Starting phenix.real_space_refine on Sun Jun 15 20:50:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8crt_26958/06_2025/8crt_26958.cif Found real_map, /net/cci-nas-00/data/ceres_data/8crt_26958/06_2025/8crt_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_26958/06_2025/8crt_26958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8crt_26958/06_2025/8crt_26958.map" model { file = "/net/cci-nas-00/data/ceres_data/8crt_26958/06_2025/8crt_26958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8crt_26958/06_2025/8crt_26958.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17925 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 2943 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2962 Chain: "L" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2938 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2954 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 248 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "B" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR K 34 " occ=0.55 ... (22 atoms not shown) pdb=" OH BTYR K 34 " occ=0.45 residue: pdb=" N ATYR K 242 " occ=0.55 ... (22 atoms not shown) pdb=" OH BTYR K 242 " occ=0.45 Time building chain proxies: 12.93, per 1000 atoms: 0.72 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: 4.48 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.68 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: 5.91 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3120 1.33 - 1.45: 4630 1.45 - 1.57: 10424 1.57 - 1.69: 0 1.69 - 1.82: 190 Bond restraints: 18364 Sorted by residual: bond pdb=" N VAL K 223 " pdb=" CA VAL K 223 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.03e+01 bond pdb=" N VAL Q 57 " pdb=" CA VAL Q 57 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 9.10e+00 bond pdb=" N ARG K 229 " pdb=" CA ARG K 229 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.25e-02 6.40e+03 7.87e+00 bond pdb=" N TRP K 220 " pdb=" CA TRP K 220 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.04e-02 9.25e+03 7.63e+00 bond pdb=" N VAL Q 59 " pdb=" CA VAL Q 59 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.21e-02 6.83e+03 7.43e+00 ... (remaining 18359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 24369 1.66 - 3.31: 505 3.31 - 4.97: 55 4.97 - 6.62: 27 6.62 - 8.28: 4 Bond angle restraints: 24960 Sorted by residual: angle pdb=" C BTYR K 34 " pdb=" N ASP K 35 " pdb=" CA ASP K 35 " ideal model delta sigma weight residual 121.70 129.98 -8.28 1.80e+00 3.09e-01 2.12e+01 angle pdb=" N ILE Q 116 " pdb=" CA ILE Q 116 " pdb=" C ILE Q 116 " ideal model delta sigma weight residual 111.58 107.15 4.43 1.06e+00 8.90e-01 1.75e+01 angle pdb=" C PRO K 226 " pdb=" CA PRO K 226 " pdb=" CB PRO K 226 " ideal model delta sigma weight residual 113.06 106.68 6.38 1.59e+00 3.96e-01 1.61e+01 angle pdb=" N ASP Q 119 " pdb=" CA ASP Q 119 " pdb=" C ASP Q 119 " ideal model delta sigma weight residual 113.23 108.62 4.61 1.24e+00 6.50e-01 1.38e+01 angle pdb=" N ASN K 224 " pdb=" CA ASN K 224 " pdb=" C ASN K 224 " ideal model delta sigma weight residual 112.93 108.77 4.16 1.12e+00 7.97e-01 1.38e+01 ... (remaining 24955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 10375 21.24 - 42.47: 349 42.47 - 63.71: 73 63.71 - 84.94: 11 84.94 - 106.18: 21 Dihedral angle restraints: 10829 sinusoidal: 4238 harmonic: 6591 Sorted by residual: dihedral pdb=" C2 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" C4 NAG A 2 " pdb=" C5 NAG A 2 " ideal model delta sinusoidal sigma weight residual 53.78 -52.40 106.18 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" C4 NAG A 2 " pdb=" O4 NAG A 2 " ideal model delta sinusoidal sigma weight residual 175.11 68.97 106.14 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG F 2 " pdb=" C3 NAG F 2 " pdb=" C4 NAG F 2 " pdb=" O4 NAG F 2 " ideal model delta sinusoidal sigma weight residual 175.11 69.31 105.80 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 10826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1956 0.034 - 0.068: 744 0.068 - 0.102: 194 0.102 - 0.136: 79 0.136 - 0.170: 9 Chirality restraints: 2982 Sorted by residual: chirality pdb=" CA ILE Q 116 " pdb=" N ILE Q 116 " pdb=" C ILE Q 116 " pdb=" CB ILE Q 116 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA MET K 238 " pdb=" N MET K 238 " pdb=" C MET K 238 " pdb=" CB MET K 238 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA PHE Q 47 " pdb=" N PHE Q 47 " pdb=" C PHE Q 47 " pdb=" CB PHE Q 47 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 2979 not shown) Planarity restraints: 3034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR K 241 " -0.027 2.00e-02 2.50e+03 5.45e-02 2.98e+01 pdb=" C THR K 241 " 0.094 2.00e-02 2.50e+03 pdb=" O THR K 241 " -0.035 2.00e-02 2.50e+03 pdb=" N ATYR K 242 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ATYR K 242 " -0.026 2.00e-02 2.50e+03 5.32e-02 2.83e+01 pdb=" C ATYR K 242 " 0.092 2.00e-02 2.50e+03 pdb=" O ATYR K 242 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR K 243 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BTYR K 242 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C BTYR K 242 " 0.091 2.00e-02 2.50e+03 pdb=" O BTYR K 242 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR K 243 " -0.031 2.00e-02 2.50e+03 ... (remaining 3031 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1535 2.74 - 3.28: 18546 