Starting phenix.real_space_refine on Sat Jul 4 02:31:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8crt_26958/07_2026/8crt_26958.cif Found real_map, /net/cci-nas-00/data/ceres_data/8crt_26958/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8crt_26958/07_2026/8crt_26958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8crt_26958/07_2026/8crt_26958.map" model { file = "/net/cci-nas-00/data/ceres_data/8crt_26958/07_2026/8crt_26958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8crt_26958/07_2026/8crt_26958.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8crt_26958/07_2026/8crt_26958.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8crt_26958/07_2026/8crt_26958.cif" } 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-6108/lib/python3.11/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 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 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: 3.92, per 1000 atoms: 0.22 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: 1.26 Conformation dependent library (CDL) restraints added in 891.0 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: 0.35 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: 2.46 Time building geometry restraints manager: 1.69 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 - 17.59: 10056 17.59 - 35.19: 444 35.19 - 52.78: 98 52.78 - 70.37: 24 70.37 - 87.96: 11 Dihedral angle restraints: 10633 sinusoidal: 4042 harmonic: 6591 Sorted by residual: dihedral pdb=" CA BTYR K 34 " pdb=" C BTYR K 34 " pdb=" N ASP K 35 " pdb=" CA ASP K 35 " ideal model delta harmonic sigma weight residual -180.00 -163.35 -16.65 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CB GLU Q 262 " pdb=" CG GLU Q 262 " pdb=" CD GLU Q 262 " pdb=" OE1 GLU Q 262 " ideal model delta sinusoidal sigma weight residual 0.00 87.96 -87.96 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU L 156 " pdb=" CG GLU L 156 " pdb=" CD GLU L 156 " pdb=" OE1 GLU L 156 " ideal model delta sinusoidal sigma weight residual 0.00 -85.05 85.05 1 3.00e+01 1.11e-03 9.75e+00 ... (remaining 10630 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: 6.310 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: 0.960 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 14.530 Find NCS groups from input model: 0.270 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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 : 11.341 87.962 6403 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/Z covalent geometry : bond 0.00325 / 0.19 (18364) covalent geometry : angle 0.58208 / 0.35 (24960) hydrogen bonds : bond 0.13864 / 9.39 ( 1244) hydrogen bonds : angle 5.26000 / 3.93 ( 3646) link_BETA1-4 : bond 0.00444 / 0.23 ( 2) link_BETA1-4 : angle 1.20910 / 0.68 ( 6) link_NAG-ASN : bond 0.00115 / 0.06 ( 2) link_NAG-ASN : angle 0.66435 / 0.37 ( 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 : 0.739 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: 0.5047 time to fit residues: 214.1598 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 : 0.688 ------------------------------------------------------------------------------- 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... 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 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4337 r_free = 0.4337 target = 0.225996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.133477 restraints weight = 30060.869| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.88 r_work: 0.3291 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1199 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= 0.132 Angle : 0.518 6.972 24972 Z= 0.270 Chirality : 0.040 0.156 2982 Planarity : 0.005 0.070 3032 Dihedral : 5.400 58.735 2489 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.41 % Favored : 98.55 % Rotamer: Outliers : 2.62 % Allowed : 10.58 % 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: 2.35 (0.17), residues: 2276 helix: 2.12 (0.13), residues: 1599 sheet: None (None), residues: 0 loop : 0.28 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 589 TYR 0.018 0.001 TYR K 178 PHE 0.017 0.001 PHE E 659 TRP 0.011 0.001 TRP C 831 HIS 0.005 0.001 HIS Q 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (18364) covalent geometry : angle 0.51822 / 0.27 (24960) hydrogen bonds : bond 0.04717 / 3.13 ( 1244) hydrogen bonds : angle 4.37443 / 3.24 ( 3646) link_BETA1-4 : bond 0.00707 / 0.37 ( 2) link_BETA1-4 : angle 0.98813 / 0.57 ( 6) link_NAG-ASN : bond 0.00148 / 0.07 ( 2) link_NAG-ASN : angle 