Starting phenix.real_space_refine on Sat Sep 28 01:29:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/09_2024/8crt_26958.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/09_2024/8crt_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/09_2024/8crt_26958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/09_2024/8crt_26958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/09_2024/8crt_26958.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crt_26958/09_2024/8crt_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-5461/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: 12.85, 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: 4.58 Conformation dependent library (CDL) restraints added in 2.7 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: 1.74 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: 6.08 Time building geometry restraints manager: 5.33 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: 6.890 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: 1.290 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.290 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.670 ------------------------------------------------------------------------------- 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 18364 Z= 0.206 Angle : 0.582 8.279 24960 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 *********************** 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 fitting. rotamer outliers: 44 poor density : 335 time to evaluate : 1.733 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: 0.9833 time to fit residues: 417.4815 Evaluate side-chains 305 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 293 time to evaluate : 1.858 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 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 18364 Z= 0.246 Angle : 0.560 7.003 24960 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 *********************** 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 fitting. rotamer outliers: 55 poor density : 283 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 235 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7842 (ttmm) REVERT: K 338 LEU cc_start: 0.7458 (tm) cc_final: 0.7016 (pp) REVERT: K 362 GLN cc_start: 0.5919 (OUTLIER) cc_final: 0.5479 (tp40) REVERT: K 382 LEU cc_start: 0.8109 (mt) cc_final: 0.7785 (tp) REVERT: K 383 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7609 (mp) REVERT: L 196 LYS cc_start: 0.7748 (mttp) cc_final: 0.7224 (tptp) REVERT: L 312 LYS cc_start: 0.8365 (tptt) cc_final: 0.8074 (tptt) REVERT: L 321 LYS cc_start: 0.8332 (mmtp) cc_final: 0.8105 (mmtt) REVERT: L 323 ARG cc_start: 0.8279 (mpt-90) cc_final: 0.7787 (mtm-85) REVERT: L 358 MET cc_start: 0.6636 (ttp) cc_final: 0.5812 (ttp) REVERT: Q 80 VAL cc_start: 0.8589 (p) cc_final: 0.8382 (t) REVERT: Q 378 MET cc_start: 0.8167 (mtm) cc_final: 0.7456 (tmm) REVERT: Q 404 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8038 (tmtt) REVERT: P 83 TYR cc_start: 0.5340 (OUTLIER) cc_final: 0.5099 (t80) REVERT: C 442 ILE cc_start: 0.6382 (mt) cc_final: 0.6132 (mt) REVERT: C 833 MET cc_start: 0.4714 (ttp) cc_final: 0.4464 (mtp) REVERT: E 488 VAL cc_start: 0.5201 (t) cc_final: 0.4959 (t) REVERT: E 587 MET cc_start: 0.3764 (OUTLIER) cc_final: 0.3443 (mmm) outliers start: 55 outliers final: 21 residues processed: 309 average time/residue: 1.0991 time to fit residues: 393.9857 Evaluate side-chains 296 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 269 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 235 LYS 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 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 115 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 205 optimal weight: 30.0000 chunk 70 optimal weight: 0.9980 chunk 166 optimal weight: 20.