Starting phenix.real_space_refine on Thu Mar 5 00:45:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8crt_26958/03_2026/8crt_26958.cif Found real_map, /net/cci-nas-00/data/ceres_data/8crt_26958/03_2026/8crt_26958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8crt_26958/03_2026/8crt_26958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8crt_26958/03_2026/8crt_26958.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8crt_26958/03_2026/8crt_26958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8crt_26958/03_2026/8crt_26958.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.100 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: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 11913 2.51 5 N 2872 2.21 5 O 3034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17925 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 2943 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2962 Chain: "L" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2938 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2954 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 248 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "B" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR K 34 " occ=0.55 ... (22 atoms not shown) pdb=" OH BTYR K 34 " occ=0.45 residue: pdb=" N ATYR K 242 " occ=0.55 ... (22 atoms not shown) pdb=" OH BTYR K 242 " occ=0.45 Time building chain proxies: 4.31, per 1000 atoms: 0.24 Number of scatterers: 17925 At special positions: 0 Unit cell: (163.095, 115.37, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 3034 8.00 N 2872 7.00 C 11913 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 1 " - " ASN C 642 " " NAG F 1 " - " ASN E 642 " Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 823.3 milliseconds 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 7 sheets defined 76.7% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'K' and resid 11 through 31 removed outlier: 3.562A pdb=" N LEU K 15 " --> pdb=" O ARG K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 66 removed outlier: 3.781A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY K 51 " --> pdb=" O SER K 47 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU K 62 " --> pdb=" O ALA K 58 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 99 removed outlier: 3.869A pdb=" N GLN K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 127 removed outlier: 3.520A pdb=" N VAL K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 130 No H-bonds generated for 'chain 'K' and resid 128 through 130' Processing helix chain 'K' and resid 135 through 162 Processing helix chain 'K' and resid 165 through 170 removed outlier: 3.758A pdb=" N ARG K 170 " --> pdb=" O MET K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 187 Processing helix chain 'K' and resid 202 through 220 Processing helix chain 'K' and resid 221 through 223 No H-bonds generated for 'chain 'K' and resid 221 through 223' Processing helix chain 'K' and resid 230 through 256 Processing helix chain 'K' and resid 266 through 274 Processing helix chain 'K' and resid 275 through 281 Processing helix chain 'K' and resid 284 through 288 Processing helix chain 'K' and resid 290 through 312 removed outlier: 3.664A pdb=" N ALA K 294 " --> pdb=" O SER K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 315 No H-bonds generated for 'chain 'K' and resid 313 through 315' Processing helix chain 'K' and resid 326 through 350 removed outlier: 3.736A pdb=" N VAL K 348 " --> pdb=" O ILE K 344 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU K 349 " --> pdb=" O VAL K 345 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS K 350 " --> pdb=" O LEU K 346 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 389 Processing helix chain 'K' and resid 390 through 394 removed outlier: 3.513A pdb=" N TRP K 393 " --> pdb=" O LEU K 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 401 removed outlier: 3.877A pdb=" N TYR K 401 " --> pdb=" O VAL K 398 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 23 Processing helix chain 'L' and resid 50 through 69 removed outlier: 4.176A pdb=" N PHE L 65 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY L 66 " --> pdb=" O PHE L 62 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET L 69 " --> pdb=" O PHE L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 104 removed outlier: 3.840A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 132 removed outlier: 3.881A pdb=" N ALA L 131 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL L 132 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 162 removed outlier: 3.624A pdb=" N VAL L 150 " --> pdb=" O ILE L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 189 Processing helix chain 'L' and resid 204 through 228 removed outlier: 3.720A pdb=" N ILE L 213 " --> pdb=" O LEU L 209 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY L 214 " --> pdb=" O PHE L 210 " (cutoff:3.500A) Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 233 through 262 removed outlier: 3.641A pdb=" N CYS L 237 " --> pdb=" O GLY L 233 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU L 252 " --> pdb=" O ALA L 248 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU L 262 " --> pdb=" O SER L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 266 Processing helix chain 'L' and resid 268 through 275 Processing helix chain 'L' and resid 277 through 283 removed outlier: 3.702A pdb=" N VAL L 281 " --> pdb=" O LEU L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 321 removed outlier: 3.546A pdb=" N GLY L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR L 315 " --> pdb=" O TYR L 311 " (cutoff:3.500A) Proline residue: L 316 - end of helix Processing helix chain 'L' and resid 329 through 351 removed outlier: 3.592A pdb=" N LEU L 333 " --> pdb=" O GLY L 329 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU L 336 " --> pdb=" O ASN L 332 " (cutoff:3.500A) Proline residue: L 337 - end of helix Processing helix chain 'L' and resid 357 through 384 Processing helix chain 'L' and resid 398 through 402 removed outlier: 3.791A pdb=" N VAL L 401 " --> pdb=" O ASP L 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 23 Processing helix chain 'Q' and resid 47 through 69 Proline residue: Q 52 - end of helix removed outlier: 4.241A pdb=" N PHE Q 65 " --> pdb=" O ILE Q 61 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY Q 66 " --> pdb=" O PHE Q 62 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET Q 69 " --> pdb=" O PHE Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 104 removed