Starting phenix.real_space_refine on Tue Dec 31 16:59:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qru_14124/12_2024/7qru_14124.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qru_14124/12_2024/7qru_14124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qru_14124/12_2024/7qru_14124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qru_14124/12_2024/7qru_14124.map" model { file = "/net/cci-nas-00/data/ceres_data/7qru_14124/12_2024/7qru_14124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qru_14124/12_2024/7qru_14124.cif" } resolution = 2.24 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= 0.002 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 92 5.16 5 C 10600 2.51 5 N 2388 2.21 5 O 3017 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-5532/modules/chem_data/mon_lib" Total number of atoms: 16100 Number of models: 1 Model: "" Number of chains: 18 Chain: "D" Number of atoms: 3906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 491, 3844 Classifications: {'peptide': 491} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 474} Conformer: "B" Number of residues, atoms: 491, 3844 Classifications: {'peptide': 491} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 474} bond proxies already assigned to first conformer: 3877 Chain: "A" Number of atoms: 6440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 805, 6306 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 776} Conformer: "B" Number of residues, atoms: 805, 6306 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 776} bond proxies already assigned to first conformer: 6327 Chain: "B" Number of atoms: 1089 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 140, 1078 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Conformer: "B" Number of residues, atoms: 140, 1078 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} bond proxies already assigned to first conformer: 1090 Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "E" Number of atoms: 1305 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 158, 1297 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Conformer: "B" Number of residues, atoms: 158, 1297 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} bond proxies already assigned to first conformer: 1317 Chain: "F" Number of atoms: 723 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 701 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 89} Conformer: "B" Number of residues, atoms: 91, 701 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 89} bond proxies already assigned to first conformer: 685 Chain: "G" Number of atoms: 888 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 113, 877 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Conformer: "B" Number of residues, atoms: 113, 877 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} bond proxies already assigned to first conformer: 883 Chain: "e" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 395 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 140 Classifications: {'water': 140} Link IDs: {None: 139} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "F" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 29 residue: pdb=" N AMET D 139 " occ=0.47 ... (14 atoms not shown) pdb=" CE BMET D 139 " occ=0.53 residue: pdb=" N ALEU D 172 " occ=0.43 ... (14 atoms not shown) pdb=" CD2BLEU D 172 " occ=0.57 residue: pdb=" N AMET D 218 " occ=0.45 ... (14 atoms not shown) pdb=" CE BMET D 218 " occ=0.55 residue: pdb=" N ALYS D 219 " occ=0.45 ... (16 atoms not shown) pdb=" NZ BLYS D 219 " occ=0.55 residue: pdb=" N AGLN D 307 " occ=0.69 ... (16 atoms not shown) pdb=" NE2BGLN D 307 " occ=0.31 residue: pdb=" N ATYR D 328 " occ=0.54 ... (22 atoms not shown) pdb=" OH BTYR D 328 " occ=0.46 residue: pdb=" N AMET D 423 " occ=0.54 ... (14 atoms not shown) pdb=" CE BMET D 423 " occ=0.46 residue: pdb=" N AMET A 118 " occ=0.45 ... (14 atoms not shown) pdb=" CE BMET A 118 " occ=0.55 residue: pdb=" N APHE A 119 " occ=0.45 ... (20 atoms not shown) pdb=" CZ BPHE A 119 " occ=0.55 residue: pdb=" N AMET A 167 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 167 " occ=0.50 residue: pdb=" N ATYR A 246 " occ=0.43 ... (22 atoms not shown) pdb=" OH BTYR A 246 " occ=0.57 residue: pdb=" N ALEU A 247 " occ=0.43 ... (14 atoms not shown) pdb=" CD2BLEU A 247 " occ=0.57 ... (remaining 17 not shown) Time building chain proxies: 15.67, per 1000 atoms: 0.97 Number of scatterers: 16100 At special positions: 0 Unit cell: (175.703, 92.137, 