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- 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 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 18364 Z= 0.416 Angle : 0.651 9.489 24960 Z= 0.335 Chirality : 0.046 0.277 2982 Planarity : 0.005 0.048 3032 Dihedral : 7.093 59.065 2681 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.46 % Allowed : 11.83 % Favored : 84.71 % 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: 1.74 (0.17), residues: 2276 helix: 1.70 (0.13), residues: 1595 sheet: None (None), residues: 0 loop : -0.05 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 831 HIS 0.011 0.002 HIS Q 58 PHE 0.024 0.002 PHE C 582 TYR 0.024 0.002 TYR L 180 ARG 0.004 0.001 ARG C 832 *********************** 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 355 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 290 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8724 (tt) REVERT: K 338 LEU cc_start: 0.7535 (tm) cc_final: 0.7095 (pp) REVERT: K 362 GLN cc_start: 0.5975 (OUTLIER) cc_final: 0.5510 (tp40) REVERT: K 382 LEU cc_start: 0.8192 (mt) cc_final: 0.7896 (tp) REVERT: K 383 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7623 (mp) REVERT: L 196 LYS cc_start: 0.7905 (mttp) cc_final: 0.7323 (mtpp) REVERT: L 199 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7272 (tm-30) REVERT: L 321 LYS cc_start: 0.8336 (mmtp) cc_final: 0.8119 (mmtt) REVERT: L 323 ARG cc_start: 0.8308 (mpt-90) cc_final: 0.7794 (mtm-85) REVERT: Q 101 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8441 (mp) REVERT: Q 369 ILE cc_start: 0.8821 (mt) cc_final: 0.8609 (mt) REVERT: Q 378 MET cc_start: 0.8217 (mtm) cc_final: 0.7474 (tmm) REVERT: Q 404 LYS cc_start: 0.8752 (tmtm) cc_final: 0.8107 (tmtt) REVERT: P 83 TYR cc_start: 0.5391 (OUTLIER) cc_final: 0.5143 (t80) REVERT: C 442 ILE cc_start: 0.6523 (mt) cc_final: 0.6260 (mt) REVERT: C 864 ILE cc_start: 0.4542 (OUTLIER) cc_final: 0.4312 (mp) REVERT: E 435 MET cc_start: 0.4384 (OUTLIER) cc_final: 0.2788 (mtm) REVERT: E 679 PHE cc_start: 0.3404 (t80) cc_final: 0.3123 (t80) REVERT: E 712 MET cc_start: 0.4547 (mmp) cc_final: 0.4275 (mmp) outliers start: 65 outliers final: 34 residues processed: 320 average time/residue: 0.9776 time to fit residues: 362.0358 Evaluate side-chains 317 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 276 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 294 PHE 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 162 ILE Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 358 MET Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 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 732 VAL Chi-restraints excluded: chain E residue 826 LYS Chi-restraints excluded: chain E residue 841 ILE 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 204 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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 175 HIS 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18364 Z= 0.180 Angle : 0.517 7.809 24960 Z= 0.267 Chirality : 0.040 0.141 2982 Planarity : 0.004 0.046 3032 Dihedral : 6.059 57.058 2665 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.98 % Allowed : 14.03 % Favored : 82.98 % 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: 1588 sheet: None (None), residues: 0 loop : 0.10 (0.23), residues: 688 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 0.023 0.001 PHE E 591 TYR 0.018 0.001 TYR K 178 ARG 0.007 0.000 ARG P 87 *********************** 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 331 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 275 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 235 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7712 (mtmt) REVERT: K 338 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6986 (pp) REVERT: K 362 GLN cc_start: 0.5944 (OUTLIER) cc_final: 0.5475 (tp40) REVERT: K 382 LEU cc_start: 0.8093 (mt) cc_final: 0.7850 (tp) REVERT: K 383 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7630 (mp) REVERT: L 196 LYS cc_start: 0.7925 (mttp) cc_final: 0.7338 (tptp) REVERT: L 199 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7252 (tm-30) REVERT: L 312 LYS cc_start: 0.8434 (tptt) cc_final: 0.7937 (tmtt) REVERT: L 321 LYS cc_start: 0.8323 (mmtp) cc_final: 0.8116 (mmtt) REVERT: L 323 ARG cc_start: 0.8282 (mpt-90) cc_final: 0.7763 (mtm-85) REVERT: Q 378 MET cc_start: 0.8169 (mtm) cc_final: 0.7445 (tmm) REVERT: Q 404 LYS cc_start: 0.8703 (tmtm) cc_final: 0.8017 (tmtt) REVERT: P 83 TYR cc_start: 0.5404 (OUTLIER) cc_final: 0.5137 (t80) REVERT: C 442 ILE cc_start: 0.6360 (mt) cc_final: 0.6098 (mt) REVERT: C 473 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5977 (tm-30) REVERT: E 435 MET cc_start: 0.4246 (OUTLIER) cc_final: 0.2508 (mtm) REVERT: E 587 MET cc_start: 0.3989 (OUTLIER) cc_final: 0.3640 (mmm) REVERT: E 679 PHE cc_start: 0.3286 (t80) cc_final: 0.3022 (t80) REVERT: E 741 MET cc_start: 