3.28 - 3.82: 31930 3.82 - 4.36: 37190 4.36 - 4.90: 65115 Nonbonded interactions: 154316 Sorted by model distance: nonbonded pdb=" OE1 GLU C 472 " pdb=" OH TYR C 486 " model vdw 2.205 3.040 nonbonded pdb=" O PHE K 28 " pdb=" OG1 THR K 32 " model vdw 2.212 3.040 nonbonded pdb=" OE1 GLU E 472 " pdb=" OH TYR E 486 " model vdw 2.213 3.040 nonbonded pdb=" OD2 ASP K 404 " pdb=" OH TYR L 205 " model vdw 2.255 3.040 nonbonded pdb=" OG SER L 171 " pdb=" O VAL L 281 " model vdw 2.276 3.040 ... (remaining 154311 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'L' selection = (chain 'Q' and (resid 1 through 26 or resid 48 through 409)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.340 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 43.970 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.110 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:14.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18368 Z= 0.195 Angle : 0.582 8.279 24972 Z= 0.353 Chirality : 0.041 0.170 2982 Planarity : 0.005 0.060 3032 Dihedral : 12.634 106.176 6599 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.010 0.001 TRP K 217 HIS 0.009 0.001 HIS Q 58 PHE 0.011 0.001 PHE L 129 TYR 0.017 0.001 TYR Q 244 ARG 0.004 0.000 ARG Q 2 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 2) link_NAG-ASN : angle 0.66435 ( 6) link_BETA1-4 : bond 0.00444 ( 2) link_BETA1-4 : angle 1.20910 ( 6) hydrogen bonds : bond 0.13864 ( 1244) hydrogen bonds : angle 5.26000 ( 3646) covalent geometry : bond 0.00325 (18364) covalent geometry : angle 0.58208 (24960) *********************** 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 : 1.736 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: 0.8142 (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: 1.1733 time to fit residues: 496.6673 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 : 4.264 ------------------------------------------------------------------------------- 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 192 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 0.0770 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 133 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 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 651 HIS ** E 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 703 HIS E 834 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.224085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131448 restraints weight = 31773.530| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.37 r_work: 0.3239 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18368 Z= 0.169 Angle : 0.560 7.003 24972 Z= 0.290 Chirality : 0.042 0.202 2982 Planarity : 0.005 0.069 3032 Dihedral : 8.547 74.870 2685 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.54 % Favored : 98.41 % Rotamer: Outliers : 2.93 % Allowed : 10.31 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.17), residues: 2276 helix: 2.03 (0.13), residues: 1589 sheet: None (None), residues: 0 loop : 0.18 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 831 HIS 0.007 0.001 HIS Q 58 PHE 0.018 0.002 PHE E 659 TYR 0.019 0.002 TYR K 178 ARG 0.006 0.000 ARG C 730 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 2) link_NAG-ASN : angle 0.77975 ( 6) link_BETA1-4 : bond 0.00261 ( 2) link_BETA1-4 : angle 1.16857 ( 6) hydrogen bonds : bond 0.05054 ( 1244) hydrogen bonds : angle 4.45049 ( 3646) covalent geometry : bond 0.00380 (18364) covalent geometry : angle 0.55997 (24960) *********************** 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 338 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 283 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 338 LEU cc_start: 0.7511 (tm) cc_final: 0.7029 (pp) REVERT: K 362 GLN cc_start: 0.5995 (OUTLIER) cc_final: 0.5599 (tp40) REVERT: K 382 LEU cc_start: 0.8179 (mt) cc_final: 0.7810 (tp) REVERT: K 383 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7511 (mp) REVERT: L 196 LYS cc_start: 0.7820 (mttp) cc_final: 0.7032 (tptp) REVERT: L 312 LYS cc_start: 0.8471 (tptt) cc_final: 0.8184 (tptt) REVERT: L 321 LYS cc_start: 0.8466 (mmtp) cc_final: 0.8144 (mmtt) REVERT: L 323 ARG cc_start: 0.8698 (mpt-90) cc_final: 0.7773 (mtm-85) REVERT: L 358 MET cc_start: 0.6778 (ttp) cc_final: 0.5946 (ttp) REVERT: L 378 MET cc_start: 0.7920 (mtp) cc_final: 0.7713 (mtp) REVERT: Q 378 MET cc_start: 0.8396 (mtm) cc_final: 0.7385 (tmm) REVERT: Q 404 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8247 (tmtt) REVERT: P 83 TYR cc_start: 0.4986 (OUTLIER) cc_final: 0.4705 (t80) REVERT: C 435 MET cc_start: 0.4428 (mtm) cc_final: 0.3839 (ttp) REVERT: C 442 ILE cc_start: 0.6713 (mt) cc_final: 0.6492 (mt) REVERT: C 539 LYS cc_start: 0.7127 (mtmm) cc_final: 0.6667 (tptt) REVERT: C 832 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5920 (mmm-85) REVERT: C 833 MET cc_start: 0.3612 (ttp) cc_final: 0.3387 (mtp) REVERT: E 587 MET cc_start: 0.4817 (OUTLIER) cc_final: 0.3969 (mmm) REVERT: E 617 MET cc_start: 0.7010 (mmm) cc_final: 0.6562 (mmm) outliers start: 55 outliers final: 21 residues processed: 309 average time/residue: 1.4694 time to fit residues: 525.2037 Evaluate side-chains 299 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 272 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 337 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 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 