outlier: 3.789A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR Q 95 " --> pdb=" O LEU Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 130 removed outlier: 3.623A pdb=" N MET Q 115 " --> pdb=" O GLY Q 111 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA Q 118 " --> pdb=" O ASN Q 114 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP Q 119 " --> pdb=" O MET Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 162 removed outlier: 3.665A pdb=" N VAL Q 150 " --> pdb=" O ILE Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 189 Processing helix chain 'Q' and resid 191 through 195 removed outlier: 3.501A pdb=" N ARG Q 195 " --> pdb=" O SER Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 204 through 228 Proline residue: Q 223 - end of helix Processing helix chain 'Q' and resid 233 through 262 removed outlier: 3.566A pdb=" N CYS Q 237 " --> pdb=" O GLY Q 233 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU Q 252 " --> pdb=" O ALA Q 248 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 266 Processing helix chain 'Q' and resid 268 through 275 Processing helix chain 'Q' and resid 277 through 283 Processing helix chain 'Q' and resid 292 through 321 removed outlier: 4.744A pdb=" N THR Q 315 " --> pdb=" O TYR Q 311 " (cutoff:3.500A) Proline residue: Q 316 - end of helix Processing helix chain 'Q' and resid 329 through 351 removed outlier: 5.305A pdb=" N LEU Q 336 " --> pdb=" O ASN Q 332 " (cutoff:3.500A) Proline residue: Q 337 - end of helix Processing helix chain 'Q' and resid 357 through 384 removed outlier: 3.571A pdb=" N GLN Q 361 " --> pdb=" O SER Q 357 " (cutoff:3.500A) Processing helix chain 'Q' and resid 398 through 402 removed outlier: 3.757A pdb=" N VAL Q 401 " --> pdb=" O ASP Q 398 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 91 removed outlier: 3.924A pdb=" N ALA P 91 " --> pdb=" O ARG P 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 114 Processing helix chain 'D' and resid 88 through 114 Processing helix chain 'C' and resid 379 through 390 removed outlier: 3.518A pdb=" N ARG C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 402 through 431 removed outlier: 3.578A pdb=" N LEU C 406 " --> pdb=" O SER C 402 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'C' and resid 436 through 455 Processing helix chain 'C' and resid 465 through 483 Processing helix chain 'C' and resid 485 through 507 removed outlier: 3.797A pdb=" N LEU C 499 " --> pdb=" O PHE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 516 removed outlier: 3.543A pdb=" N LEU C 512 " --> pdb=" O GLY C 509 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 513 " --> pdb=" O SER C 510 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 514 " --> pdb=" O PHE C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 547 removed outlier: 3.558A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 593 removed outlier: 3.613A pdb=" N ASN C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 608 Processing helix chain 'C' and resid 608 through 623 Processing helix chain 'C' and resid 660 through 667 removed outlier: 3.811A pdb=" N MET C 664 " --> pdb=" O PRO C 660 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 690 Processing helix chain 'C' and resid 691 through 695 Processing helix chain 'C' and resid 701 through 719 Processing helix chain 'C' and resid 727 through 738 Processing helix chain 'C' and resid 760 through 772 Processing helix chain 'C' and resid 776 through 781 Processing helix chain 'C' and resid 784 through 799 removed outlier: 3.794A pdb=" N LEU C 788 " --> pdb=" O PRO C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 811 Processing helix chain 'C' and resid 812 through 814 No H-bonds generated for 'chain 'C' and resid 812 through 814' Processing helix chain 'C' and resid 815 through 819 Processing helix chain 'C' and resid 822 through 827 Processing helix chain 'C' and resid 829 through 852 Processing helix chain 'C' and resid 855 through 857 No H-bonds generated for 'chain 'C' and resid 855 through 857' Processing helix chain 'C' and resid 858 through 865 Processing helix chain 'C' and resid 865 through 872 Processing helix chain 'C' and resid 872 through 878 removed outlier: 4.095A pdb=" N LEU C 876 " --> pdb=" O VAL C 872 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 887 Processing helix chain 'E' and resid 379 through 390 Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 394 through 399 Processing helix chain 'E' and resid 402 through 431 removed outlier: 3.627A pdb=" N LEU E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE E 414 " --> pdb=" O ILE E 410 " (cutoff:3.500A) Proline residue: E 419 - end of helix Processing helix chain 'E' and resid 436 through 455 Processing helix chain 'E' and resid 465 through 483 Processing helix chain 'E' and resid 485 through 507 removed outlier: 3.524A pdb=" N LEU E 499 " --> pdb=" O PHE E 495 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU E 503 " --> pdb=" O LEU E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 516 removed outlier: 3.654A pdb=" N LEU E 512 " --> pdb=" O GLY E 509 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL E 513 " --> pdb=" O SER E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 547 removed outlier: 3.597A pdb=" N LEU E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 593 removed outlier: 3.694A pdb=" N ASN E 593 " --> pdb=" O ARG E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 608 Processing helix chain 'E' and resid 608 through 623 Processing helix chain 'E' and resid 660 through 667 removed outlier: 3.714A pdb=" N MET E 664 " --> pdb=" O PRO E 660 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE E 665 " --> pdb=" O ILE E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 667 through 690 Processing helix chain 'E' and resid 691 through 695 removed outlier: 3.651A pdb=" N LYS E 695 " --> pdb=" O PRO E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 719 removed outlier: 3.671A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE E 719 " --> pdb=" O VAL E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 727 through 738 Processing helix chain 'E' and resid 760 through 772 Processing helix chain 'E' and resid 776 through 781 Processing helix chain 'E' and resid 784 through 799 removed outlier: 3.902A pdb=" N LEU E 788 " --> pdb=" O PRO E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 803 through 812 removed outlier: 3.536A pdb=" N ASP E 807 " --> pdb=" O ILE E 803 " (cutoff:3.500A) Processing helix chain 'E' and resid 813 through 814 No H-bonds generated