0.3532 (mmt) cc_final: 0.3118 (mmt) outliers start: 56 outliers final: 21 residues processed: 307 average time/residue: 1.0128 time to fit residues: 358.8633 Evaluate side-chains 293 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 264 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 235 LYS Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 338 LEU Chi-restraints excluded: chain K residue 362 GLN Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 614 ILE 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 682 SER Chi-restraints excluded: chain E residue 826 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 188 optimal weight: 30.0000 chunk 152 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 0.1980 chunk 197 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 18364 Z= 0.360 Angle : 0.593 8.295 24960 Z= 0.306 Chirality : 0.043 0.147 2982 Planarity : 0.005 0.043 3032 Dihedral : 6.004 57.966 2665 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.87 % Allowed : 13.98 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.02 (0.17), residues: 2276 helix: 1.95 (0.13), residues: 1581 sheet: None (None), residues: 0 loop : -0.02 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 831 HIS 0.008 0.001 HIS Q 58 PHE 0.025 0.002 PHE C 582 TYR 0.020 0.002 TYR L 180 ARG 0.004 0.000 ARG P 87 *********************** 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 347 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 274 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 235 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7813 (mtmt) REVERT: K 338 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7054 (pp) REVERT: K 362 GLN cc_start: 0.5981 (OUTLIER) cc_final: 0.5498 (tp40) REVERT: K 382 LEU cc_start: 0.8167 (mt) cc_final: 0.7887 (tp) REVERT: K 383 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7582 (mp) REVERT: L 196 LYS cc_start: 0.7968 (mttp) cc_final: 0.7409 (mtpp) REVERT: L 199 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7277 (tm-30) REVERT: L 312 LYS cc_start: 0.8503 (tptt) cc_final: 0.8004 (tmtt) REVERT: L 323 ARG cc_start: 0.8304 (mpt-90) cc_final: 0.7784 (mtm-85) REVERT: Q 25 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6894 (tt0) REVERT: Q 378 MET cc_start: 0.8183 (mtm) cc_final: 0.7456 (tmm) REVERT: Q 404 LYS cc_start: 0.8728 (tmtm) cc_final: 0.8043 (tmtt) REVERT: P 83 TYR cc_start: 0.5435 (OUTLIER) cc_final: 0.5158 (t80) REVERT: C 442 ILE cc_start: 0.6429 (mt) cc_final: 0.6162 (mt) REVERT: C 473 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6025 (tm-30) REVERT: E 435 MET cc_start: 0.4321 (OUTLIER) cc_final: 0.2440 (mtm) REVERT: E 587 MET cc_start: 0.4076 (OUTLIER) cc_final: 0.3772 (mmm) REVERT: E 679 PHE cc_start: 0.3360 (t80) cc_final: 0.3055 (t80) REVERT: E 741 MET cc_start: 0.3660 (mmt) cc_final: 0.3121 (mmt) outliers start: 73 outliers final: 44 residues processed: 317 average time/residue: 0.9758 time to fit residues: 358.0051 Evaluate side-chains 318 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 265 time to evaluate : 1.774 ------------------------------------------------------------------------------- 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 60 LEU Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 235 LYS 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 60 MET Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 294 PHE 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 101 LEU Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 528 ILE 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 684 ILE Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 832 ARG Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 587 MET Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 682 SER Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 826 LYS 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 74 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 52 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18364 Z= 0.190 Angle : 0.520 9.754 24960 Z= 0.268 Chirality : 0.040 0.138 2982 Planarity : 0.004 0.044 3032 Dihedral : 5.744 55.811 2665 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.30 % Allowed : 14.82 % Favored : 81.88 % 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: 2.31 (0.17), residues: 2276 helix: 2.17 (0.13), residues: 1587 sheet: None (None), residues: 