B residue 100 MET 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 587 MET 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 90 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 331 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 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 = 0.4302 r_free = 0.4302 target = 0.221823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.130217 restraints weight = 37379.581| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.39 r_work: 0.3175 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 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 = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18368 Z= 0.233 Angle : 0.605 8.472 24972 Z= 0.311 Chirality : 0.044 0.339 2982 Planarity : 0.005 0.045 3032 Dihedral : 7.029 58.842 2677 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.30 % Allowed : 11.68 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.17), residues: 2276 helix: 1.98 (0.13), residues: 1577 sheet: None (None), residues: 0 loop : 0.05 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 492 HIS 0.010 0.001 HIS Q 58 PHE 0.026 0.002 PHE C 582 TYR 0.020 0.002 TYR L 180 ARG 0.003 0.000 ARG C 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 2) link_NAG-ASN : angle 0.98381 ( 6) link_BETA1-4 : bond 0.00211 ( 2) link_BETA1-4 : angle 1.51308 ( 6) hydrogen bonds : bond 0.05483 ( 1244) hydrogen bonds : angle 4.52664 ( 3646) covalent geometry : bond 0.00542 (18364) covalent geometry : angle 0.60451 (24960) *********************** 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 340 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 278 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8699 (tt) REVERT: K 338 LEU cc_start: 0.7614 (tm) cc_final: 0.7146 (pp) REVERT: K 362 GLN cc_start: 0.6081 (OUTLIER) cc_final: 0.5671 (tp40) REVERT: K 382 LEU cc_start: 0.8255 (mt) cc_final: 0.7938 (tp) REVERT: K 383 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7552 (mp) REVERT: L 196 LYS cc_start: 0.7949 (mttp) cc_final: 0.7234 (mtpp) REVERT: L 199 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7575 (tm-30) REVERT: L 312 LYS cc_start: 0.8573 (tptt) cc_final: 0.8204 (tmtt) REVERT: L 321 LYS cc_start: 0.8495 (mmtp) cc_final: 0.8188 (mmtt) REVERT: L 323 ARG cc_start: 0.8757 (mpt-90) cc_final: 0.7800 (mtm-85) REVERT: L 378 MET cc_start: 0.8041 (mtp) cc_final: 0.7818 (mtt) REVERT: Q 378 MET cc_start: 0.8462 (mtm) cc_final: 0.7426 (tmm) REVERT: Q 404 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8324 (tmtt) REVERT: P 83 TYR cc_start: 0.5130 (OUTLIER) cc_final: 0.4793 (t80) REVERT: P 87 ARG cc_start: 0.5448 (OUTLIER) cc_final: 0.5234 (ppt90) REVERT: C 442 ILE cc_start: 0.6788 (mt) cc_final: 0.6539 (mt) REVERT: C 537 PHE cc_start: 0.6914 (m-80) cc_final: 0.6620 (m-80) REVERT: C 539 LYS cc_start: 0.7188 (mtmm) cc_final: 0.6724 (tptt) REVERT: C 864 ILE cc_start: 0.5373 (OUTLIER) cc_final: 0.5166 (mp) REVERT: E 435 MET cc_start: 0.5743 (OUTLIER) cc_final: 0.4696 (mtm) REVERT: E 617 MET cc_start: 0.7050 (mmm) cc_final: 0.6686 (mmm) REVERT: E 624 ILE cc_start: 0.5370 (mt) cc_final: 0.4741 (tp) outliers start: 62 outliers final: 32 residues processed: 306 average time/residue: 1.1319 time to fit residues: 398.7897 Evaluate side-chains 312 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 272 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 101 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 646 ARG Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 864 ILE 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 605 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 826 LYS Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 218 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 224 ASN L 92 GLN L 331 HIS Q 102 GLN Q 114 ASN 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.221561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.129104 restraints weight = 34145.939| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.04 r_work: 0.3224 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18368 Z= 0.169 Angle : 0.541 7.410 24972 Z= 0.279 Chirality : 0.041 0.146 2982 Planarity : 0.004 0.046 3032 Dihedral : 6.367 58.546 2677 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.98 % Allowed : 13.61 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.17), residues: 2276 helix: 2.11 (0.13), residues: 1578 sheet: None (None), residues: 0 loop : 0.07 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 492 HIS 0.006 0.001 HIS Q 58 PHE 0.020 0.001 PHE Q 257 TYR 0.018 0.002 TYR K 178 ARG 0.004 0.000 ARG E 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00012 ( 2) link_NAG-ASN : angle 1.02113 ( 6) link_BETA1-4 : bond 0.00504 ( 2) link_BETA1-4 : angle 1.82182 ( 6) hydrogen bonds : bond 0.04863 ( 1244) hydrogen bonds : angle 4.40959 ( 3646) covalent geometry : bond 0.00386 (18364) covalent geometry : angle 0.53994 (24960) *********************** 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 325 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 269 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 338 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7078 (pp) REVERT: K 362 GLN cc_start: 0.6044 (OUTLIER) cc_final: 0.5618 (tp40) REVERT: K 382 LEU cc_start: 0.8222 (mt) cc_final: 0.7931 (tp) REVERT: K 383 