for 'chain 'E' and resid 813 through 814' Processing helix chain 'E' and resid 815 through 819 Processing helix chain 'E' and resid 822 through 827 Processing helix chain 'E' and resid 829 through 852 Processing helix chain 'E' and resid 855 through 857 No H-bonds generated for 'chain 'E' and resid 855 through 857' Processing helix chain 'E' and resid 858 through 865 Processing helix chain 'E' and resid 865 through 872 removed outlier: 3.502A pdb=" N LEU E 869 " --> pdb=" O LEU E 865 " (cutoff:3.500A) Processing helix chain 'E' and resid 873 through 877 Processing helix chain 'E' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'K' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'L' and resid 24 through 25 Processing sheet with id=AA3, first strand: chain 'Q' and resid 24 through 25 Processing sheet with id=AA4, first strand: chain 'C' and resid 462 through 463 Processing sheet with id=AA5, first strand: chain 'C' and resid 739 through 742 removed outlier: 5.394A pdb=" N GLY C 742 " --> pdb=" O ILE C 753 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE C 753 " --> pdb=" O GLY C 742 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 462 through 463 Processing sheet with id=AA7, first strand: chain 'E' and resid 739 through 741 1244 hydrogen bonds defined for protein. 3646 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.37 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3120 1.33 - 1.45: 4630 1.45 - 1.57: 10424 1.57 - 1.69: 0 1.69 - 1.82: 190 Bond restraints: 18364 Sorted by residual: bond pdb=" N VAL K 223 " pdb=" CA VAL K 223 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.03e+01 bond pdb=" N VAL Q 57 " pdb=" CA VAL Q 57 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 9.10e+00 bond pdb=" N ARG K 229 " pdb=" CA ARG K 229 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.25e-02 6.40e+03 7.87e+00 bond pdb=" N TRP K 220 " pdb=" CA TRP K 220 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.04e-02 9.25e+03 7.63e+00 bond pdb=" N VAL Q 59 " pdb=" CA VAL Q 59 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.21e-02 6.83e+03 7.43e+00 ... (remaining 18359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 24369 1.66 - 3.31: 505 3.31 - 4.97: 55 4.97 - 6.62: 27 6.62 - 8.28: 4 Bond angle restraints: 24960 Sorted by residual: angle pdb=" C BTYR K 34 " pdb=" N ASP K 35 " pdb=" CA ASP K 35 " ideal model delta sigma weight residual 121.70 129.98 -8.28 1.80e+00 3.09e-01 2.12e+01 angle pdb=" N ILE Q 116 " pdb=" CA ILE Q 116 " pdb=" C ILE Q 116 " ideal model delta sigma weight residual 111.58 107.15 4.43 1.06e+00 8.90e-01 1.75e+01 angle pdb=" C PRO K 226 " pdb=" CA PRO K 226 " pdb=" CB PRO K 226 " ideal model delta sigma weight residual 113.06 106.68 6.38 1.59e+00 3.96e-01 1.61e+01 angle pdb=" N ASP Q 119 " pdb=" CA ASP Q 119 " pdb=" C ASP Q 119 " ideal model delta sigma weight residual 113.23 108.62 4.61 1.24e+00 6.50e-01 1.38e+01 angle pdb=" N ASN K 224 " pdb=" CA ASN K 224 " pdb=" C ASN K 224 " ideal model delta sigma weight residual 112.93 108.77 4.16 1.12e+00 7.97e-01 1.38e+01 ... (remaining 24955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 10375 21.24 - 42.47: 349 42.47 - 63.71: 73 63.71 - 84.94: 11 84.94 - 106.18: 21 Dihedral angle restraints: 10829 sinusoidal: 4238 harmonic: 6591 Sorted by residual: dihedral pdb=" C2 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" C4 NAG A 2 " pdb=" C5 NAG A 2 " ideal model delta sinusoidal sigma weight residual 53.78 -52.40 106.18 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" C4 NAG A 2 " pdb=" O4 NAG A 2 " ideal model delta sinusoidal sigma weight residual 175.11 68.97 106.14 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG F 2 " pdb=" C3 NAG F 2 " pdb=" C4 NAG F 2 " pdb=" O4 NAG F 2 " ideal model delta sinusoidal sigma weight residual 175.11 69.31 105.80 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 10826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1956 0.034 - 0.068: 744 0.068 - 0.102: 194 0.102 - 0.136: 79 0.136 - 0.170: 9 Chirality restraints: 2982 Sorted by residual: chirality pdb=" CA ILE Q 116 " pdb=" N ILE Q 116 " pdb=" C ILE Q 116 " pdb=" CB ILE Q 116 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA MET K 238 " pdb=" N MET K 238 " pdb=" C MET K 238 " pdb=" CB MET K 238 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA PHE Q 47 " pdb=" N PHE Q 47 " pdb=" C PHE Q 47 " pdb=" CB PHE Q 47 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 2979 not shown) Planarity restraints: 3034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR K 241 " -0.027 2.00e-02 2.50e+03 5.45e-02 2.98e+01 pdb=" C THR K 241 " 0.094 2.00e-02 2.50e+03 pdb=" O THR K 241 " -0.035 2.00e-02 2.50e+03 pdb=" N ATYR K 242 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ATYR K 242 " -0.026 2.00e-02 2.50e+03 5.32e-02 2.83e+01 pdb=" C ATYR K 242 " 0.092 2.00e-02 2.50e+03 pdb=" O ATYR K 242 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR K 243 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BTYR K 242 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C BTYR K 242 " 0.091 2.00e-02 2.50e+03 pdb=" O BTYR K 242 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR K 243 " -0.031 2.00e-02 2.50e+03 ... (remaining 3031 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1535 2.74 - 3.28: 18546 3.28 - 3.82: 31930 3.82 - 4.36: 37190 4.36 - 4.90: 65115 Nonbonded interactions: 154316 Sorted by model distance: nonbonded pdb=" OE1 GLU C 472 " pdb=" OH TYR C 486 " model vdw 2.205 3.040 nonbonded pdb=" O PHE K 28 " pdb=" OG1 THR K 32 " model vdw 2.212 3.040 nonbonded pdb=" OE1 GLU E 472 " pdb=" OH TYR E 486 " model vdw 2.213 3.040 nonbonded pdb=" OD2 ASP K 404 " pdb=" OH TYR L 205 " model vdw 2.255 3.040 nonbonded pdb=" OG SER L 171 " pdb=" O VAL L 281 " model vdw 2.276 3.040 ... (remaining 154311 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'L' selection = (chain 'Q' and (resid 1 through 26 or resid 48 through 409)) } 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=0.45 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: 8.060 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: 0.010 Extract box with map and model: 1.430 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.670 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 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 : 0.003 0.039 18368 Z= 0.195 Angle : 0.582 8.279 24972 Z= 0.353 Chirality : 0.041 0.170 2982 Planarity : 0.005 0.060 3032 Dihedral : 12.634 106.176 6599 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.45 % Favored : 98.50 % Rotamer: Outliers : 2.36 % Allowed : 4.45 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.17), residues: 2276 helix: 1.75 (0.13), residues: 1581 sheet: None (None), residues: 0 loop : 0.15 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 2 TYR 0.017 0.001 TYR Q 244 PHE 0.011 0.001 PHE L 129 TRP 0.010 0.001 TRP K 217 HIS 0.009 0.001 HIS Q 58 Details of bonding type rmsd covalent geometry : bond 0.00325 (18364) covalent geometry : angle 0.58208 (24960) hydrogen bonds : bond 0.13864 ( 1244) hydrogen bonds : angle 5.26000 ( 3646) link_BETA1-4 : bond 0.00444 ( 2) link_BETA1-4 : angle 1.20910 ( 6) link_NAG-ASN : bond 0.00115 ( 2) link_NAG-ASN : angle 0.66435 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 335 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 225 SER cc_start: 0.8495 (p) cc_final: 0.8142 (m) REVERT: K 235 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7635 (mtmt) REVERT: K 338 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7014 (pp) REVERT: K 382 LEU cc_start: 0.8001 (mt) cc_final: 0.7785 (tp) REVERT: K 383 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7661 (mp) REVERT: L 196 LYS cc_start: 0.7708 (mttp) cc_final: 0.7302 (mtpp) REVERT: L 305 MET cc_start: 0.8933 (ttp) cc_final: 0.8708 (ttm) REVERT: L 312 LYS cc_start: 0.8336 (tptt) cc_final: 0.8057 (tptt) REVERT: L 321 LYS cc_start: 0.8323 (mmtp) cc_final: 0.8089 (mmtt) REVERT: L 323 ARG cc_start: 0.8249 (mpt-90) cc_final: 0.7780 (mtm-85) REVERT: L 358 MET cc_start: 0.6785 (ttp) cc_final: 0.5966 (ttp) REVERT: L 378 MET cc_start: 0.7444 (mtp) cc_final: 0.7169 (mtp) REVERT: Q 378 MET cc_start: 0.8114 (mtm) cc_final: 0.7478 (tmm) REVERT: Q 404 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8092 (ttpt) REVERT: P 83 TYR cc_start: 0.5297 (OUTLIER) cc_final: 0.5096 (t80) REVERT: C 729 VAL cc_start: 0.7116 (OUTLIER) cc_final: 0.6914 (t) REVERT: E 624 ILE cc_start: 0.6676 (mt) cc_final: 0.6243 (tp) REVERT: E 785 LEU cc_start: 0.4034 (mt) cc_final: 0.3127 (mt) outliers start: 44 outliers final: 6 residues processed: 368 average time/residue: 0.4823 time to fit residues: 203.4690 Evaluate side-chains 305 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 293 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 235 LYS Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain E residue 826 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN L 92 GLN L 331 HIS Q 98 GLN Q 102 GLN Q 200 ASN Q 331 HIS C 377 GLN C 521 GLN C 630 GLN C 651 HIS C 683 GLN C 819 HIS E 377 GLN E 593 ASN E 651 HIS ** E 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 703 HIS ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 834 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.226136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.133619 restraints weight = 30059.107| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.87 r_work: 0.3290 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18368 Z= 0.132 Angle : 0.532 6.994 24972 Z= 0.274 Chirality : 0.041 0.199 2982 Planarity : 0.005 0.070 3032 Dihedral : 8.506 74.623 2685 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.41 % Favored : 98.55 % Rotamer: Outliers : 2.72 % Allowed : 10.47 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.17), residues: 2276 helix: 2.15 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : 0.24 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 589 TYR 0.018 0.001 TYR K 178 PHE 0.019 0.001 PHE E 659 TRP 0.011 0.001 TRP C 831 HIS 0.004 0.001 HIS Q 58 Details of bonding type rmsd covalent geometry : bond 0.00274 (18364) covalent geometry : angle 0.53136 (24960) hydrogen bonds : bond 0.04657 ( 1244) hydrogen bonds : angle 4.37090 ( 3646) link_BETA1-4 : bond 0.00544 ( 2) link_BETA1-4 : angle 1.09051 ( 6) link_NAG-ASN : bond 0.00169 ( 2) link_NAG-ASN : angle 0.69972 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 278 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 338 LEU cc_start: 0.7504 (tm) cc_final: 0.7031 (pp) REVERT: K 362 GLN cc_start: 0.6000 (OUTLIER) cc_final: 0.5602 (tp40) REVERT: K 382 LEU cc_start: 0.8140 (mt) cc_final: 0.7868 (tp) REVERT: K 383 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7548 (mp) REVERT: L 196 LYS cc_start: 0.7810 (mttp) cc_final: 0.7040 (tptp) REVERT: L 199 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7683 (tm-30) REVERT: L 312 LYS cc_start: 0.8403 (tptt) cc_final: 0.8138 (tptt) REVERT: L 321 LYS cc_start: 0.8469 (mmtp) cc_final: 0.8145 (mmtt) REVERT: L 323 ARG cc_start: 0.8682 (mpt-90) cc_final: 0.7773 (mtm-85) REVERT: L 358 MET cc_start: 0.6645 (ttp) cc_final: 0.5816 (ttp) REVERT: L 378 MET cc_start: 0.7856 (mtp) cc_final: 0.7596 (mtt) REVERT: Q 378 MET cc_start: 0.8363 (mtm) cc_final: 0.7409 (tmm) REVERT: Q 404 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8329 (ttpt) REVERT: P 83 TYR cc_start: 0.5056 (OUTLIER) cc_final: 0.4764 (t80) REVERT: C 435 MET cc_start: 0.4526 (mtm) cc_final: 0.3993 (ttp) REVERT: C 442 ILE cc_start: 0.6709 (mt) cc_final: 0.6480 (mt) REVERT: C 539 LYS cc_start: 0.7181 (mtmm) cc_final: 0.6746 (tptt) REVERT: C 587 MET cc_start: 0.5206 (mmp) cc_final: 0.5004 (mmp) REVERT: C 832 ARG cc_start: 0.6213 (OUTLIER) cc_final: 0.5934 (mmm-85) REVERT: E 617 MET cc_start: 0.6981 (mmm) cc_final: 0.6526 (mmm) outliers start: 51 outliers final: 20 residues processed: 305 average time/residue: 0.4612 time to fit residues: 161.6692 Evaluate side-chains 295 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 270 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 832 ARG Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 826 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 171 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 210 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 108 optimal weight: 0.1980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.225535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.133744 restraints weight = 26896.364| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.73 r_work: 0.3301 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18368 Z= 0.128 Angle : 0.506 7.463 24972 Z= 0.260 Chirality : 0.040 0.152 2982 Planarity : 0.004 0.048 3032 Dihedral : 6.651 55.447 2677 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.57 % Allowed : 11.88 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.17), residues: 2276 helix: 2.35 (0.13), residues: 1586 sheet: None (None), residues: 0 loop : 0.21 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 646 TYR 0.017 0.001 TYR K 178 PHE 0.025 0.001 PHE C 582 TRP 0.012 