0 loop : 0.07 (0.23), residues: 689 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 0.018 0.001 PHE C 789 TYR 0.017 0.001 TYR K 178 ARG 0.004 0.000 ARG P 87 *********************** 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 325 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 263 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 275 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7871 (mm) REVERT: K 338 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6985 (pp) REVERT: K 362 GLN cc_start: 0.5958 (OUTLIER) cc_final: 0.5470 (tp40) REVERT: K 382 LEU cc_start: 0.8112 (mt) cc_final: 0.7806 (tp) REVERT: K 383 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7613 (mp) REVERT: L 196 LYS cc_start: 0.7984 (mttp) cc_final: 0.7456 (mtpp) REVERT: L 199 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7253 (tm-30) REVERT: L 312 LYS cc_start: 0.8439 (tptt) cc_final: 0.8024 (tptt) REVERT: L 323 ARG cc_start: 0.8313 (mpt-90) cc_final: 0.7781 (mtm-85) REVERT: Q 25 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6830 (tt0) REVERT: Q 378 MET cc_start: 0.8146 (mtm) cc_final: 0.7431 (tmm) REVERT: Q 404 LYS cc_start: 0.8703 (tmtm) cc_final: 0.7989 (tmtt) REVERT: P 83 TYR cc_start: 0.5396 (OUTLIER) cc_final: 0.5125 (t80) REVERT: C 442 ILE cc_start: 0.6350 (mt) cc_final: 0.6087 (mt) REVERT: C 473 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.6007 (tm-30) REVERT: C 586 MET cc_start: 0.6183 (mmm) cc_final: 0.5884 (mmt) REVERT: E 435 MET cc_start: 0.4205 (OUTLIER) cc_final: 0.2217 (mtm) REVERT: E 587 MET cc_start: 0.4006 (OUTLIER) cc_final: 0.3689 (mmm) REVERT: E 624 ILE cc_start: 0.6681 (mt) cc_final: 0.6349 (tp) REVERT: E 741 MET cc_start: 0.3615 (mmt) cc_final: 0.3094 (mmt) outliers start: 62 outliers final: 35 residues processed: 299 average time/residue: 1.0217 time to fit residues: 351.1740 Evaluate side-chains 303 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 259 time to evaluate : 2.045 ------------------------------------------------------------------------------- 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 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 60 MET Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 387 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 277 LEU Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 528 ILE 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 663 MET Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 537 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 185 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 219 optimal weight: 0.9980 chunk 137 optimal weight: 30.0000 chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 52 GLN L 331 HIS Q 102 GLN Q 114 ASN Q 331 HIS Q 332 ASN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 18364 Z= 0.464 Angle : 0.649 9.477 24960 Z= 0.335 Chirality : 0.046 0.154 2982 Planarity : 0.005 0.042 3032 Dihedral : 5.818 55.612 2661 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.82 % Allowed : 14.71 % Favored : 81.47 % 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: 1.77 (0.17), residues: 2276 helix: 1.76 (0.13), residues: 1578 sheet: None (None), residues: 0 loop : -0.10 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 831 HIS 0.010 0.001 HIS Q 58 PHE 0.034 0.002 PHE E 591 TYR 0.024 0.002 TYR L 180 ARG 0.005 0.001 ARG K 234 *********************** 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 335 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 263 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 16 TRP cc_start: 0.7415 (OUTLIER) cc_final: 0.7087 (t-100) REVERT: K 235 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7835 (mtmt) REVERT: K 275 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8001 (mm) REVERT: K 338 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7068 (pp) REVERT: K 362 GLN cc_start: 0.6003 (OUTLIER) cc_final: 0.5513 (tp40) REVERT: K 382 LEU cc_start: 0.8214 (mt) cc_final: 0.7887 (tp) REVERT: K 383 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7633 (mp) REVERT: L 196 LYS cc_start: 0.8010 (mttp) cc_final: 0.7410 (mtpp) REVERT: L 199 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7266 (tm-30) REVERT: L 312 LYS cc_start: 0.8516 (tptt) cc_final: 0.8014 (tmtt) REVERT: L 323 ARG cc_start: 0.8325 (mpt-90) cc_final: 0.7799 (mtm-85) REVERT: Q 25 