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7580 (mp) REVERT: L 196 LYS cc_start: 0.8012 (mttp) cc_final: 0.7187 (tptp) REVERT: L 199 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7529 (tm-30) REVERT: L 312 LYS cc_start: 0.8522 (tptt) cc_final: 0.8157 (tmtt) REVERT: L 321 LYS cc_start: 0.8485 (mmtp) cc_final: 0.8188 (mmtt) REVERT: L 323 ARG cc_start: 0.8722 (mpt-90) cc_final: 0.7800 (mtm-85) REVERT: L 378 MET cc_start: 0.7966 (mtp) cc_final: 0.7742 (mtt) REVERT: Q 378 MET cc_start: 0.8408 (mtm) cc_final: 0.7395 (tmm) REVERT: Q 404 LYS cc_start: 0.8960 (tmtm) cc_final: 0.8297 (tmtt) REVERT: P 83 TYR cc_start: 0.5049 (OUTLIER) cc_final: 0.4715 (t80) REVERT: P 87 ARG cc_start: 0.5441 (OUTLIER) cc_final: 0.5198 (ppt90) REVERT: C 435 MET cc_start: 0.4717 (mtm) cc_final: 0.4515 (mtm) REVERT: C 442 ILE cc_start: 0.6751 (mt) cc_final: 0.6518 (mt) REVERT: C 481 THR cc_start: 0.5518 (m) cc_final: 0.5307 (p) REVERT: C 537 PHE cc_start: 0.6910 (m-80) cc_final: 0.6609 (m-80) REVERT: E 435 MET cc_start: 0.5618 (OUTLIER) cc_final: 0.4481 (mtm) REVERT: E 587 MET cc_start: 0.5036 (OUTLIER) cc_final: 0.4084 (mmm) REVERT: E 617 MET cc_start: 0.6908 (mmm) cc_final: 0.6581 (mmm) REVERT: E 624 ILE cc_start: 0.5358 (mt) cc_final: 0.4711 (tp) outliers start: 56 outliers final: 32 residues processed: 297 average time/residue: 1.0441 time to fit residues: 357.0489 Evaluate side-chains 307 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 268 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 259 SER 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 162 ILE Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 358 MET Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 587 MET Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 826 LYS Chi-restraints excluded: chain E residue 841 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 105 optimal weight: 0.6980 chunk 213 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 185 optimal weight: 0.5980 chunk 151 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 150 optimal weight: 6.9990 chunk 209 optimal weight: 30.0000 chunk 142 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 52 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.222142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130540 restraints weight = 27848.206| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.74 r_work: 0.3251 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18368 Z= 0.155 Angle : 0.527 9.003 24972 Z= 0.272 Chirality : 0.041 0.139 2982 Planarity : 0.004 0.045 3032 Dihedral : 6.002 59.184 2673 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.82 % Allowed : 13.09 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.17), residues: 2276 helix: 2.18 (0.13), residues: 1579 sheet: None (None), residues: 0 loop : 0.10 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 492 HIS 0.005 0.001 HIS Q 58 PHE 0.027 0.001 PHE C 582 TYR 0.018 0.002 TYR K 178 ARG 0.003 0.000 ARG E 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00014 ( 2) link_NAG-ASN : angle 1.07531 ( 6) link_BETA1-4 : bond 0.00505 ( 2) link_BETA1-4 : angle 2.01321 ( 6) hydrogen bonds : bond 0.04674 ( 1244) hydrogen bonds : angle 4.35717 ( 3646) covalent geometry : bond 0.00349 (18364) covalent geometry : angle 0.52591 (24960) *********************** 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 344 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 272 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7833 (mtt) REVERT: K 338 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7027 (pp) REVERT: K 362 GLN cc_start: 0.6039 (OUTLIER) cc_final: 0.5605 (tp40) REVERT: K 382 LEU cc_start: 0.8178 (mt) cc_final: 0.7835 (tp) REVERT: K 383 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7531 (mp) REVERT: L 196 LYS cc_start: 0.8019 (mttp) cc_final: 0.7365 (mtpp) REVERT: L 199 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7459 (tm-30) REVERT: L 312 LYS cc_start: 0.8495 (tptt) cc_final: 0.8122 (tmtt) REVERT: L 321 LYS cc_start: 0.8492 (mmtp) cc_final: 0.8202 (mmtt) REVERT: L 323 ARG cc_start: 0.8685 (mpt-90) cc_final: 0.7782 (mtm-85) REVERT: L 378 MET cc_start: 0.7927 (mtp) cc_final: 0.7704 (mtt) REVERT: Q 25 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6996 (tt0) REVERT: Q 378 MET cc_start: 0.8373 (mtm) cc_final: 0.7383 (tmm) REVERT: Q 404 LYS cc_start: 0.8912 (tmtm) cc_final: 0.8185 (tmtt) REVERT: P 83 TYR cc_start: 0.5013 (OUTLIER) cc_final: 0.4688 (t80) REVERT: P 87 ARG cc_start: 0.5441 (OUTLIER) cc_final: 0.5168 (ppt90) REVERT: C 442 ILE cc_start: 0.6741 (mt) cc_final: 0.6501 (mt) REVERT: C 473 GLU cc_start: 0.5649 (OUTLIER) cc_final: 0.5301 (tm-30) REVERT: C 481 THR cc_start: 0.5482 (m) cc_final: 0.5271 (p) REVERT: C 539 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6702 (tptt) REVERT: E 435 MET cc_start: 0.5498 (OUTLIER) cc_final: 0.4285 (mtm) REVERT: E 587 MET cc_start: 0.4914 (OUTLIER) cc_final: 0.4014 (mmm) REVERT: E 617 MET cc_start: 0.6812 (mmm) cc_final: 0.6483 (mmm) REVERT: E 679 PHE cc_start: 0.4318 (t80) cc_final: 0.3981 (t80) REVERT: E 712 MET cc_start: 0.3869 (mmp) cc_final: 0.3658 (mmp) outliers start: 72 outliers final: 34 residues processed: 314 average time/residue: 1.0667 time to fit residues: 386.7686 Evaluate side-chains 313 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 238 MET 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 