0.001 TRP E 492 HIS 0.005 0.001 HIS Q 58 Details of bonding type rmsd covalent geometry : bond 0.00275 (18364) covalent geometry : angle 0.50564 (24960) hydrogen bonds : bond 0.04402 ( 1244) hydrogen bonds : angle 4.25767 ( 3646) link_BETA1-4 : bond 0.00377 ( 2) link_BETA1-4 : angle 1.41571 ( 6) link_NAG-ASN : bond 0.00068 ( 2) link_NAG-ASN : angle 0.84999 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 338 LEU cc_start: 0.7496 (tm) cc_final: 0.7019 (pp) REVERT: K 362 GLN cc_start: 0.6018 (OUTLIER) cc_final: 0.5612 (tp40) REVERT: K 382 LEU cc_start: 0.8128 (mt) cc_final: 0.7868 (tp) REVERT: K 383 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7544 (mp) REVERT: L 196 LYS cc_start: 0.7866 (mttp) cc_final: 0.7091 (tptp) REVERT: L 199 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7613 (tm-30) REVERT: L 312 LYS cc_start: 0.8391 (tptt) cc_final: 0.8118 (tptt) REVERT: L 321 LYS cc_start: 0.8465 (mmtp) cc_final: 0.8139 (mmtt) REVERT: L 323 ARG cc_start: 0.8675 (mpt-90) cc_final: 0.7769 (mtm-85) REVERT: L 358 MET cc_start: 0.6553 (ttp) cc_final: 0.5484 (tmt) REVERT: L 378 MET cc_start: 0.7842 (mtp) cc_final: 0.7577 (mtt) REVERT: Q 378 MET cc_start: 0.8358 (mtm) cc_final: 0.7415 (tmm) REVERT: Q 404 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8295 (ttpt) REVERT: P 83 TYR cc_start: 0.5032 (OUTLIER) cc_final: 0.4726 (t80) REVERT: C 435 MET cc_start: 0.4527 (mtm) cc_final: 0.4147 (ttp) REVERT: C 442 ILE cc_start: 0.6728 (mt) cc_final: 0.6491 (mt) REVERT: C 539 LYS cc_start: 0.7119 (mtmm) cc_final: 0.6701 (tptt) REVERT: C 587 MET cc_start: 0.5134 (mmp) cc_final: 0.4927 (mmp) REVERT: C 757 LYS cc_start: 0.5639 (mmtp) cc_final: 0.5088 (mtpp) REVERT: E 435 MET cc_start: 0.5627 (OUTLIER) cc_final: 0.4719 (mtm) REVERT: E 617 MET cc_start: 0.6865 (mmm) cc_final: 0.6507 (mmm) outliers start: 48 outliers final: 23 residues processed: 303 average time/residue: 0.4887 time to fit residues: 169.6612 Evaluate side-chains 300 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 358 MET Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 615 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 140 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 215 optimal weight: 30.0000 chunk 171 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 102 GLN C 447 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.221825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.139657 restraints weight = 22545.047| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 4.62 r_work: 0.3215 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18368 Z= 0.209 Angle : 0.559 7.786 24972 Z= 0.289 Chirality : 0.042 0.148 2982 Planarity : 0.005 0.049 3032 Dihedral : 6.071 56.069 2673 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.98 % Allowed : 13.09 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.17), residues: 2276 helix: 2.18 (0.13), residues: 1584 sheet: None (None), residues: 0 loop : 0.15 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 234 TYR 0.019 0.002 TYR Q 244 PHE 0.018 0.002 PHE Q 257 TRP 0.012 0.001 TRP C 831 HIS 0.009 0.001 HIS Q 58 Details of bonding type rmsd covalent geometry : bond 0.00490 (18364) covalent geometry : angle 0.55855 (24960) hydrogen bonds : bond 0.05045 ( 1244) hydrogen bonds : angle 4.38346 ( 3646) link_BETA1-4 : bond 0.00584 ( 2) link_BETA1-4 : angle 1.88356 ( 6) link_NAG-ASN : bond 0.00054 ( 2) link_NAG-ASN : angle 0.99728 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 338 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7010 (pp) REVERT: K 362 GLN cc_start: 0.5986 (OUTLIER) cc_final: 0.5587 (tp40) REVERT: K 382 LEU cc_start: 0.8208 (mt) cc_final: 0.7887 (tp) REVERT: K 383 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7518 (mp) REVERT: L 196 LYS cc_start: 0.7910 (mttp) cc_final: 0.7070 (tptp) REVERT: L 199 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7779 (tm-30) REVERT: L 312 LYS cc_start: 0.8516 (tptt) cc_final: 0.8182 (tmtt) REVERT: L 321 LYS cc_start: 0.8469 (mmtp) cc_final: 0.8147 (mmtt) REVERT: L 323 ARG cc_start: 0.8733 (mpt-90) cc_final: 0.7780 (mtm-85) REVERT: Q 378 MET cc_start: 0.8431 (mtm) cc_final: 0.7393 (tmm) REVERT: Q 404 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8283 (tmtt) REVERT: P 83 TYR cc_start: 0.4939 (OUTLIER) cc_final: 0.4656 (t80) REVERT: C 412 ILE cc_start: 0.7342 (mm) cc_final: 0.7138 (mp) REVERT: C 442 ILE cc_start: 0.6749 (mt) cc_final: 0.6546 (mt) REVERT: C 537 PHE cc_start: 0.6863 (m-80) cc_final: 0.6557 (m-80) REVERT: C 539 LYS cc_start: 0.7098 (mtmm) cc_final: 0.6640 (tptt) REVERT: C 586 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.5679 (mmm) REVERT: C 587 MET cc_start: 0.5168 (mmp) cc_final: 0.4965 (mmp) REVERT: C 712 MET cc_start: 0.4520 (mmm) cc_final: 0.4310 (tpt) REVERT: C 757 LYS cc_start: 0.5574 (mmtp) cc_final: 0.5013 (mtpp) REVERT: E 435 MET cc_start: 0.5596 (OUTLIER) cc_final: 0.4828 (mtm) REVERT: E 587 MET cc_start: 0.4833 (OUTLIER) cc_final: 0.3987 (mmm) REVERT: E 617 MET cc_start: 0.6822 (mmm) cc_final: 0.6528 (mmm) outliers start: 56 outliers final: 30 residues processed: 306 average time/residue: 0.4759 time to fit residues: 167.1547 Evaluate side-chains 301 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 263 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 358 MET Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 404 LYS Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 832 ARG Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 587 MET Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 841 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 161 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.0070 chunk 172 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 224 ASN Q 102 GLN C 447 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.221667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.128935 restraints weight = 29158.952| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.81 r_work: 0.3236 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18368 Z= 0.184 Angle : 0.553 8.734 24972 Z= 0.284 Chirality : 0.042 0.218 2982 Planarity : 0.005 0.044 3032 Dihedral : 6.035 55.369 2673 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.04 % Allowed : 13.82 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.17), residues: 2276 helix: 2.17 (0.13), residues: 1576 sheet: None (None), residues: 0 loop : 0.08 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 646 TYR 0.018 0.002 TYR K 178 PHE 0.020 0.002 PHE Q 257 TRP 0.011 0.001 TRP C 831 HIS 0.007 0.001 HIS Q 58 Details