0.70677 / 0.41 ( 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 330 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 281 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 338 LEU cc_start: 0.7516 (tm) cc_final: 0.7046 (pp) REVERT: K 362 GLN cc_start: 0.6001 (OUTLIER) cc_final: 0.5600 (tp40) REVERT: K 382 LEU cc_start: 0.8130 (mt) cc_final: 0.7864 (tp) REVERT: K 383 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7544 (mp) REVERT: L 196 LYS cc_start: 0.7816 (mttp) cc_final: 0.7054 (tptp) REVERT: L 199 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7687 (tm-30) REVERT: L 312 LYS cc_start: 0.8400 (tptt) cc_final: 0.8132 (tptt) REVERT: L 321 LYS cc_start: 0.8465 (mmtp) cc_final: 0.8141 (mmtt) REVERT: L 323 ARG cc_start: 0.8671 (mpt-90) cc_final: 0.7767 (mtm-85) REVERT: L 358 MET cc_start: 0.6638 (ttp) cc_final: 0.5808 (ttp) REVERT: L 378 MET cc_start: 0.7850 (mtp) cc_final: 0.7588 (mtt) REVERT: Q 378 MET cc_start: 0.8357 (mtm) cc_final: 0.7400 (tmm) REVERT: Q 404 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8321 (ttpt) REVERT: P 83 TYR cc_start: 0.5038 (OUTLIER) cc_final: 0.4746 (t80) REVERT: C 435 MET cc_start: 0.4485 (mtm) cc_final: 0.3949 (ttp) REVERT: C 442 ILE cc_start: 0.6703 (mt) cc_final: 0.6482 (mt) REVERT: C 539 LYS cc_start: 0.7181 (mtmm) cc_final: 0.6736 (tptt) REVERT: C 587 MET cc_start: 0.5160 (mmp) cc_final: 0.4924 (mmp) REVERT: C 695 LYS cc_start: 0.7483 (mmtt) cc_final: 0.6723 (tmtt) REVERT: C 832 ARG cc_start: 0.6189 (OUTLIER) cc_final: 0.5900 (mmm-85) REVERT: E 617 MET cc_start: 0.7003 (mmm) cc_final: 0.6509 (mmm) outliers start: 49 outliers final: 19 residues processed: 306 average time/residue: 0.5069 time to fit residues: 178.9416 Evaluate side-chains 301 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 277 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 68 ASN 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: 5.9990 chunk 200 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 158 optimal weight: 0.0670 chunk 211 optimal weight: 5.9990 chunk 168 optimal weight: 0.7980 chunk 199 optimal weight: 5.9990 chunk 108 optimal weight: 0.3980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 102 GLN Q 175 HIS 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 = 0.4339 r_free = 0.4339 target = 0.226207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.139396 restraints weight = 27042.450| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.54 r_work: 0.3258 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18368 Z= 0.118 Angle : 0.488 6.961 24972 Z= 0.253 Chirality : 0.039 0.140 2982 Planarity : 0.004 0.048 3032 Dihedral : 5.166 55.662 2481 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.46 % Allowed : 11.99 % 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: 2.61 (0.17), residues: 2276 helix: 2.38 (0.13), residues: 1586 sheet: None (None), residues: 0 loop : 0.23 (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 0.022 0.001 PHE C 582 TRP 0.011 0.001 TRP C 831 HIS 0.004 0.001 HIS Q 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (18364) covalent geometry : angle 0.48791 / 0.25 (24960) hydrogen bonds : bond 0.04274 / 2.84 ( 1244) hydrogen bonds : angle 4.24358 / 3.14 ( 3646) link_BETA1-4 : bond 0.00367 / 0.18 ( 2) link_BETA1-4 : angle 0.95745 / 0.54 ( 6) link_NAG-ASN : bond 0.00086 / 0.04 ( 2) link_NAG-ASN : angle 0.70901 / 0.40 ( 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 322 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 276 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 338 LEU cc_start: 0.7342 (tm) cc_final: 0.6828 (pp) REVERT: K 362 GLN cc_start: 0.5909 (OUTLIER) cc_final: 0.5532 (tp40) REVERT: K 382 LEU cc_start: 0.8093 (mt) cc_final: 0.7796 (tp) REVERT: K 383 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7409 (mp) REVERT: L 196 LYS cc_start: 0.7792 (mttp) cc_final: 0.6986 (tptp) REVERT: L 199 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7658 (tm-30) REVERT: L 312 LYS cc_start: 0.8370 (tptt) cc_final: 0.8038 (tptt) REVERT: L 321 LYS cc_start: 0.8409 (mmtp) cc_final: 0.8057 (mmtt) REVERT: L 323 ARG cc_start: 0.8704 (mpt-90) cc_final: 0.7684 (mtm-85) REVERT: L 358 MET cc_start: 0.6624 (ttp) cc_final: 0.5442 (tmt) REVERT: L 378 MET cc_start: 0.7783 (mtp) cc_final: 0.7496 (mtt) REVERT: Q 378 MET cc_start: 0.8326 (mtm) cc_final: 0.7237 (tmm) REVERT: Q 404 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8304 (ttpt) REVERT: P 83 TYR cc_start: 0.4899 (OUTLIER) cc_final: 0.4627 (t80) REVERT: C 435 MET cc_start: 