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 7 LEU Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 358 MET Chi-restraints excluded: chain Q residue 367 SER Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 539 LYS Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 602 ARG 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 587 MET Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 841 ILE Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 99 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 209 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 GLN Q 58 HIS Q 102 GLN Q 114 ASN ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 840 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.223463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131618 restraints weight = 37372.000| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.64 r_work: 0.3218 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1997 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= 0.131 Angle : 0.513 9.651 24972 Z= 0.264 Chirality : 0.040 0.133 2982 Planarity : 0.004 0.044 3032 Dihedral : 5.735 55.934 2669 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.14 % Allowed : 14.29 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.17), residues: 2276 helix: 2.24 (0.13), residues: 1594 sheet: None (None), residues: 0 loop : 0.13 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 492 HIS 0.004 0.001 HIS K 329 PHE 0.022 0.001 PHE E 591 TYR 0.017 0.001 TYR K 178 ARG 0.003 0.000 ARG E 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00050 ( 2) link_NAG-ASN : angle 1.05712 ( 6) link_BETA1-4 : bond 0.00418 ( 2) link_BETA1-4 : angle 1.94889 ( 6) hydrogen bonds : bond 0.04387 ( 1244) hydrogen bonds : angle 4.28133 ( 3646) covalent geometry : bond 0.00284 (18364) covalent geometry : angle 0.51152 (24960) *********************** 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 318 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 259 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 275 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7843 (mm) REVERT: K 338 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.6987 (pp) REVERT: K 362 GLN cc_start: 0.5973 (OUTLIER) cc_final: 0.5574 (tp40) REVERT: K 382 LEU cc_start: 0.8191 (mt) cc_final: 0.7839 (tp) REVERT: K 383 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7557 (mp) REVERT: L 196 LYS cc_start: 0.8013 (mttp) cc_final: 0.7197 (tptp) REVERT: L 199 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7575 (tm-30) REVERT: L 312 LYS cc_start: 0.8516 (tptt) cc_final: 0.8175 (tmtt) REVERT: L 321 LYS cc_start: 0.8486 (mmtp) cc_final: 0.8187 (mmtt) REVERT: L 323 ARG cc_start: 0.8764 (mpt-90) cc_final: 0.7780 (mtm-85) REVERT: L 378 MET cc_start: 0.7977 (mtp) cc_final: 0.7749 (mtt) REVERT: Q 378 MET cc_start: 0.8410 (mtm) cc_final: 0.7344 (tmm) REVERT: Q 404 LYS cc_start: 0.8956 (tmtm) cc_final: 0.8240 (tmtt) REVERT: P 83 TYR cc_start: 0.4962 (OUTLIER) cc_final: 0.4645 (t80) REVERT: P 87 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.5140 (ppt90) REVERT: C 435 MET cc_start: 0.4597 (mtm) cc_final: 0.4355 (ttp) REVERT: C 442 ILE cc_start: 0.6746 (mt) cc_final: 0.6523 (mt) REVERT: C 473 GLU cc_start: 0.5592 (OUTLIER) cc_final: 0.5258 (tm-30) REVERT: C 539 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6717 (tptt) REVERT: C 587 MET cc_start: 0.5305 (mmp) cc_final: 0.5091 (mmp) REVERT: E 435 MET cc_start: 0.5445 (mtm) cc_final: 0.4238 (mtm) REVERT: E 587 MET cc_start: 0.5045 (OUTLIER) cc_final: 0.4109 (mmm) REVERT: E 617 MET cc_start: 0.6788 (mmm) cc_final: 0.6470 (mmm) REVERT: E 624 ILE cc_start: 0.5180 (mt) cc_final: 0.4779 (tp) outliers start: 59 outliers final: 31 residues processed: 298 average time/residue: 1.0319 time to fit residues: 353.4005 Evaluate side-chains 301 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 1.901 ------------------------------------------------------------------------------- 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 275 LEU 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 155 ASN 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 539 LYS Chi-restraints excluded: chain C residue 602 ARG 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 528 ILE Chi-restraints excluded: chain E residue 587 MET Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 841 ILE Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 46 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 GLN Q 102 GLN Q 332 ASN ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4393 r_free = 0.4393 target = 0.230362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.153660 restraints weight = 26098.248| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.76 r_work: 0.3266 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 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 = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18368 Z= 0.117 Angle : 0.502 9.890 24972 Z= 0.256 Chirality : 0.039 0.142 2982 Planarity : 0.004 0.044 3032 Dihedral : 5.553 56.293 2669 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.67 % Allowed : 15.39 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.18), residues: 2276 helix: 2.33 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : 0.20 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 