96.4224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 3 15.00 O 3017 8.00 N 2388 7.00 C 10600 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 Time building additional restraints: 4.75 Conformation dependent library (CDL) restraints added in 3.6 seconds 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3678 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 4 sheets defined 81.7% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'D' and resid 2 through 5 Processing helix chain 'D' and resid 6 through 19 Proline residue: D 12 - end of helix Processing helix chain 'D' and resid 25 through 55 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 75 through 98 removed outlier: 3.699A pdb=" N GLN D 98 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 removed outlier: 3.900A pdb=" N GLU D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 126 Processing helix chain 'D' and resid 128 through 149 removed outlier: 3.687A pdb=" N VAL D 148 " --> pdb=" O TYR D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 185 Processing helix chain 'D' and resid 188 through 199 Processing helix chain 'D' and resid 203 through 221 removed outlier: 4.001A pdb=" N VAL D 207 " --> pdb=" O GLY D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 237 through 263 removed outlier: 5.540A pdb=" N THR D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS D 250 " --> pdb=" O GLY D 246 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 292 removed outlier: 4.250A pdb=" N MET D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 318 removed outlier: 3.954A pdb=" N ILE D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 311 " --> pdb=" O AGLN D 307 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 315 " --> pdb=" O MET D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 352 Processing helix chain 'D' and resid 355 through 359 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.524A pdb=" N THR D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 381 Processing helix chain 'D' and resid 386 through 402 removed outlier: 3.649A pdb=" N PHE D 390 " --> pdb=" O LEU D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 430 Processing helix chain 'D' and resid 437 through 442 Processing helix chain 'D' and resid 445 through 465 Proline residue: D 451 - end of helix Proline residue: D 454 - end of helix Processing helix chain 'D' and resid 465 through 481 removed outlier: 3.706A pdb=" N ILE D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 491 removed outlier: 4.134A pdb=" N TYR D 486 " --> pdb=" O ASP D 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 24 Proline residue: A 11 - end of helix Proline residue: A 19 - end of helix Processing helix chain 'A' and resid 29 through 47 removed outlier: 4.342A pdb=" N PHE A 33 " --> pdb=" O HIS A 29 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU A 37 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Proline residue: A 38 - end of helix Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 66 through 69 Processing helix chain 'A' and resid 77 through 102 removed outlier: 3.814A pdb=" N PHE A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 129 Processing helix chain 'A' and resid 131 through 151 Processing helix chain 'A' and resid 156 through 189 Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 208 through 224 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.034A pdb=" N ASP A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 250 removed outlier: 3.577A pdb=" N BHIS A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N BSER A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N AALA A 250 " --> pdb=" O ATYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 removed outlier: 3.501A pdb=" N ALA A 255 " --> pdb=" O BTHR A 251 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A 256 " --> pdb=" O AMET A 252 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 270 through 294 removed outlier: 3.876A pdb=" N ARG A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 321 Processing helix chain 'A' and resid 321 through 327 removed outlier: 3.777A pdb=" N TYR A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 332 through 368 removed outlier: 5.003A pdb=" N ALA A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 402 through 420 removed outlier: 3.824A pdb=" N LEU A 406 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 457 removed outlier: 5.985A pdb=" N ILE A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE A 432 " --> pdb=" O THR A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 