0.4369 (mtm) cc_final: 0.3868 (ttp) REVERT: C 539 LYS cc_start: 0.7059 (mtmm) cc_final: 0.6613 (tptt) REVERT: C 587 MET cc_start: 0.5175 (mmp) cc_final: 0.4954 (mmp) REVERT: C 695 LYS cc_start: 0.7318 (mmtt) cc_final: 0.6594 (tmmt) REVERT: E 586 MET cc_start: 0.6819 (mmm) cc_final: 0.6619 (mmm) REVERT: E 617 MET cc_start: 0.6881 (mmm) cc_final: 0.6510 (mmm) outliers start: 46 outliers final: 22 residues processed: 299 average time/residue: 0.5155 time to fit residues: 177.1251 Evaluate side-chains 293 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 140 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 331 HIS 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 = 0.4304 r_free = 0.4304 target = 0.222109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.142875 restraints weight = 22453.751| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 4.96 r_work: 0.3218 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18368 Z= 0.209 Angle : 0.564 8.004 24972 Z= 0.293 Chirality : 0.042 0.152 2982 Planarity : 0.005 0.048 3032 Dihedral : 5.186 53.671 2477 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.19 % Allowed : 12.51 % Favored : 84.29 % 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 : 0.16 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 827 TYR 0.020 0.002 TYR Q 244 PHE 0.018 0.002 PHE Q 257 TRP 0.012 0.001 TRP C 831 HIS 0.010 0.001 HIS Q 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (18364) covalent geometry : angle 0.56391 / 0.29 (24960) hydrogen bonds : bond 0.05134 / 3.39 ( 1244) hydrogen bonds : angle 4.39177 / 3.25 ( 3646) link_BETA1-4 : bond 0.00244 / 0.13 ( 2) link_BETA1-4 : angle 1.07721 / 0.62 ( 6) link_NAG-ASN : bond 0.00019 / 0.01 ( 2) link_NAG-ASN : angle 0.85930 / 0.49 ( 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 342 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 282 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 338 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.6966 (pp) REVERT: K 362 GLN cc_start: 0.5946 (OUTLIER) cc_final: 0.5573 (tp40) REVERT: K 382 LEU cc_start: 0.8198 (mt) cc_final: 0.7870 (tp) REVERT: K 383 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7485 (mp) REVERT: L 196 LYS cc_start: 0.7892 (mttp) cc_final: 0.7040 (tptp) REVERT: L 199 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7806 (tm-30) REVERT: L 312 LYS cc_start: 0.8521 (tptt) cc_final: 0.8180 (tmtt) REVERT: L 321 LYS cc_start: 0.8462 (mmtp) cc_final: 0.8137 (mmtt) REVERT: L 323 ARG cc_start: 0.8739 (mpt-90) cc_final: 0.7764 (mtm-85) REVERT: Q 378 MET cc_start: 0.8408 (mtm) cc_final: 0.7363 (tmm) REVERT: Q 404 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8281 (tmtt) REVERT: P 83 TYR cc_start: 0.4950 (OUTLIER) cc_final: 0.4674 (t80) REVERT: C 412 ILE cc_start: 0.7329 (mm) cc_final: 0.7122 (mp) REVERT: C 442 ILE cc_start: 0.6714 (mt) cc_final: 0.6490 (mt) REVERT: C 537 PHE cc_start: 0.6840 (m-80) cc_final: 0.6531 (m-80) REVERT: C 539 LYS cc_start: 0.7068 (mtmm) cc_final: 0.6592 (tptt) REVERT: C 587 MET cc_start: 0.5133 (mmp) cc_final: 0.4931 (mmp) REVERT: E 435 MET cc_start: 0.5601 (OUTLIER) cc_final: 0.4865 (mtm) REVERT: E 617 MET cc_start: 0.6848 (mmm) cc_final: 0.6542 (mmm) outliers start: 60 outliers final: 31 residues processed: 314 average time/residue: 0.4510 time to fit residues: 164.1058 Evaluate side-chains 308 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 223 VAL Chi-restraints excluded: chain K residue 290 SER 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 60 MET 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 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 614 ILE 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 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 869 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 161 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 27 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 224 ASN L 92 GLN Q 102 GLN Q 331 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.224254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.132906 restraints weight = 29250.207| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.78 r_work: 0.3273 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- 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 = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18368 Z= 0.133 Angle : 0.516 8.932 24972 Z= 0.265 Chirality : 0.040 0.218 2982 Planarity : 0.004 0.044 3032 Dihedral : 5.075 56.554 2477 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.98 % Allowed : 13.56 % Favored : 83.46 % 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: 2.50 (0.17), residues: 2276 helix: 2.30 (0.13), residues: 1583 sheet: None (None), residues: 0 loop : 0.19 (0.23), residues: 693 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 0.019 0.001 PHE Q 257 TRP 0.011 0.001 TRP C 831 HIS 0.005 0.001 HIS K 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (18364) covalent geometry : angle 0.51542 / 0.26 (24960) hydrogen bonds : bond 0.04396 / 2.90 ( 1244) hydrogen bonds : angle 4.27394 / 3.16 ( 3646) link_BETA1-4 : bond 0.00232 / 0.12 ( 2) link_BETA1-4 : angle 0.95209 / 0.54 ( 6) link_NAG-ASN : bond 0.00046 / 0.02 ( 2) link_NAG-ASN : angle 0.79633 / 0.45 ( 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 334 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 278 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 335 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7372 (mp) REVERT: K 338 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7050 (pp) REVERT: K 362 GLN cc_start: 0.6014 (OUTLIER) cc_final: 0.5592 (tp40) REVERT: K 382 LEU cc_start: 0.8160 (mt) cc_final: 0.7829 (tp) REVERT: K 383 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7588 (mp) REVERT: L 196 LYS cc_start: 0.7957 (mttp) cc_final: 0.7193 (tptp) REVERT: L 199 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7748 (tm-30) REVERT: L 312 LYS cc_start: 0.8445 (tptt) cc_final: 0.8141 (tptt) REVERT: L 321 LYS cc_start: 0.8479 (mmtp) cc_final: 0.8174 (mmtt) REVERT: L 323 ARG cc_start: 0.8690 (mpt-90) cc_final: 0.7795 (mtm-85) REVERT: L 358 MET cc_start: 0.6736 (ttp) cc_final: 0.5625 (tmt) REVERT: Q 378 MET cc_start: 0.8370 (mtm) cc_final: 0.7403 (tmm) REVERT: Q 404 LYS cc_start: 0.8911 (tmtm) cc_final: 0.8206 (tmtt) REVERT: P 83 TYR cc_start: 0.4979 (OUTLIER) cc_final: 0.4673 (t80) REVERT: C 412 ILE cc_start: 0.7326 (mm) cc_final: 0.7116 (mp) REVERT: C 435 MET cc_start: 0.4756 (mtm) cc_final: 0.4287 (ttp) REVERT: C 442 ILE cc_start: 0.6706 (mt) cc_final: 0.6479 (mt) REVERT: C 473 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.5300 (tm-30) REVERT: C 539 LYS cc_start: 0.7133 (mtmm) cc_final: 0.6731 (tptt) REVERT: C 587 MET cc_start: 0.5180 (mmp) cc_final: 0.4968 (mmp) REVERT: E 435 MET cc_start: 0.5628 (mtm) cc_final: 0.4630 (mtm) REVERT: E 617 MET cc_start: 0.6755 (mmm) cc_final: 0.6432 (mmm) outliers start: 56 outliers final: 25 residues processed: 310 average time/residue: 0.5029 time to fit residues: 179.5984 Evaluate side-chains 299 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 268 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 335 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 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 85 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 528 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 528 ILE Chi-restraints excluded: chain E residue 646 ARG 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: 4.9990 chunk 23 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 58 HIS Q 102 GLN Q 331 HIS 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 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.222116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.131717 restraints weight = 31183.698| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.18 r_work: 0.3201 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18368 Z= 0.214 Angle : 0.571 9.627 24972 Z= 0.295 Chirality : 0.043 0.191 2982 Planarity : 0.005 0.053 3032 Dihedral : 5.036 53.919 2473 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.98 % Allowed : 14.61 % Favored : 82.41 % 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: 2.24 (0.17), residues: 2276 helix: 2.13 (0.13), residues: 1576 sheet: None (None), residues: 0 loop : 0.06 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 234 TYR 0.019 0.002 TYR L 180 PHE 0.030 0.002 PHE E 591 TRP 0.012 0.001 TRP C 831 HIS 0.008 0.001 HIS Q 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (18364) covalent geometry : angle 0.57113 / 0.30 (24960) hydrogen bonds : bond 0.05121 / 3.38 ( 1244) hydrogen bonds : angle 4.42472 / 3.27 ( 3646) link_BETA1-4 : bond 0.00240 / 0.12 ( 2) link_BETA1-4 : angle 1.03315 / 0.58 ( 6) link_NAG-ASN : bond 0.00028 / 0.01 ( 2) link_NAG-ASN : angle 0.91456 / 0.52 ( 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: 56 poor density : 275 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 338 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7085 (pp) REVERT: K 362 GLN cc_start: 