831 HIS 0.004 0.001 HIS K 329 PHE 0.022 0.001 PHE E 591 TYR 0.016 0.001 TYR K 178 ARG 0.003 0.000 ARG C 832 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 2) link_NAG-ASN : angle 0.99795 ( 6) link_BETA1-4 : bond 0.00267 ( 2) link_BETA1-4 : angle 1.76034 ( 6) hydrogen bonds : bond 0.04100 ( 1244) hydrogen bonds : angle 4.22024 ( 3646) covalent geometry : bond 0.00246 (18364) covalent geometry : angle 0.50088 (24960) *********************** 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 323 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7826 (mtt) REVERT: K 275 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7764 (mm) REVERT: K 338 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6920 (pp) REVERT: K 362 GLN cc_start: 0.5990 (OUTLIER) cc_final: 0.5587 (tp40) REVERT: K 382 LEU cc_start: 0.8156 (mt) cc_final: 0.7814 (tp) REVERT: K 383 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7533 (mp) REVERT: L 196 LYS cc_start: 0.8018 (mttp) cc_final: 0.7207 (tptp) REVERT: L 199 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7517 (tm-30) REVERT: L 312 LYS cc_start: 0.8452 (tptt) cc_final: 0.8129 (tptt) REVERT: L 321 LYS cc_start: 0.8471 (mmtp) cc_final: 0.8186 (mmtt) REVERT: L 323 ARG cc_start: 0.8735 (mpt-90) cc_final: 0.7761 (mtm-85) REVERT: L 358 MET cc_start: 0.7006 (ttm) cc_final: 0.5813 (tmt) REVERT: L 378 MET cc_start: 0.7909 (mtp) cc_final: 0.7673 (mtt) REVERT: Q 378 MET cc_start: 0.8375 (mtm) cc_final: 0.7309 (tmm) REVERT: Q 404 LYS cc_start: 0.8927 (tmtm) cc_final: 0.8134 (tmtt) REVERT: P 83 TYR cc_start: 0.4949 (OUTLIER) cc_final: 0.4634 (t80) REVERT: P 87 ARG cc_start: 0.5461 (OUTLIER) cc_final: 0.5148 (ppt90) REVERT: C 388 ARG cc_start: 0.7070 (ttp-170) cc_final: 0.6761 (ttp-170) REVERT: C 473 GLU cc_start: 0.5391 (OUTLIER) cc_final: 0.5107 (tm-30) REVERT: C 539 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6598 (tptt) REVERT: E 435 MET cc_start: 0.5324 (mtm) cc_final: 0.4198 (mtm) REVERT: E 617 MET cc_start: 0.6697 (mmm) cc_final: 0.6382 (mmm) REVERT: E 624 ILE cc_start: 0.4933 (mt) cc_final: 0.4608 (pp) REVERT: E 791 ILE cc_start: 0.5277 (mm) cc_final: 0.5076 (mm) outliers start: 50 outliers final: 29 residues processed: 305 average time/residue: 1.0855 time to fit residues: 379.5356 Evaluate side-chains 297 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 259 time to evaluate : 1.760 ------------------------------------------------------------------------------- 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 275 LEU 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 155 ASN 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 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 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 539 LYS Chi-restraints excluded: chain C residue 602 ARG 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 615 LEU 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 117 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 142 optimal weight: 0.9990 chunk 173 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 102 GLN Q 114 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.222244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.131697 restraints weight = 24732.443| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.99 r_work: 0.3250 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18368 Z= 0.164 Angle : 0.542 10.654 24972 Z= 0.277 Chirality : 0.041 0.179 2982 Planarity : 0.004 0.049 3032 Dihedral : 5.573 56.274 2669 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.67 % Allowed : 15.65 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.17), residues: 2276 helix: 2.27 (0.13), residues: 1575 sheet: None (None), residues: 0 loop : 0.16 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 831 HIS 0.005 0.001 HIS K 329 PHE 0.031 0.002 PHE E 591 TYR 0.017 0.002 TYR K 178 ARG 0.003 0.000 ARG C 832 Details of bonding type rmsd link_NAG-ASN : bond 0.00044 ( 2) link_NAG-ASN : angle 0.97063 ( 6) link_BETA1-4 : bond 0.00362 ( 2) link_BETA1-4 : angle 1.66535 ( 6) hydrogen bonds : bond 0.04624 ( 1244) hydrogen bonds : angle 4.30639 ( 3646) covalent geometry : bond 0.00378 (18364) covalent geometry : angle 0.54143 (24960) *********************** 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 316 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 266 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7822 (mtt) REVERT: K 275 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7795 (mm) REVERT: K 338 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6925 (pp) REVERT: K 362 GLN cc_start: 0.6060 (OUTLIER) cc_final: 0.5641 (tp40) REVERT: K 382 LEU cc_start: 0.8162 (mt) cc_final: 0.7815 (tp) REVERT: K 383 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7400 (mp) REVERT: L 196 LYS cc_start: 0.8044 (mttp) cc_final: 0.7356 (mtpp) REVERT: L 199 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7456 (tm-30) REVERT: L 312 LYS cc_start: 0.8486 (tptt) cc_final: 0.8124 (tmtt) REVERT: L 321 LYS cc_start: 0.8470 (mmtp) cc_final: 0.8187 (mmtt) REVERT: L 323 ARG cc_start: 0.8694 (mpt-90) cc_final: 0.7746 (mtm-85) REVERT: L 358 MET cc_start: 0.7091 (ttm) cc_final: 0.5891 (tmt) REVERT: L 378 MET cc_start: 0.7895 (mtp) cc_final: 0.7656 (mtt) REVERT: Q 378 MET cc_start: 0.8376 (mtm) cc_final: 0.7347 (tmm) REVERT: Q 404 LYS cc_start: 0.8894 (tmtm) cc_final: 0.8091 (tmtt) REVERT: P 83 TYR cc_start: 0.5016 (OUTLIER) cc_final: 0.4701 (t80) REVERT: P 87 ARG cc_start: 0.5453 (OUTLIER) cc_final: 0.5126 (ppt90) REVERT: C 388 ARG cc_start: 0.7130 (ttp-170) cc_final: 0.6756 (ttp-170) REVERT: C 435 MET cc_start: 0.4630 (mtm) cc_final: 0.3250 (mtm) REVERT: C 442 ILE cc_start: 0.6666 (mt) cc_final: 0.6443 (mt) REVERT: C 473 GLU cc_start: 0.5579 (OUTLIER) cc_final: 0.5273 (tm-30) REVERT: C 539 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6625 (tptt) REVERT: C 741 MET cc_start: 0.4482 (mmm) cc_final: 0.2987 (tmm) REVERT: E 435 MET cc_start: 0.5422 (mtm) cc_final: 0.4108 (mtm) REVERT: E 617 MET cc_start: 0.6700 (mmm) cc_final: 0.6385 (mmm) REVERT: E 841 ILE cc_start: 0.4624 (OUTLIER) cc_final: 0.4413 (mm) outliers start: 50 outliers final: 30 residues processed: 299 average time/residue: 1.1245 time to fit residues: 387.4311 Evaluate side-chains 306 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 275 LEU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 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 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 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 539 LYS Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 841 ILE 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 203 optimal weight: 7.9990 chunk 204 optimal weight: 30.0000 chunk 86 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 211 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 199 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 102 GLN ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.228823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.152199 restraints weight = 27378.289| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.32 r_work: 0.3241 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2240 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= 0.140 Angle : 0.531 9.368 24972 Z= 0.271 Chirality : 0.040 0.157 2982 Planarity : 0.004 0.048 3032 Dihedral : 5.498 58.248 2665 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.67 % Allowed : 16.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.17), residues: 2276 helix: 2.24 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : 0.20 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 831 HIS 0.005 0.001 HIS K 329 PHE 0.030 0.001 PHE E 591 TYR 0.020 0.001 TYR K 178 ARG 0.005 0.000 ARG C 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 2) link_NAG-ASN : angle 0.90208 ( 6) link_BETA1-4 : bond 0.00390 ( 2) link_BETA1-4 : angle 1.56433 ( 6) hydrogen bonds : bond 0.04391 ( 1244) hydrogen bonds : angle 4.28188 ( 3646) covalent geometry : bond 0.00312 (18364) covalent geometry : angle 0.53087 (24960) *********************** 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 311 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7893 (mtt) REVERT: K 275 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7806 (mm) REVERT: K 338 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6935 (pp) REVERT: K 362 GLN cc_start: 0.6031 (OUTLIER) cc_final: 0.5614 (tp40) REVERT: K 382 LEU cc_start: 0.8205 (mt) cc_final: 0.7910 (tp) REVERT: K 383 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7428 (mp) REVERT: L 196 LYS cc_start: 0.8041 (mttp) cc_final: 0.7355 (mtpp) REVERT: L 199 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7511 (tm-30) REVERT: L 312 LYS cc_start: 0.8502 (tptt) cc_final: 0.8175 (tptt) REVERT: L 321 LYS cc_start: 0.8492 (mmtp) cc_final: 0.8209 (mmtt) REVERT: L 323 ARG cc_start: 0.8734 (mpt-90) cc_final: 0.7761 (mtm-85) REVERT: L 378 MET cc_start: 0.7943 (mtp) cc_final: 0.7712 (mtt) REVERT: Q 378 MET cc_start: 0.8400 (mtm) cc_final: 0.7327 (tmm) REVERT: Q 404 LYS cc_start: 0.8937 (tmtm) cc_final: 0.8153 (tmtt) REVERT: P 83 TYR cc_start: 0.4953 (OUTLIER) cc_final: 0.4649 (t80) REVERT: P 87 ARG cc_start: 0.5439 (OUTLIER) cc_final: 0.5084 (ppt90) REVERT: C 388 ARG cc_start: 0.7063 (ttp-170) cc_final: 0.6842 (ttp80) REVERT: C 473 GLU cc_start: 0.5389 (OUTLIER) cc_final: 0.5135 (tm-30) REVERT: C 539 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6558 (tptt) REVERT: E 435 MET cc_start: 0.5223 (mtm) cc_final: 0.4054 (mtm) REVERT: E 617 MET cc_start: 0.6683 (mmm) cc_final: 0.6455 (mmm) outliers start: 50 outliers final: 29 residues processed: 294 average time/residue: 1.0598 time to fit residues: 358.3130 Evaluate side-chains 297 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 259 time to evaluate : 1.719 ------------------------------------------------------------------------------- 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 275 LEU 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 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 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 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 539 LYS Chi-restraints excluded: chain C residue 602 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 615 LEU Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 869 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 27 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 127 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 152 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 102 GLN Q 114 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.221667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128565 