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: Q 358 MET cc_start: 0.8770 (ptm) cc_final: 0.8496 (ptp) REVERT: Q 378 MET cc_start: 0.8197 (mtm) cc_final: 0.7462 (tmm) REVERT: Q 404 LYS cc_start: 0.8757 (tmtm) cc_final: 0.8069 (tmtt) REVERT: P 83 TYR cc_start: 0.5474 (OUTLIER) cc_final: 0.5183 (t80) REVERT: C 442 ILE cc_start: 0.6428 (mt) cc_final: 0.6156 (mt) REVERT: C 473 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6297 (tm-30) REVERT: C 586 MET cc_start: 0.6323 (mmm) cc_final: 0.6065 (OUTLIER) REVERT: E 435 MET cc_start: 0.4343 (OUTLIER) cc_final: 0.2362 (mtm) REVERT: E 587 MET cc_start: 0.4152 (OUTLIER) cc_final: 0.3876 (mmm) REVERT: E 624 ILE cc_start: 0.6822 (mt) cc_final: 0.6341 (tp) REVERT: E 679 PHE cc_start: 0.3380 (t80) cc_final: 0.3019 (t80) outliers start: 72 outliers final: 46 residues processed: 307 average time/residue: 1.0091 time to fit residues: 358.0823 Evaluate side-chains 311 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 255 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 235 LYS 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 60 MET Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 294 PHE Chi-restraints excluded: chain L residue 356 THR 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 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 D residue 100 MET Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 528 ILE 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 664 MET Chi-restraints excluded: chain C residue 684 ILE 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 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 537 PHE 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 682 SER Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 740 VAL Chi-restraints excluded: chain E residue 828 VAL Chi-restraints excluded: chain E residue 841 ILE 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 135 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 52 GLN L 331 HIS Q 58 HIS Q 102 GLN Q 331 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18364 Z= 0.197 Angle : 0.540 10.673 24960 Z= 0.277 Chirality : 0.040 0.154 2982 Planarity : 0.004 0.044 3032 Dihedral : 5.578 55.080 2661 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.04 % Allowed : 15.86 % Favored : 81.10 % 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: 2.14 (0.17), residues: 2276 helix: 2.06 (0.13), residues: 1578 sheet: None (None), residues: 0 loop : -0.00 (0.23), residues: 698 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 0.029 0.001 PHE E 591 TYR 0.017 0.001 TYR K 178 ARG 0.004 0.000 ARG P 87 *********************** 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 326 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 269 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 235 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7763 (mtmt) REVERT: K 275 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7885 (mm) REVERT: K 338 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.6977 (pp) REVERT: K 362 GLN cc_start: 0.5994 (OUTLIER) cc_final: 0.5489 (tp40) REVERT: K 382 LEU cc_start: 0.8113 (mt) cc_final: 0.7777 (tp) REVERT: K 383 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7644 (mp) REVERT: L 196 LYS cc_start: 0.8011 (mttp) cc_final: 0.7455 (mtpp) REVERT: L 199 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7216 (tm-30) REVERT: L 312 LYS cc_start: 0.8450 (tptt) cc_final: 0.8023 (tptt) REVERT: L 323 ARG cc_start: 0.8319 (mpt-90) cc_final: 0.7775 (mtm-85) REVERT: Q 351 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7897 (mtt) REVERT: Q 358 MET cc_start: 0.8676 (ptm) cc_final: 0.8425 (ptp) REVERT: Q 378 MET cc_start: 0.8156 (mtm) cc_final: 0.7424 (tmm) REVERT: Q 404 LYS cc_start: 0.8713 (tmtm) cc_final: 0.7998 (tmtt) REVERT: P 83 TYR cc_start: 0.5414 (OUTLIER) cc_final: 0.5132 (t80) REVERT: C 442 ILE cc_start: 0.6265 (mt) cc_final: 0.6013 (mt) REVERT: C 473 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6301 (tm-30) REVERT: E 435 MET cc_start: 0.4182 (OUTLIER) cc_final: 0.2160 (mtm) REVERT: E 624 ILE cc_start: 0.6747 (mt) cc_final: 0.6391 (tp) REVERT: E 679 PHE cc_start: 0.3266 (t80) cc_final: 0.2919 (t80) outliers start: 57 outliers final: 32 residues processed: 306 average time/residue: 0.9677 time to fit residues: 343.0292 Evaluate side-chains 308 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 