493 removed outlier: 4.526A pdb=" N SER A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Proline residue: A 480 - end of helix removed outlier: 3.547A pdb=" N ILE A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 531 through 550 Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'A' and resid 557 through 562 removed outlier: 3.684A pdb=" N LYS A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 590 removed outlier: 4.510A pdb=" N PHE A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 616 Processing helix chain 'A' and resid 630 through 647 removed outlier: 3.800A pdb=" N TRP A 634 " --> pdb=" O ALA A 630 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 652 through 674 Processing helix chain 'A' and resid 676 through 699 removed outlier: 3.527A pdb=" N TYR A 699 " --> pdb=" O MET A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 743 Processing helix chain 'A' and resid 748 through 755 Processing helix chain 'A' and resid 763 through 771 Processing helix chain 'A' and resid 773 through 797 removed outlier: 3.835A pdb=" N THR A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 33 removed outlier: 3.908A pdb=" N PHE B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 58 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 70 through 86 removed outlier: 3.551A pdb=" N GLY B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.767A pdb=" N LEU B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 92' Processing helix chain 'B' and resid 116 through 141 Processing helix chain 'C' and resid 2 through 21 Processing helix chain 'C' and resid 24 through 47 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 66 through 99 removed outlier: 4.195A pdb=" N GLN C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.517A pdb=" N ARG C 107 " --> pdb=" O ASP C 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 19 removed outlier: 3.654A pdb=" N ASN E 17 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 42 removed outlier: 4.037A pdb=" N PHE E 27 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 80 removed outlier: 4.414A pdb=" N ARG E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 113 Processing helix chain 'E' and resid 137 through 148 removed outlier: 3.597A pdb=" N MET E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 158 removed outlier: 3.724A pdb=" N VAL E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 27 removed outlier: 3.925A pdb=" N ARG F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 24 " --> pdb=" O CYS F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 55 removed outlier: 3.538A pdb=" N ILE F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY F 46 " --> pdb=" O ILE F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 85 removed outlier: 3.533A pdb=" N VAL F 64 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU F 65 " --> pdb=" O SER F 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 29 Processing helix chain 'G' and resid 31 through 63 removed outlier: 3.570A pdb=" N ALA G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR G 44 " --> pdb=" O THR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 95 removed outlier: 3.981A pdb=" N LEU G 70 " --> pdb=" O VAL G 66 " (cutoff:3.500A) Proline residue: G 81 - end of helix Processing helix chain 'G' and resid 105 through 111 removed outlier: 4.234A pdb=" N LYS G 109 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 20 removed outlier: 4.001A pdb=" N ASN e 17 " --> pdb=" O VAL e 13 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE e 18 " --> pdb=" O ILE e 14 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN e 19 " --> pdb=" O TRP e 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 41 Processing sheet with id=AA1, first strand: chain 'D' and resid 57 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 65 removed outlier: 7.188A pdb=" N ILE A 70 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 105 Processing sheet with id=AA4, first strand: chain 'E' and resid 89 through 94 removed outlier: 6.826A pdb=" N TYR E 127 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE E 121 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR E 129 " --> pdb=" O AMET E 119 " (cutoff:3.500A) 1213 hydrogen bonds defined for protein. 3611 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.24 Time building geometry restraints manager: 5.