restraints weight = 38871.645| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.36 r_work: 0.3214 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 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 = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18368 Z= 0.172 Angle : 0.559 13.535 24972 Z= 0.286 Chirality : 0.041 0.169 2982 Planarity : 0.004 0.051 3032 Dihedral : 5.513 58.037 2665 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.41 % Allowed : 16.28 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.17), residues: 2276 helix: 2.15 (0.13), residues: 1582 sheet: None (None), residues: 0 loop : 0.11 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 831 HIS 0.005 0.001 HIS K 329 PHE 0.029 0.002 PHE E 591 TYR 0.021 0.002 TYR K 178 ARG 0.003 0.000 ARG E 589 Details of bonding type rmsd link_NAG-ASN : bond 0.00038 ( 2) link_NAG-ASN : angle 0.96078 ( 6) link_BETA1-4 : bond 0.00440 ( 2) link_BETA1-4 : angle 1.45267 ( 6) hydrogen bonds : bond 0.04750 ( 1244) hydrogen bonds : angle 4.35168 ( 3646) covalent geometry : bond 0.00396 (18364) covalent geometry : angle 0.55841 (24960) ********************** 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 306 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 3.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 238 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7934 (mtt) REVERT: K 275 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7864 (mm) REVERT: K 338 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7021 (pp) REVERT: K 362 GLN cc_start: 0.6051 (OUTLIER) cc_final: 0.5624 (tp40) REVERT: K 382 LEU cc_start: 0.8259 (mt) cc_final: 0.7947 (tp) REVERT: K 383 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7457 (mp) REVERT: L 196 LYS cc_start: 0.8079 (mttp) cc_final: 0.7379 (mtpp) REVERT: L 199 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7542 (tm-30) REVERT: L 312 LYS cc_start: 0.8538 (tptt) cc_final: 0.8181 (tmtt) REVERT: L 321 LYS cc_start: 0.8504 (mmtp) cc_final: 0.8225 (mmtt) REVERT: L 323 ARG cc_start: 0.8739 (mpt-90) cc_final: 0.7791 (mtm-85) REVERT: L 378 MET cc_start: 0.7996 (mtp) cc_final: 0.7775 (mtt) REVERT: Q 358 MET cc_start: 0.8884 (ptm) cc_final: 0.8572 (ptp) REVERT: Q 378 MET cc_start: 0.8443 (mtm) cc_final: 0.7410 (tmm) REVERT: Q 404 LYS cc_start: 0.8954 (tmtm) cc_final: 0.8176 (tmtt) REVERT: P 83 TYR cc_start: 0.4945 (OUTLIER) cc_final: 0.4650 (t80) REVERT: P 87 ARG cc_start: 0.5428 (OUTLIER) cc_final: 0.5055 (ppt90) REVERT: C 473 GLU cc_start: 0.5635 (OUTLIER) cc_final: 0.5334 (tm-30) REVERT: C 539 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6687 (tptt) REVERT: C 586 MET cc_start: 0.5852 (mmm) cc_final: 0.5640 (mmt) REVERT: C 587 MET cc_start: 0.5361 (mmp) cc_final: 0.5128 (mmp) REVERT: C 639 LYS cc_start: 0.5999 (pttp) cc_final: 0.5601 (ttmt) REVERT: C 741 MET cc_start: 0.4456 (mmm) cc_final: 0.3899 (mmt) REVERT: E 435 MET cc_start: 0.5309 (mtm) cc_final: 0.3971 (mtm) REVERT: E 617 MET cc_start: 0.6738 (mmm) cc_final: 0.6508 (mmm) outliers start: 45 outliers final: 33 residues processed: 290 average time/residue: 1.5797 time to fit residues: 526.3804 Evaluate side-chains 302 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 260 time to evaluate : 2.131 ------------------------------------------------------------------------------- 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 275 LEU Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 305 MET 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 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 539 LYS Chi-restraints excluded: chain C residue 544 PHE Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 664 MET Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 646 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 175 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 203 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 214 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 GLN Q 102 GLN ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 840 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.224871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.137316 restraints weight = 27152.205| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.52 r_work: 0.3261 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2360 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= 0.116 Angle : 0.517 12.241 24972 Z= 0.262 Chirality : 0.040 0.170 2982 Planarity : 0.004 0.046 3032 Dihedral : 5.317 56.672 2665 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.30 % Allowed : 16.49 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.18), residues: 2276 helix: 2.29 (0.13), residues: 1592 sheet: None (None), residues: 0 loop : 0.18 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 831 HIS 0.004 0.001 HIS K 329 PHE 0.028 0.001 PHE E 591 TYR 0.017 0.001 TYR K 178 ARG 0.004 0.000 ARG E 589 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 2) link_NAG-ASN : angle 0.93110 ( 6) link_BETA1-4 : bond 0.00339 ( 2) link_BETA1-4 : angle 1.36444 ( 6) hydrogen bonds : bond 0.04090 ( 1244) hydrogen bonds : angle 4.24300 ( 3646) covalent geometry : bond 0.00246 (18364) covalent geometry : angle 0.51631 (24960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21282.25 seconds wall clock time: 371 minutes 41.91 seconds (22301.91 seconds total)