of bonding type rmsd covalent geometry : bond 0.00426 (18364) covalent geometry : angle 0.55172 (24960) hydrogen bonds : bond 0.04868 ( 1244) hydrogen bonds : angle 4.38294 ( 3646) link_BETA1-4 : bond 0.00375 ( 2) link_BETA1-4 : angle 1.95858 ( 6) link_NAG-ASN : bond 0.00022 ( 2) link_NAG-ASN : angle 1.04128 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 269 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 338 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7085 (pp) REVERT: K 362 GLN cc_start: 0.6049 (OUTLIER) cc_final: 0.5615 (tp40) REVERT: K 382 LEU cc_start: 0.8219 (mt) cc_final: 0.7925 (tp) REVERT: K 383 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7519 (mp) REVERT: L 196 LYS cc_start: 0.7977 (mttp) cc_final: 0.7160 (tptp) REVERT: L 199 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7709 (tm-30) REVERT: L 312 LYS cc_start: 0.8509 (tptt) cc_final: 0.8149 (tmtt) REVERT: L 321 LYS cc_start: 0.8472 (mmtp) cc_final: 0.8174 (mmtt) REVERT: L 323 ARG cc_start: 0.8704 (mpt-90) cc_final: 0.7792 (mtm-85) REVERT: Q 378 MET cc_start: 0.8386 (mtm) cc_final: 0.7402 (tmm) REVERT: Q 404 LYS cc_start: 0.8951 (tmtm) cc_final: 0.8233 (tmtt) REVERT: P 83 TYR cc_start: 0.5083 (OUTLIER) cc_final: 0.4765 (t80) REVERT: C 442 ILE cc_start: 0.6764 (mt) cc_final: 0.6530 (mt) REVERT: C 473 GLU cc_start: 0.5705 (OUTLIER) cc_final: 0.5329 (tm-30) REVERT: C 481 THR cc_start: 0.5549 (m) cc_final: 0.5335 (p) REVERT: C 539 LYS cc_start: 0.7170 (mtmm) cc_final: 0.6735 (tptt) REVERT: C 587 MET cc_start: 0.5208 (mmp) cc_final: 0.4984 (mmp) REVERT: C 757 LYS cc_start: 0.5570 (mmtp) cc_final: 0.5022 (mtpp) REVERT: E 435 MET cc_start: 0.5623 (OUTLIER) cc_final: 0.4560 (mtm) REVERT: E 587 MET cc_start: 0.4902 (OUTLIER) cc_final: 0.4008 (mmm) REVERT: E 617 MET cc_start: 0.6795 (mmm) cc_final: 0.6466 (mmm) outliers start: 57 outliers final: 32 residues processed: 299 average time/residue: 0.4968 time to fit residues: 169.7556 Evaluate side-chains 298 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 259 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 294 PHE Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 358 MET Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 587 MET Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 841 ILE Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 GLN Q 102 GLN C 447 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 840 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.221612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.129350 restraints weight = 30922.186| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.12 r_work: 0.3231 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18368 Z= 0.172 Angle : 0.539 9.462 24972 Z= 0.278 Chirality : 0.041 0.138 2982 Planarity : 0.005 0.052 3032 Dihedral : 5.812 58.719 2669 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.35 % Allowed : 13.98 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.17), residues: 2276 helix: 2.19 (0.13), residues: 1581 sheet: None (None), residues: 0 loop : 0.04 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 234 TYR 0.018 0.002 TYR K 178 PHE 0.029 0.002 PHE E 591 TRP 0.012 0.001 TRP C 831 HIS 0.006 0.001 HIS Q 58 Details of bonding type rmsd covalent geometry : bond 0.00396 (18364) covalent geometry : angle 0.53791 (24960) hydrogen bonds : bond 0.04768 ( 1244) hydrogen bonds : angle 4.36524 ( 3646) link_BETA1-4 : bond 0.00399 ( 2) link_BETA1-4 : angle 1.93026 ( 6) link_NAG-ASN : bond 0.00014 ( 2) link_NAG-ASN : angle 1.04523 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 268 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 338 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7048 (pp) REVERT: K 362 GLN cc_start: 0.6022 (OUTLIER) cc_final: 0.5607 (tp40) REVERT: K 382 LEU cc_start: 0.8197 (mt) cc_final: 0.7811 (tp) REVERT: K 383 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7526 (mp) REVERT: L 196 LYS cc_start: 0.7999 (mttp) cc_final: 0.7183 (tptp) REVERT: L 199 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7667 (tm-30) REVERT: L 312 LYS cc_start: 0.8502 (tptt) cc_final: 0.8133 (tmtt) REVERT: L 321 LYS cc_start: 0.8485 (mmtp) cc_final: 0.8181 (mmtt) REVERT: L 323 ARG cc_start: 0.8711 (mpt-90) cc_final: 0.7780 (mtm-85) REVERT: Q 378 MET cc_start: 0.8397 (mtm) cc_final: 0.7382 (tmm) REVERT: Q 404 LYS cc_start: 0.8950 (tmtm) cc_final: 0.8232 (tmtt) REVERT: P 83 TYR cc_start: 0.4978 (OUTLIER) cc_final: 0.4687 (t80) REVERT: C 412 ILE cc_start: 0.7389 (mm) cc_final: 0.7179 (mp) REVERT: C 442 ILE cc_start: 0.6777 (mt) cc_final: 0.6542 (mt) REVERT: C 473 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.5278 (tm-30) REVERT: C 481 THR cc_start: 0.5506 (m) cc_final: 0.5296 (p) REVERT: C 539 LYS cc_start: 0.7200 (mtmm) cc_final: 0.6785 (tptt) REVERT: C 712 MET cc_start: 0.4377 (OUTLIER) cc_final: 0.4034 (tpt) REVERT: C 757 LYS cc_start: 0.5583 (mmtp) cc_final: 0.5043 (mtpp) REVERT: E 435 MET cc_start: 0.5552 (OUTLIER) cc_final: 0.4337 (mtm) REVERT: E 587 MET cc_start: 0.5054 (OUTLIER) cc_final: 0.4124 (mmm) REVERT: E 617 MET cc_start: 0.6759 (mmm) cc_final: 0.6427 (mmm) outliers start: 63 outliers final: 33 residues processed: 303 average time/residue: 0.4970 time to fit residues: 172.4710 Evaluate side-chains 306 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 265 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 587 MET Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 828 VAL Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 133 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 GLN Q 102 GLN C 447 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 804 GLN E 840 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.223956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.132547 restraints weight = 29946.035| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.19 r_work: 0.3261 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18368 Z= 0.128 Angle : 0.515 9.913 24972 Z= 0.265 Chirality : 0.040 0.143 2982 Planarity : 0.004 0.049 3032 Dihedral : 5.766 57.370 2669 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.93 % Allowed : 14.76 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.17), residues: 2276 helix: 2.27 (0.13), residues: 1592 sheet: None (None), residues: 0 loop : 0.13 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 646 TYR 0.017 0.001 TYR K 178 PHE 0.026 0.001 PHE E 591 TRP 0.012 0.001 TRP C 831 HIS 0.004 0.001 HIS K 329 Details of bonding type rmsd covalent geometry : bond 0.00275 (18364) covalent geometry : angle 