267 time to evaluate : 1.950 ------------------------------------------------------------------------------- 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 200 GLN Chi-restraints excluded: chain K residue 235 LYS Chi-restraints excluded: chain K residue 275 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 60 MET Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 351 MET Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 602 ARG 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 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 537 PHE Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 682 SER 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 199 optimal weight: 5.9990 chunk 210 optimal weight: 0.6980 chunk 192 optimal weight: 6.9990 chunk 204 optimal weight: 30.0000 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 52 GLN Q 102 GLN Q 114 ASN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18364 Z= 0.272 Angle : 0.579 11.481 24960 Z= 0.295 Chirality : 0.042 0.216 2982 Planarity : 0.005 0.048 3032 Dihedral : 5.557 55.486 2661 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.93 % Allowed : 16.44 % Favored : 80.63 % 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: 2.03 (0.13), residues: 1576 sheet: None (None), residues: 0 loop : -0.08 (0.23), residues: 700 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 0.027 0.002 PHE E 591 TYR 0.018 0.002 TYR K 178 ARG 0.004 0.000 ARG P 87 *********************** 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 318 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 263 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 235 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7807 (mtmt) REVERT: K 275 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7916 (mm) REVERT: K 338 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.6987 (pp) REVERT: K 362 GLN cc_start: 0.6001 (OUTLIER) cc_final: 0.5485 (tp40) REVERT: K 382 LEU cc_start: 0.8145 (mt) cc_final: 0.7858 (tp) REVERT: K 383 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7635 (mp) REVERT: L 196 LYS cc_start: 0.8015 (mttp) cc_final: 0.7459 (mtpp) REVERT: L 199 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7230 (tm-30) REVERT: L 312 LYS cc_start: 0.8483 (tptt) cc_final: 0.8060 (tptt) REVERT: L 323 ARG cc_start: 0.8327 (mpt-90) cc_final: 0.7789 (mtm-85) REVERT: Q 351 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7903 (mtt) REVERT: Q 358 MET cc_start: 0.8716 (ptm) cc_final: 0.8467 (ptp) REVERT: Q 378 MET cc_start: 0.8164 (mtm) cc_final: 0.7437 (tmm) REVERT: Q 404 LYS cc_start: 0.8727 (tmtm) cc_final: 0.8044 (tmtt) REVERT: P 83 TYR cc_start: 0.5429 (OUTLIER) cc_final: 0.5145 (t80) REVERT: C 473 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6167 (tm-30) REVERT: C 741 MET cc_start: 0.3901 (mmm) cc_final: 0.3442 (tmm) REVERT: E 435 MET cc_start: 0.4144 (OUTLIER) cc_final: 0.1959 (mtm) REVERT: E 624 ILE cc_start: 0.6759 (mt) cc_final: 0.6408 (tp) REVERT: E 679 PHE cc_start: 0.3300 (t80) cc_final: 0.2945 (t80) outliers start: 55 outliers final: 36 residues processed: 300 average time/residue: 1.0456 time to fit residues: 363.1618 Evaluate side-chains 307 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 262 time to evaluate : 1.808 ------------------------------------------------------------------------------- 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 200 GLN Chi-restraints excluded: chain K residue 235 LYS 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 60 MET Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 115 MET Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 351 MET Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 602 ARG 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 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 537 PHE Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 682 SER Chi-restraints excluded: chain E residue 841 ILE 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 216 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 52 GLN Q 102 GLN Q 114 ASN ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18364 Z= 0.228 Angle : 0.566 12.958 24960 Z= 0.288 Chirality : 0.041 0.275 2982 Planarity : 0.005 0.116 3032 Dihedral : 5.522 56.954 2661 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.72 % Allowed : 16.81 % Favored : 80.47 % 