006 0.073 5253 Dihedral : 15.694 178.869 6528 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.39 % Allowed : 23.74 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3878 helix: 1.14 (0.11), residues: 2345 sheet: -0.97 (0.35), residues: 221 loop : -1.85 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP u 149 HIS 0.010 0.002 HIS v 216 PHE 0.027 0.002 PHE 6 311 TYR 0.042 0.003 TYR 5 158 ARG 0.018 0.001 ARG y 563 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 1892) hydrogen bonds : angle 4.78788 ( 5442) metal coordination : bond 0.00929 ( 4) metal coordination : angle 16.79886 ( 6) SS BOND : bond 0.03282 ( 1) SS BOND : angle 8.22287 ( 2) covalent geometry : bond 0.00861 (32132) covalent geometry : angle 0.83906 (44343) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18432.99 seconds wall clock time: 318 minutes 46.66 seconds (19126.66 seconds total)