0.6033 (OUTLIER) cc_final: 0.5621 (tp40) REVERT: K 382 LEU cc_start: 0.8239 (mt) cc_final: 0.7929 (tp) REVERT: K 383 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7522 (mp) REVERT: L 196 LYS cc_start: 0.7983 (mttp) cc_final: 0.7170 (tptp) REVERT: L 199 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7802 (tm-30) REVERT: L 312 LYS cc_start: 0.8541 (tptt) cc_final: 0.8175 (tmtt) REVERT: L 321 LYS cc_start: 0.8501 (mmtp) cc_final: 0.8192 (mmtt) REVERT: L 323 ARG cc_start: 0.8740 (mpt-90) cc_final: 0.7805 (mtm-85) REVERT: Q 378 MET cc_start: 0.8435 (mtm) cc_final: 0.7423 (tmm) REVERT: Q 404 LYS cc_start: 0.8963 (tmtm) cc_final: 0.8262 (tmtt) REVERT: P 83 TYR cc_start: 0.5003 (OUTLIER) cc_final: 0.4704 (t80) REVERT: C 442 ILE cc_start: 0.6776 (mt) cc_final: 0.6541 (mt) REVERT: C 473 GLU cc_start: 0.5601 (OUTLIER) cc_final: 0.5235 (tm-30) REVERT: C 481 THR cc_start: 0.5513 (m) cc_final: 0.5308 (p) REVERT: C 537 PHE cc_start: 0.6874 (m-80) cc_final: 0.6571 (m-80) REVERT: C 539 LYS cc_start: 0.7194 (mtmm) cc_final: 0.6758 (tptt) REVERT: C 587 MET cc_start: 0.5264 (mmp) cc_final: 0.5029 (mmp) REVERT: E 435 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.4423 (mtm) REVERT: E 587 MET cc_start: 0.5027 (OUTLIER) cc_final: 0.4103 (mmm) REVERT: E 617 MET cc_start: 0.6792 (mmm) cc_final: 0.6473 (mmm) REVERT: E 679 PHE cc_start: 0.4345 (t80) cc_final: 0.4017 (t80) outliers start: 56 outliers final: 33 residues processed: 311 average time/residue: 0.5030 time to fit residues: 180.2545 Evaluate side-chains 310 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 270 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 290 SER 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 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 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 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 567 LEU 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 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 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: 1.9990 chunk 137 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 9 optimal weight: 0.0570 chunk 186 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 52 GLN L 92 GLN Q 102 GLN Q 331 HIS 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** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 840 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.223551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.131850 restraints weight = 29834.637| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.84 r_work: 0.3270 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18368 Z= 0.127 Angle : 0.510 9.766 24972 Z= 0.262 Chirality : 0.040 0.149 2982 Planarity : 0.004 0.049 3032 Dihedral : 4.894 55.961 2473 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.98 % Allowed : 14.97 % Favored : 82.04 % 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: 2.29 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : 0.15 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 646 TYR 0.016 0.001 TYR K 178 PHE 0.026 0.001 PHE E 591 TRP 0.012 0.001 TRP K 16 HIS 0.004 0.001 HIS K 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (18364) covalent geometry : angle 0.50930 / 0.26 (24960) hydrogen bonds : bond 0.04331 / 2.85 ( 1244) hydrogen bonds : angle 4.26427 / 3.16 ( 3646) link_BETA1-4 : bond 0.00300 / 0.15 ( 2) link_BETA1-4 : angle 1.00711 / 0.56 ( 6) link_NAG-ASN : bond 0.00073 / 0.04 ( 2) link_NAG-ASN : angle 0.83562 / 0.47 ( 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 329 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 273 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7823 (mtt) REVERT: K 338 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7024 (pp) REVERT: K 362 GLN cc_start: 0.6032 (OUTLIER) cc_final: 0.5616 (tp40) REVERT: K 382 LEU cc_start: 0.8148 (mt) cc_final: 0.7803 (tp) REVERT: K 383 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7541 (mp) REVERT: L 196 LYS cc_start: 0.8004 (mttp) cc_final: 0.7229 (tptp) REVERT: L 199 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7650 (tm-30) REVERT: L 312 LYS cc_start: 0.8469 (tptt) cc_final: 0.8153 (tptt) REVERT: L 321 LYS cc_start: 0.8483 (mmtp) cc_final: 0.8180 (mmtt) REVERT: L 323 ARG cc_start: 0.8691 (mpt-90) cc_final: 0.7777 (mtm-85) REVERT: L 358 MET cc_start: 0.6755 (ttp) cc_final: 0.5615 (tmt) REVERT: Q 378 MET cc_start: 0.8376 (mtm) cc_final: 0.7370 (tmm) REVERT: Q 404 LYS cc_start: 0.8912 (tmtm) cc_final: 0.8137 (tmtt) REVERT: P 83 TYR cc_start: 