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 2498 1.31 - 1.46: 5800 1.46 - 1.61: 7651 1.61 - 1.76: 20 1.76 - 1.91: 168 Bond restraints: 16137 Sorted by residual: bond pdb=" CE1 HIS D 266 " pdb=" NE2 HIS D 266 " ideal model delta sigma weight residual 1.321 1.451 -0.130 1.00e-02 1.00e+04 1.70e+02 bond pdb=" C29 3PE A 901 " pdb=" C2A 3PE A 901 " ideal model delta sigma weight residual 1.524 1.292 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" CE1 HIS D 303 " pdb=" NE2 HIS D 303 " ideal model delta sigma weight residual 1.321 1.428 -0.107 1.00e-02 1.00e+04 1.15e+02 bond pdb=" C29 3PE E 201 " pdb=" C2A 3PE E 201 " ideal model delta sigma weight residual 1.524 1.331 0.193 2.00e-02 2.50e+03 9.30e+01 bond pdb=" C29 3PE E 202 " pdb=" C2A 3PE E 202 " ideal model delta sigma weight residual 1.524 1.337 0.187 2.00e-02 2.50e+03 8.76e+01 ... (remaining 16132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 17697 2.69 - 5.38: 3747 5.38 - 8.07: 425 8.07 - 10.76: 56 10.76 - 13.45: 14 Bond angle restraints: 21939 Sorted by residual: angle pdb=" O VAL D 453 " pdb=" C VAL D 453 " pdb=" N PRO D 454 " ideal model delta sigma weight residual 120.42 114.51 5.91 6.40e-01 2.44e+00 8.54e+01 angle pdb=" O PRO C 54 " pdb=" C PRO C 54 " pdb=" N PRO C 55 " ideal model delta sigma weight residual 121.31 117.11 4.20 4.60e-01 4.73e+00 8.32e+01 angle pdb=" N PRO B 68 " pdb=" CA PRO B 68 " pdb=" CB PRO B 68 " ideal model delta sigma weight residual 102.81 96.80 6.01 6.70e-01 2.23e+00 8.04e+01 angle pdb=" CA ASP A 297 " pdb=" CB ASP A 297 " pdb=" CG ASP A 297 " ideal model delta sigma weight residual 112.60 121.15 -8.55 1.00e+00 1.00e+00 7.30e+01 angle pdb=" C PRO A 473 " pdb=" CA PRO A 473 " pdb=" CB PRO A 473 " ideal model delta sigma weight residual 111.56 100.82 10.74 1.27e+00 6.20e-01 7.16e+01 ... (remaining 21934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8468 17.96 - 35.91: 713 35.91 - 53.86: 166 53.86 - 71.81: 28 71.81 - 89.77: 10 Dihedral angle restraints: 9385 sinusoidal: 3631 harmonic: 5754 Sorted by residual: dihedral pdb=" CA ARG F 90 " pdb=" C ARG F 90 " pdb=" N GLY F 91 " pdb=" CA GLY F 91 " ideal model delta harmonic sigma weight residual -180.00 -150.61 -29.39 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ALA A 333 " pdb=" C ALA A 333 " pdb=" N PHE A 334 " pdb=" CA PHE A 334 " ideal model delta harmonic sigma weight residual -180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ASP C 111 " pdb=" C ASP C 111 " pdb=" N GLU C 112 " pdb=" CA GLU C 112 " ideal model delta harmonic sigma weight residual 180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 9382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1723 0.093 - 0.186: 725 0.186 - 0.278: 159 0.278 - 0.371: 25 0.371 - 0.464: 1 Chirality restraints: 2633 Sorted by residual: chirality pdb=" CA PRO A 265 " pdb=" N PRO A 265 " pdb=" C PRO A 265 " pdb=" CB PRO A 265 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA ARG F 90 " pdb=" N ARG F 90 " pdb=" C ARG F 90 " pdb=" CB ARG F 90 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA TYR A 113 " pdb=" N TYR A 113 " pdb=" C TYR A 113 " pdb=" CB TYR A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 2630 not shown) Planarity restraints: 2637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE e 18 " 0.099 2.00e-02 2.50e+03 6.98e-02 8.54e+01 pdb=" CG PHE e 18 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE e 18 " -0.102 2.00e-02 2.50e+03 pdb=" CD2 PHE e 18 " -0.090 2.00e-02 2.50e+03 pdb=" CE1 PHE e 18 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 PHE e 18 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE e 18 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 28 " -0.122 2.00e-02 2.50e+03 6.32e-02 7.98e+01 pdb=" CG TYR B 28 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B 28 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR B 28 " 0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR B 28 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR B 28 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 28 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR B 28 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 431 " -0.078 2.00e-02 2.50e+03 5.32e-02 7.07e+01 pdb=" CG TRP D 431 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 TRP D 431 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 431 " 0.078 2.00e-02 2.50e+03 pdb=" NE1 TRP D 431 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TRP D 431 " -0.050 2.00e-02 2.50e+03 pdb=" CE3 TRP D 431 " -0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 431 " -0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 431 " 0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP D 431 " -0.008 2.00e-02 2.50e+03 ... (remaining 2634 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 407 2.63 - 3.20: 15861 3.20 - 3.76: 28235 3.76 - 4.33: 40867 4.33 - 4.90: 64070 Nonbonded interactions: 149440 Sorted by model distance: nonbonded pdb=" OD1 ASP A 678 " pdb=" O HOH A1001 " model vdw 2.058 3.040 nonbonded pdb=" CE2APHE B 41 " pdb=" CD1 LEU B 45 " model vdw 2.083 3.760 nonbonded pdb=" NH1 ARG D 231 " pdb=" O HOH D 501 " model vdw 2.106 3.120 nonbonded pdb=" O HOH A1002 " pdb=" O HOH A1008 " model vdw 2.117 3.040 nonbonded pdb=" OG1 THR E 113 " pdb=" O HOH E 301 " model vdw 2.181 3.040 ... (remaining 149435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.24 max=1.00 mean=0.98 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: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 44.930 Find NCS groups from input model: 0.190 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:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 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 : 0.020 0.232 16137 Z= 1.296 Angle : 2.179 13.447 21939 Z= 1.477 Chirality : 0.102 0.464 2633 Planarity : 0.022 0.249 2637 Dihedral : 14.727 89.768 5707 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 2.50 % Allowed : 6.60 % Favored : 90.90 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 9.68 % 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: -1.62 (0.16), residues: 2010 helix: -0.87 (0.11), residues: 1509 sheet: -0.81 (0.71), residues: 48 loop : -1.15 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.024 TRP A 273 HIS 0.074 0.013 HIS A 349 PHE 0.102 0.022 PHE e 18 TYR 0.122 0.023 TYR B 28 ARG 0.059 0.007 ARG F 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 40 MET cc_start: 0.9295 (mtp) cc_final: 0.9010 (mtp) REVERT: D 103 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8601 (mm-30) REVERT: D 189 MET cc_start: 0.9283 (mtt) cc_final: 0.9028 (mtp) REVERT: D 283 MET cc_start: 0.9419 (mtm) cc_final: 0.9203 (mtm) REVERT: D 311 MET cc_start: 0.9389 (mtt) cc_final: 0.8988 (mtt) REVERT: D 396 ILE cc_start: 0.8857 (pt) cc_final: 0.8506 (mt) REVERT: D 439 GLN cc_start: 0.8928 (tt0) cc_final: 0.8159 (pm20) REVERT: D 467 GLU cc_start: 0.9242 (tp30) cc_final: 0.9005 (tp30) REVERT: D 488 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8749 (mm-30) REVERT: A 207 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8329 (mp0) REVERT: A 314 MET cc_start: 0.9301 (tpp) cc_final: 0.8782 (tpp) REVERT: A 382 MET cc_start: 0.9371 (mtt) cc_final: 0.9160 (mtp) REVERT: A 421 MET cc_start: 0.9216 (mtp) cc_final: 0.8879 (mtm) REVERT: A 459 LYS cc_start: 0.8326 (tttt) cc_final: 0.8107 (mtmm) REVERT: A 461 LYS cc_start: 0.8174 (mmtp) cc_final: 0.7797 (mtpt) REVERT: A 496 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8886 (mt) REVERT: A 518 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7951 (mt-10) REVERT: A 551 MET cc_start: 0.9057 (ttp) cc_final: 0.8802 (ttt) REVERT: A 561 MET cc_start: 0.8463 (mmt) cc_final: 0.8116 (mmm) REVERT: A 563 GLU cc_start: 0.8587 (pt0) cc_final: 0.8177 (pm20) REVERT: A 706 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7640 (tttm) REVERT: A 715 ILE cc_start: 0.8589 (mt) cc_final: 0.8319 (tp) REVERT: B 69 PHE cc_start: 0.8861 (m-80) cc_final: 0.8587 (m-10) REVERT: B 74 MET cc_start: 0.9392 (ttm) cc_final: 0.9159 (ttp) REVERT: B 102 GLU cc_start: 0.8403 (tt0) cc_final: 0.8180 (tp30) REVERT: B 142 ASP cc_start: 0.8977 (t0) cc_final: 0.8756 (t0) REVERT: C 1 MET cc_start: 0.8863 (tpp) cc_final: 0.8569 (tpt) REVERT: C 14 MET cc_start: 0.9259 (ttp) cc_final: 0.8953 (ttp) REVERT: C 46 MET cc_start: 0.9510 (mmp) cc_final: 0.9050 (mmp) REVERT: C 80 SER cc_start: 0.9224 (t) cc_final: 0.8882 (p) REVERT: E 51 MET cc_start: 0.8878 (mmm) cc_final: 0.8659 (mmm) REVERT: E 53 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8151 (ttm-80) REVERT: E 146 HIS cc_start: 0.8496 (m90) cc_final: 0.8224 (m170) REVERT: G 1 MET cc_start: 0.8251 (ttt) cc_final: 0.7987 (ttm) REVERT: G 92 TYR cc_start: 0.9363 (t80) cc_final: 0.8842 (t80) REVERT: G 109 LYS cc_start: 0.7978 (mmtm) cc_final: 0.7745 (mmmt) REVERT: e 19 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.7142 (mm-40) outliers start: 37 outliers final: 14 residues processed: 285 average time/residue: 1.4612 time to fit residues: 458.0415 Evaluate side-chains 239 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 222 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 PRO Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 