0.51420 (24960) hydrogen bonds : bond 0.04288 ( 1244) hydrogen bonds : angle 4.28431 ( 3646) link_BETA1-4 : bond 0.00395 ( 2) link_BETA1-4 : angle 1.79182 ( 6) link_NAG-ASN : bond 0.00082 ( 2) link_NAG-ASN : angle 0.97030 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7810 (mtt) REVERT: K 338 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6954 (pp) REVERT: K 362 GLN cc_start: 0.5990 (OUTLIER) cc_final: 0.5586 (tp40) REVERT: K 382 LEU cc_start: 0.8145 (mt) cc_final: 0.7800 (tp) REVERT: K 383 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7560 (mp) REVERT: L 196 LYS cc_start: 0.8003 (mttp) cc_final: 0.7209 (tptp) REVERT: L 199 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7661 (tm-30) REVERT: L 312 LYS cc_start: 0.8455 (tptt) cc_final: 0.8125 (tptt) REVERT: L 321 LYS cc_start: 0.8496 (mmtp) cc_final: 0.8188 (mmtt) REVERT: L 323 ARG cc_start: 0.8722 (mpt-90) cc_final: 0.7777 (mtm-85) REVERT: Q 378 MET cc_start: 0.8366 (mtm) cc_final: 0.7305 (tmm) REVERT: Q 404 LYS cc_start: 0.8928 (tmtm) cc_final: 0.8198 (tmtt) REVERT: P 83 TYR cc_start: 0.4956 (OUTLIER) cc_final: 0.4663 (t80) REVERT: C 442 ILE cc_start: 0.6683 (mt) cc_final: 0.6451 (mt) REVERT: C 473 GLU cc_start: 0.5578 (OUTLIER) cc_final: 0.5261 (tm-30) REVERT: C 481 THR cc_start: 0.5493 (m) cc_final: 0.5286 (p) REVERT: C 539 LYS cc_start: 0.7128 (mtmm) cc_final: 0.6753 (tmtt) REVERT: C 712 MET cc_start: 0.4214 (OUTLIER) cc_final: 0.3964 (tpt) REVERT: C 757 LYS cc_start: 0.5487 (mmtp) cc_final: 0.4881 (mtpp) REVERT: E 435 MET cc_start: 0.5458 (mtm) cc_final: 0.4202 (mtm) REVERT: E 587 MET cc_start: 0.4871 (OUTLIER) cc_final: 0.4012 (mmm) REVERT: E 617 MET cc_start: 0.6683 (mmm) cc_final: 0.6426 (mmm) REVERT: E 624 ILE cc_start: 0.5177 (mt) cc_final: 0.4861 (pp) REVERT: E 791 ILE cc_start: 0.5318 (mm) cc_final: 0.5105 (mm) outliers start: 55 outliers final: 26 residues processed: 303 average time/residue: 0.4774 time to fit residues: 165.3229 Evaluate side-chains 296 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 238 MET Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 155 ASN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 587 MET Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 828 VAL Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 95 optimal weight: 0.9980 chunk 143 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 180 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 214 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 58 HIS Q 102 GLN ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.225041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.142732 restraints weight = 24728.610| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.42 r_work: 0.3279 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18368 Z= 0.115 Angle : 0.504 10.833 24972 Z= 0.259 Chirality : 0.039 0.180 2982 Planarity : 0.004 0.050 3032 Dihedral : 5.571 56.270 2665 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.57 % Allowed : 15.29 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.17), residues: 2276 helix: 2.38 (0.13), residues: 1584 sheet: None (None), residues: 0 loop : 0.21 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 646 TYR 0.016 0.001 TYR K 178 PHE 0.024 0.001 PHE E 591 TRP 0.013 0.001 TRP K 16 HIS 0.004 0.001 HIS C 734 Details of bonding type rmsd covalent geometry : bond 0.00240 (18364) covalent geometry : angle 0.50351 (24960) hydrogen bonds : bond 0.04087 ( 1244) hydrogen bonds : angle 4.23123 ( 3646) link_BETA1-4 : bond 0.00465 ( 2) link_BETA1-4 : angle 1.69582 ( 6) link_NAG-ASN : bond 0.00115 ( 2) link_NAG-ASN : angle 0.89722 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 260 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7764 (mtt) REVERT: K 338 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6896 (pp) REVERT: K 362 GLN cc_start: 0.6012 (OUTLIER) cc_final: 0.5603 (tp40) REVERT: K 382 LEU cc_start: 0.8095 (mt) cc_final: 0.7750 (tp) REVERT: K 383 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7424 (mp) REVERT: L 196 LYS cc_start: 0.7972 (mttp) cc_final: 0.7162 (tptp) REVERT: L 199 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7606 (tm-30) REVERT: L 312 LYS cc_start: 0.8391 (tptt) cc_final: 0.8063 (tptt) REVERT: L 321 LYS cc_start: 0.8452 (mmtp) cc_final: 0.8144 (mmtt) REVERT: L 323 ARG cc_start: 0.8706 (mpt-90) cc_final: 0.7727 (mtm-85) REVERT: L 358 MET cc_start: 0.6973 (ttm) cc_final: 0.5757 (tmt) REVERT: Q 378 MET cc_start: 0.8328 (mtm) cc_final: 0.7264 (tmm) REVERT: Q 404 LYS cc_start: 0.8904 (tmtm) cc_final: 0.8099 (tmtt) REVERT: P 83 TYR cc_start: 0.4952 (OUTLIER) cc_final: 0.4671 (t80) REVERT: C 473 GLU cc_start: 0.5430 (OUTLIER) cc_final: 0.5161 (tm-30) REVERT: C 539 LYS cc_start: 0.7039 (mtmm) cc_final: 0.6589 (tptt) REVERT: C 586 MET cc_start: 0.5705 (mmm) cc_final: 0.5334 (mmt) REVERT: C 712 MET cc_start: 0.4108 (OUTLIER) cc_final: 0.3761 (tpt) REVERT: C 741 MET cc_start: 0.4345 (mmm) cc_final: 0.2807 (tmm) REVERT: E 435 MET cc_start: 0.5371 (mtm) cc_final: 0.4211 (mtm) REVERT: E 617 MET cc_start: 0.6697 (mmm) cc_final: 0.6462 (mmm) outliers start: 48 outliers final: 26 residues processed: 288 average time/residue: 0.4673 time to fit residues: 154.3625 Evaluate side-chains 287 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 238 MET Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 155 ASN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 99 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 93 optimal weight: 0.0770 chunk 198 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 102 GLN C 447 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 593 ASN ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.220494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.129076 restraints weight = 33725.362| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.36 r_work: 0.3192 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18368 Z= 0.210 Angle : 0.583 9.362 24972 Z= 0.300 Chirality : 0.043 0.171 2982 Planarity : 0.005 0.050 3032 Dihedral : 5.671 56.141 2665 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.51 % Allowed : 15.76 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.17), residues: 2276 helix: 2.10 (0.13), residues: 1583 sheet: None (None), residues: 0 loop : 0.04 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 234 TYR 0.019 0.002 TYR Q 180 PHE 0.026 0.002 PHE E 591 TRP 0.010 0.001 TRP E 492 HIS 0.005 0.001 HIS Q 154 Details of bonding type rmsd covalent geometry : bond 0.00490 (18364) covalent geometry : angle 0.58290 (24960) hydrogen