0.4994 (OUTLIER) cc_final: 0.4698 (t80) REVERT: C 442 ILE cc_start: 0.6728 (mt) cc_final: 0.6498 (mt) REVERT: C 473 GLU cc_start: 0.5600 (OUTLIER) cc_final: 0.5255 (tm-30) REVERT: C 481 THR cc_start: 0.5547 (m) cc_final: 0.5339 (p) REVERT: C 539 LYS cc_start: 0.7157 (mtmm) cc_final: 0.6742 (tptt) REVERT: C 712 MET cc_start: 0.4342 (OUTLIER) cc_final: 0.4081 (tpt) REVERT: E 435 MET cc_start: 0.5461 (mtm) cc_final: 0.4252 (mtm) REVERT: E 617 MET cc_start: 0.6695 (mmm) cc_final: 0.6367 (mmm) outliers start: 56 outliers final: 29 residues processed: 306 average time/residue: 0.5209 time to fit residues: 183.3677 Evaluate side-chains 297 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 290 SER 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 259 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 499 LEU 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 617 MET 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 646 ARG 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: 0.8980 chunk 143 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.224858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.143551 restraints weight = 24799.833| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.63 r_work: 0.3249 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 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 = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18368 Z= 0.124 Angle : 0.520 10.824 24972 Z= 0.265 Chirality : 0.040 0.154 2982 Planarity : 0.004 0.050 3032 Dihedral : 4.835 58.245 2469 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.62 % Allowed : 15.65 % 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: 2.52 (0.18), residues: 2276 helix: 2.32 (0.13), residues: 1590 sheet: None (None), residues: 0 loop : 0.16 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 646 TYR 0.017 0.001 TYR E 824 PHE 0.025 0.001 PHE E 591 TRP 0.011 0.001 TRP C 831 HIS 0.004 0.001 HIS C 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (18364) covalent geometry : angle 0.51988 / 0.27 (24960) hydrogen bonds : bond 0.04227 / 2.78 ( 1244) hydrogen bonds : angle 4.24335 / 3.15 ( 3646) link_BETA1-4 : bond 0.00239 / 0.12 ( 2) link_BETA1-4 : angle 0.99530 / 0.56 ( 6) link_NAG-ASN : bond 0.00076 / 0.04 ( 2) link_NAG-ASN : angle 0.80570 / 0.46 ( 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 313 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 338 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6894 (pp) REVERT: K 362 GLN cc_start: 0.5994 (OUTLIER) cc_final: 0.5594 (tp40) REVERT: K 382 LEU cc_start: 0.8167 (mt) cc_final: 0.7803 (tp) REVERT: K 383 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7447 (mp) REVERT: L 196 LYS cc_start: 0.7950 (mttp) cc_final: 0.7116 (tptp) REVERT: L 199 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7752 (tm-30) REVERT: L 312 LYS cc_start: 0.8442 (tptt) cc_final: 0.8154 (tptt) REVERT: L 321 LYS cc_start: 0.8465 (mmtp) cc_final: 0.8150 (mmtt) REVERT: L 323 ARG cc_start: 0.8717 (mpt-90) cc_final: 0.7726 (mtm-85) REVERT: L 358 MET cc_start: 0.6806 (ttp) cc_final: 0.5569 (tmt) REVERT: Q 358 MET cc_start: 0.8881 (ptm) cc_final: 0.8546 (ptp) REVERT: Q 378 MET cc_start: 0.8363 (mtm) cc_final: 0.7275 (tmm) REVERT: Q 404 LYS cc_start: 0.8943 (tmtm) cc_final: 0.8157 (tmtt) REVERT: P 83 TYR cc_start: 0.4948 (OUTLIER) cc_final: 0.4667 (t80) REVERT: C 435 MET cc_start: 0.4240 (mtm) cc_final: 0.3999 (ttp) REVERT: C 442 ILE cc_start: 0.6664 (mt) cc_final: 0.6463 (mt) REVERT: C 473 GLU cc_start: 0.5424 (OUTLIER) cc_final: 0.5153 (tm-30) REVERT: C 539 LYS cc_start: 0.7071 (mtmm) cc_final: 0.6651 (tmtt) REVERT: C 586 MET cc_start: 0.5604 (mmm) cc_final: 0.5229 (mmt) REVERT: C 712 MET cc_start: 0.4129 (OUTLIER) cc_final: 0.3752 (tpt) REVERT: E 435 MET cc_start: 0.5377 (mtm) cc_final: 0.4245 (mtm) REVERT: E 617 MET cc_start: 0.6661 (mmm) cc_final: 0.6432 (mmm) REVERT: E 624 ILE cc_start: 0.4888 (mt) cc_final: 0.4308 (tp) outliers start: 49 outliers final: 32 residues processed: 294 average time/residue: 0.5235 time to fit residues: 177.0256 Evaluate side-chains 298 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 260 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 290 SER Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 376 ILE 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 259 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 499 LEU 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 617 MET 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 646 ARG Chi-restraints