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: 2.11 (0.13), residues: 1572 sheet: None (None), residues: 0 loop : -0.00 (0.23), residues: 704 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 0.001 PHE E 591 TYR 0.017 0.001 TYR K 178 ARG 0.013 0.000 ARG E 646 ********************** 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 315 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 264 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 235 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7784 (mtmt) REVERT: K 275 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7883 (mm) REVERT: K 338 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6978 (pp) REVERT: K 362 GLN cc_start: 0.5993 (OUTLIER) cc_final: 0.5467 (tp40) REVERT: K 382 LEU cc_start: 0.8124 (mt) cc_final: 0.7798 (tp) REVERT: K 383 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7632 (mp) REVERT: L 196 LYS cc_start: 0.8002 (mttp) cc_final: 0.7465 (mtpp) REVERT: L 199 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7216 (tm-30) REVERT: L 312 LYS cc_start: 0.8460 (tptt) cc_final: 0.8038 (tptt) REVERT: L 323 ARG cc_start: 0.8323 (mpt-90) cc_final: 0.7781 (mtm-85) REVERT: Q 351 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7896 (mtt) REVERT: Q 358 MET cc_start: 0.8681 (ptm) cc_final: 0.8433 (ptp) REVERT: Q 378 MET cc_start: 0.8152 (mtm) cc_final: 0.7426 (tmm) REVERT: Q 404 LYS cc_start: 0.8719 (tmtm) cc_final: 0.8006 (tmtt) REVERT: P 83 TYR cc_start: 0.5437 (OUTLIER) cc_final: 0.5155 (t80) REVERT: C 473 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6144 (tm-30) REVERT: C 741 MET cc_start: 0.3898 (mmm) cc_final: 0.3382 (tmm) REVERT: E 435 MET cc_start: 0.4145 (mtm) cc_final: 0.1950 (mtm) REVERT: E 679 PHE cc_start: 0.3298 (t80) cc_final: 0.2957 (t80) REVERT: E 740 VAL cc_start: 0.5321 (OUTLIER) cc_final: 0.5015 (m) REVERT: E 741 MET cc_start: 0.3981 (mtm) cc_final: 0.3765 (ptt) outliers start: 51 outliers final: 36 residues processed: 296 average time/residue: 0.9687 time to fit residues: 331.9076 Evaluate side-chains 309 residues out of total 1925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 264 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 235 LYS 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 376 ILE Chi-restraints excluded: chain K residue 383 LEU Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 115 MET Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 277 LEU Chi-restraints excluded: chain Q residue 351 MET Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain P residue 83 TYR Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 544 PHE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 602 ARG 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 537 PHE Chi-restraints excluded: chain E residue 605 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 682 SER Chi-restraints excluded: chain E residue 740 VAL 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 192 optimal weight: 5.9990 chunk 55 optimal weight: 0.0770 chunk 166 optimal weight: 0.0060 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 75 optimal weight: 0.0060 chunk 186 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 159 optimal weight: 20.0000 overall best weight: 0.3772 ------------------------------------------------------------------------------- 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 Q 325 HIS ** C 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.225990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.138029 restraints weight = 33034.598| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.55 r_work: 0.3282 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18364 Z= 0.145 Angle : 0.530 10.283 24960 Z= 0.265 Chirality : 0.040 0.184 2982 Planarity : 0.005 0.104 3032 Dihedral : 5.365 59.761 2661 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.04 % Allowed : 17.70 % Favored : 80.26 % 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: 2.46 (0.18), residues: 2276 helix: 2.30 (0.13), residues: 1582 sheet: None (None), residues: 0 loop : 0.11 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 16 HIS 0.004 0.001 HIS K 329 PHE 0.028 0.001 PHE E 591 TYR 0.014 0.001 TYR K 178 ARG 0.009 0.000 ARG E 646 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7691.17 seconds wall clock time: 134 minutes 57.11 seconds (8097.11 seconds total)