bonds : bond 0.05065 ( 1244) hydrogen bonds : angle 4.44172 ( 3646) link_BETA1-4 : bond 0.00366 ( 2) link_BETA1-4 : angle 1.52497 ( 6) link_NAG-ASN : bond 0.00016 ( 2) link_NAG-ASN : angle 0.96040 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 255 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7940 (mtt) REVERT: K 338 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7007 (pp) REVERT: K 362 GLN cc_start: 0.6044 (OUTLIER) cc_final: 0.5622 (tp40) REVERT: K 382 LEU cc_start: 0.8235 (mt) cc_final: 0.7864 (tp) REVERT: K 383 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7475 (mp) REVERT: L 196 LYS cc_start: 0.8025 (mttp) cc_final: 0.7337 (mtpp) REVERT: L 199 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7779 (tm-30) REVERT: L 312 LYS cc_start: 0.8538 (tptt) cc_final: 0.8167 (tmtt) REVERT: L 321 LYS cc_start: 0.8497 (mmtp) cc_final: 0.8208 (mmtt) REVERT: L 323 ARG cc_start: 0.8742 (mpt-90) cc_final: 0.7788 (mtm-85) REVERT: Q 378 MET cc_start: 0.8431 (mtm) cc_final: 0.7391 (tmm) REVERT: Q 404 LYS cc_start: 0.8971 (tmtm) cc_final: 0.8259 (tmtt) REVERT: P 83 TYR cc_start: 0.4973 (OUTLIER) cc_final: 0.4688 (t80) REVERT: C 442 ILE cc_start: 0.6716 (mt) cc_final: 0.6477 (mt) REVERT: C 473 GLU cc_start: 0.5591 (OUTLIER) cc_final: 0.5286 (tm-30) REVERT: C 537 PHE cc_start: 0.6852 (m-80) cc_final: 0.6515 (m-80) REVERT: C 539 LYS cc_start: 0.7220 (mtmm) cc_final: 0.6789 (tptt) REVERT: C 712 MET cc_start: 0.4354 (OUTLIER) cc_final: 0.4078 (tpt) REVERT: E 435 MET cc_start: 0.5411 (mtm) cc_final: 0.4155 (mtm) REVERT: E 617 MET cc_start: 0.6748 (mmm) cc_final: 0.6508 (mmm) outliers start: 47 outliers final: 29 residues processed: 286 average time/residue: 0.4913 time to fit residues: 161.1166 Evaluate side-chains 287 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 238 MET Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 47 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 211 optimal weight: 0.4980 chunk 159 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 102 GLN ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.224509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.133461 restraints weight = 33334.178| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.35 r_work: 0.3251 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18368 Z= 0.118 Angle : 0.516 11.061 24972 Z= 0.263 Chirality : 0.039 0.152 2982 Planarity : 0.004 0.047 3032 Dihedral : 5.470 54.464 2665 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.78 % Allowed : 16.70 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.18), residues: 2276 helix: 2.28 (0.13), residues: 1595 sheet: None (None), residues: 0 loop : 0.14 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 589 TYR 0.016 0.001 TYR K 178 PHE 0.022 0.001 PHE E 591 TRP 0.013 0.001 TRP K 16 HIS 0.004 0.001 HIS K 329 Details of bonding type rmsd covalent geometry : bond 0.00252 (18364) covalent geometry : angle 0.51505 (24960) hydrogen bonds : bond 0.04145 ( 1244) hydrogen bonds : angle 4.27237 ( 3646) link_BETA1-4 : bond 0.00266 ( 2) link_BETA1-4 : angle 1.42264 ( 6) link_NAG-ASN : bond 0.00082 ( 2) link_NAG-ASN : angle 0.93248 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 265 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7890 (mtt) REVERT: K 338 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6946 (pp) REVERT: K 362 GLN cc_start: 0.6060 (OUTLIER) cc_final: 0.5631 (tp40) REVERT: K 382 LEU cc_start: 0.8195 (mt) cc_final: 0.7857 (tp) REVERT: K 383 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7447 (mp) REVERT: L 196 LYS cc_start: 0.8049 (mttp) cc_final: 0.7258 (tptp) REVERT: L 199 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7743 (tm-30) REVERT: L 312 LYS cc_start: 0.8463 (tptt) cc_final: 0.8145 (tptt) REVERT: L 321 LYS cc_start: 0.8490 (mmtp) cc_final: 0.8199 (mmtt) REVERT: L 323 ARG cc_start: 0.8731 (mpt-90) cc_final: 0.7762 (mtm-85) REVERT: Q 358 MET cc_start: 0.8845 (ptm) cc_final: 0.8518 (ptp) REVERT: Q 378 MET cc_start: 0.8394 (mtm) cc_final: 0.7333 (tmm) REVERT: Q 404 LYS cc_start: 0.8948 (tmtm) cc_final: 0.8165 (tmtt) REVERT: P 83 TYR cc_start: 0.4962 (OUTLIER) cc_final: 0.4697 (t80) REVERT: C 388 ARG cc_start: 0.7139 (ttp-170) cc_final: 0.6883 (ttp-170) REVERT: C 473 GLU cc_start: 0.5558 (OUTLIER) cc_final: 0.5267 (tm-30) REVERT: C 539 LYS cc_start: 0.7165 (mtmm) cc_final: 0.6747 (tptt) REVERT: C 586 MET cc_start: 0.5735 (mmm) cc_final: 0.5394 (mmt) REVERT: C 712 MET cc_start: 0.4259 (OUTLIER) cc_final: 0.3912 (tpt) REVERT: E 435 MET cc_start: 0.5303 (mtm) cc_final: 0.4002 (mtm) REVERT: E 617 MET cc_start: 0.6706 (mmm) cc_final: 0.6486 (mmm) REVERT: E 624 ILE cc_start: 0.5134 (mt) cc_final: 0.4506 (tp) outliers start: 33 outliers final: 24 residues processed: 286 average time/residue: 0.4750 time to fit residues: 155.9928 Evaluate side-chains 286 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 238 MET Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 93 optimal weight: 0.0970 chunk 48 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 174 optimal weight: 0.7980 chunk 153 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 124 optimal weight: 40.0000 chunk 59 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 102 GLN ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 840 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.225913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.134938 restraints weight = 29736.108| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.89 r_work: 0.3313 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18368 Z= 0.113 Angle : 0.509 10.157 24972 Z= 0.259 Chirality : 0.040 0.247 2982 Planarity : 0.004 0.046 3032 Dihedral : 5.379 57.746 2665 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.94 % Allowed : 16.70 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.18), residues: 2276 helix: 2.35 (0.13), residues: 1599 sheet: None (None), residues: 0 loop : 0.17 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 589 TYR 0.016 0.001 TYR K 178 PHE 0.023 0.001 PHE E 591 TRP 0.013 0.001 TRP K 16 HIS 0.004 0.001 HIS K 329 Details of bonding type rmsd covalent geometry : bond 0.00236 (18364) covalent geometry : angle 0.50804 (24960) hydrogen bonds : bond 0.03987 ( 1244) hydrogen bonds : angle 4.22526 ( 3646) link_BETA1-4 : bond 0.00310 ( 2) link_BETA1-4 : angle 1.33923 ( 6) link_NAG-ASN : bond 0.00112 ( 2) link_NAG-ASN : angle 0.89478 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9453.65 seconds wall clock time: 161 minutes 4.73 seconds (9664.73 seconds total)