excluded: chain E residue 828 VAL 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: 4.9990 chunk 123 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 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: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 52 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.220397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.128592 restraints weight = 33691.870| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.55 r_work: 0.3172 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18368 Z= 0.224 Angle : 0.595 12.611 24972 Z= 0.306 Chirality : 0.043 0.252 2982 Planarity : 0.005 0.050 3032 Dihedral : 5.001 59.853 2469 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.72 % Allowed : 15.76 % 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: 2.14 (0.17), residues: 2276 helix: 2.05 (0.13), residues: 1583 sheet: None (None), residues: 0 loop : 0.00 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 234 TYR 0.023 0.002 TYR K 178 PHE 0.026 0.002 PHE C 582 TRP 0.010 0.001 TRP C 831 HIS 0.006 0.001 HIS K 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 (18364) covalent geometry : angle 0.59478 / 0.31 (24960) hydrogen bonds : bond 0.05179 / 3.42 ( 1244) hydrogen bonds : angle 4.44450 / 3.29 ( 3646) link_BETA1-4 : bond 0.00292 / 0.15 ( 2) link_BETA1-4 : angle 1.11695 / 0.63 ( 6) link_NAG-ASN : bond 0.00060 / 0.03 ( 2) link_NAG-ASN : angle 0.97645 / 0.56 ( 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 307 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7963 (mtt) REVERT: K 338 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.6986 (pp) REVERT: K 362 GLN cc_start: 0.6087 (OUTLIER) cc_final: 0.5661 (tp40) REVERT: K 382 LEU cc_start: 0.8259 (mt) cc_final: 0.7924 (tp) REVERT: K 383 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7374 (mp) REVERT: L 196 LYS cc_start: 0.7999 (mttp) cc_final: 0.7290 (mtpp) REVERT: L 312 LYS cc_start: 0.8568 (tptt) cc_final: 0.8205 (tmtt) REVERT: L 321 LYS cc_start: 0.8486 (mmtp) cc_final: 0.8187 (mmtt) REVERT: L 323 ARG cc_start: 0.8746 (mpt-90) cc_final: 0.7765 (mtm-85) REVERT: Q 358 MET cc_start: 0.8922 (ptm) cc_final: 0.8621 (ptp) REVERT: Q 378 MET cc_start: 0.8429 (mtm) cc_final: 0.7368 (tmm) REVERT: Q 404 LYS cc_start: 0.8987 (tmtm) cc_final: 0.8279 (tmtt) REVERT: P 83 TYR cc_start: 0.5053 (OUTLIER) cc_final: 0.4751 (t80) REVERT: C 442 ILE cc_start: 0.6687 (mt) cc_final: 0.6455 (mt) REVERT: C 473 GLU cc_start: 0.5597 (OUTLIER) cc_final: 0.5282 (tm-30) REVERT: C 537 PHE cc_start: 0.6830 (m-80) cc_final: 0.6510 (m-80) REVERT: C 539 LYS cc_start: 0.7190 (mtmm) cc_final: 0.6790 (tptt) REVERT: C 586 MET cc_start: 0.5893 (mmm) cc_final: 0.5576 (mmt) REVERT: C 712 MET cc_start: 0.4252 (OUTLIER) cc_final: 0.3953 (tpt) REVERT: C 741 MET cc_start: 0.4473 (mmm) cc_final: 0.3923 (mmt) REVERT: E 435 MET cc_start: 0.5453 (mtm) cc_final: 0.4195 (mtm) REVERT: E 617 MET cc_start: 0.6765 (mmm) cc_final: 0.6538 (mmm) outliers start: 51 outliers final: 36 residues processed: 290 average time/residue: 0.5215 time to fit residues: 174.1051 Evaluate side-chains 297 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 290 SER Chi-restraints excluded: chain K residue 293 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 259 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 326 ASP 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 528 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain C residue 684 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 417 LEU Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 828 VAL Chi-restraints excluded: chain E residue 833 MET 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: 0.9990 chunk 215 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 69 optimal weight: 0.0770 chunk 211 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 52 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.223529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.132844 restraints weight = 33128.377| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.33 r_work: 0.3263 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18368 Z= 0.125 Angle : 0.525 11.627 24972 Z= 0.268 Chirality : 0.040 0.171 2982 Planarity : 0.004 0.047 3032 Dihedral : 4.840 57.187 2469 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.99 % Allowed : 16.44 % Favored : 81.57 % 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: 2.20 (0.13), residues: 1594 sheet: None (None), residues: 0 loop : 0.08 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 832 TYR 0.018 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/Z covalent geometry : bond 0.00267 / 0.12 (18364) covalent geometry : angle 0.52512 / 0.27 (24960) hydrogen bonds : bond 0.04266 / 2.81 ( 1244) hydrogen bonds : angle 4.29633 / 3.19 ( 3646) link_BETA1-4 : bond 0.00254 / 0.13 ( 2) link_BETA1-4 : angle 1.04015 / 0.58 ( 6) link_NAG-ASN : bond 0.00058 / 0.03 ( 2) link_NAG-ASN : angle 0.89554 / 0.51 ( 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 307 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 270 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7842 (mtt) REVERT: K 338 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6982 (pp) REVERT: K 362 GLN cc_start: 0.6073 (OUTLIER) cc_final: 0.5629 (tp40) REVERT: K 382 LEU cc_start: 0.8209 (mt) cc_final: 0.7867 (tp) REVERT: K 383 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7529 (mp) REVERT: L 196 LYS cc_start: 0.8061 (mttp) cc_final: 0.7272 (tptp) REVERT: L 199 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7590 (tm-30) REVERT: L 312 LYS cc_start: 0.8483 (tptt) cc_final: 0.8165 (tptt) REVERT: L 321 LYS cc_start: 0.8500 (mmtp) cc_final: 0.8209 (mmtt) REVERT: L 323 ARG cc_start: 0.8709 (mpt-90) cc_final: 0.7780 (mtm-85) REVERT: L 358 MET cc_start: 0.6929 (ttm) cc_final: 0.5759 (tmt) REVERT: Q 358 MET cc_start: 0.8801 (ptm) cc_final: 0.8506 (ptp) REVERT: Q 378 MET cc_start: 0.8388 (mtm) cc_final: 0.7348 (tmm) REVERT: Q 404 LYS cc_start: 0.8934 (tmtm) cc_final: 0.8155 (tmtt) REVERT: P 83 TYR cc_start: 0.5045 (OUTLIER) cc_final: 0.4764 (t80) REVERT: C 388 ARG cc_start: 0.7211 (ttp-170) cc_final: 0.6922 (ttp-170) REVERT: C 442 ILE cc_start: 0.6651 (mt) cc_final: 0.6431 (mt) REVERT: C 473 GLU cc_start: 0.5643 (OUTLIER) cc_final: 0.5324 (tm-30) REVERT: C 539 LYS cc_start: 0.7213 (mtmm) cc_final: 0.6796 (tptt) REVERT: C 586 MET cc_start: 0.5912 (mmm) cc_final: 0.5555 (mmt) REVERT: C 589 ARG cc_start: 0.4189 (ttt-90) cc_final: 0.3852 (ttt180) REVERT: C 639 LYS cc_start: 0.6058 (pttp) cc_final: 0.5612 (ttmt) REVERT: C 712 MET cc_start: 0.4276 (OUTLIER) cc_final: 0.3956 (tpt) REVERT: E 435 MET cc_start: 0.5350 (mtm) cc_final: 0.3991 (mtm) REVERT: E 617 MET cc_start: 0.6691 (mmm) cc_final: 0.6452 (mmm) outliers start: 37 outliers final: 27 residues processed: 294 average time/residue: 0.5362 time to fit residues: 180.8231 Evaluate side-chains 300 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 290 SER 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 259 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 602 ARG Chi-restraints excluded: chain C residue 617 MET 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 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: 0.0020 chunk 48 optimal weight: 5.9990 chunk 208 optimal weight: 0.0570 chunk 32 optimal weight: 0.1980 chunk 174 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 190 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 59 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 overall best weight: 0.9908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.226398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.138740 restraints weight = 29555.245| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.12 r_work: 0.3279 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- 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 = 0.47 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 = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18368 Z= 0.123 Angle : 0.518 13.188 24972 Z= 0.264 Chirality : 0.040 0.173 2982 Planarity : 0.004 0.047 3032 Dihedral : 4.733 55.378 2469 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.09 % Allowed : 16.65 % Favored : 81.26 % 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: 2.48 (0.18), residues: 2276 helix: 2.30 (0.13), residues: 1593 sheet: None (None), residues: 0 loop : 0.11 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 832 TYR 0.017 0.001 TYR K 178 PHE 0.022 0.001 PHE E 591 TRP 0.011 0.001 TRP E 492 HIS 0.004 0.001 HIS K 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (18364) covalent geometry : angle 0.51765 / 0.26 (24960) hydrogen bonds : bond 0.04198 / 2.76 ( 1244) hydrogen bonds : angle 4.24069 / 3.14 ( 3646) link_BETA1-4 : bond 0.00238 / 0.12 ( 2) link_BETA1-4 : angle 1.01610 / 0.57 ( 6) link_NAG-ASN : bond 0.00052 / 0.03 ( 2) link_NAG-ASN : angle 0.90508 / 0.52 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9823.75 seconds wall clock time: 167 minutes 46.99 seconds (10066.99 seconds total)