385 PRO Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 401 PRO Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 94 PRO Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain e residue 19 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 0.0970 chunk 78 optimal weight: 0.6980 chunk 151 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 ASN E 137 ASN F 43 ASN e 8 ASN e 19 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16137 Z= 0.239 Angle : 0.653 8.278 21939 Z= 0.357 Chirality : 0.044 0.202 2633 Planarity : 0.005 0.045 2637 Dihedral : 8.987 80.984 2293 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.96 % Allowed : 10.17 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 1.51 (0.18), residues: 2010 helix: 1.52 (0.13), residues: 1523 sheet: -0.19 (0.70), residues: 48 loop : -0.54 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 139 HIS 0.011 0.002 HIS D 333 PHE 0.048 0.002 PHE A 352 TYR 0.029 0.002 TYR A 447 ARG 0.010 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 1.768 Fit side-chains revert: symmetry clash REVERT: D 103 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8083 (mm-30) REVERT: D 311 MET cc_start: 0.9259 (mtt) cc_final: 0.8830 (mtt) REVERT: D 439 GLN cc_start: 0.8885 (tt0) cc_final: 0.8174 (pm20) REVERT: D 467 GLU cc_start: 0.9179 (tp30) cc_final: 0.8918 (tp30) REVERT: D 488 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8777 (mm-30) REVERT: A 207 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8336 (mp0) REVERT: A 314 MET cc_start: 0.9089 (tpp) cc_final: 0.8794 (tpp) REVERT: A 431 ILE cc_start: 0.8375 (pp) cc_final: 0.8172 (mp) REVERT: A 459 LYS cc_start: 0.8445 (tttt) cc_final: 0.8224 (mtmm) REVERT: A 461 LYS cc_start: 0.7867 (mmtp) cc_final: 0.7522 (mtpt) REVERT: A 516 ASP cc_start: 0.8604 (m-30) cc_final: 0.8395 (t70) REVERT: A 518 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7961 (mt-10) REVERT: A 561 MET cc_start: 0.8438 (mmt) cc_final: 0.8112 (mmm) REVERT: A 563 GLU cc_start: 0.8685 (pt0) cc_final: 0.8226 (pm20) REVERT: A 706 LYS cc_start: 0.8432 (ttmt) cc_final: 0.7835 (tttm) REVERT: B 102 GLU cc_start: 0.8175 (tt0) cc_final: 0.7879 (tp30) REVERT: C 14 MET cc_start: 0.9052 (ttp) cc_final: 0.8756 (ttp) REVERT: C 46 MET cc_start: 0.9338 (mmp) cc_final: 0.8906 (mmp) REVERT: C 80 SER cc_start: 0.9263 (t) cc_final: 0.8880 (p) REVERT: E 51 MET cc_start: 0.8639 (mmm) cc_final: 0.8424 (mmm) REVERT: E 141 MET cc_start: 0.8873 (ttp) cc_final: 0.8588 (tmm) REVERT: E 151 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7700 (ttm-80) REVERT: F 38 ASP cc_start: 0.9053 (t70) cc_final: 0.8839 (t70) REVERT: G 79 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8551 (p) REVERT: G 100 GLU cc_start: 0.8550 (pt0) cc_final: 0.8335 (mp0) REVERT: e 8 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7335 (t0) REVERT: e 46 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.8485 (mtp85) outliers start: 27 outliers final: 8 residues processed: 254 average time/residue: 1.4576 time to fit residues: 407.8651 Evaluate side-chains 227 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain e residue 8 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 175 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 174 optimal weight: 0.2980 chunk 59 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN A 683 GLN E 8 ASN E 137 ASN E 146 HIS e 8 ASN e 17 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16137 Z= 0.237 Angle : 0.600 7.391 21939 Z= 0.325 Chirality : 0.043 0.244 2633 Planarity : 0.004 0.042 2637 Dihedral : 8.331 77.644 2271 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.90 % Allowed : 11.06 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.09 (0.18), residues: 2010 helix: 1.91 (0.13), residues: 1528 sheet: -0.08 (0.71), residues: 48 loop : -0.26 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 139 HIS 0.009 0.001 HIS A 349 PHE 0.041 0.002 PHE A 352 TYR 0.024 0.002 TYR C 92 ARG 0.010 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 1.657 Fit side-chains revert: symmetry clash REVERT: D 103 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8168 (mm-30) REVERT: D 311 MET cc_start: 0.9241 (mtt) cc_final: 0.8815 (mtt) REVERT: D 439 GLN cc_start: 0.8920 (tt0) cc_final: 0.8243 (pm20) REVERT: D 467 GLU cc_start: 0.9204 (tp30) cc_final: 0.8977 (tp30) REVERT: D 488 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8797 (mm-30) REVERT: A 207 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8231 (mp0) REVERT: A 459 LYS cc_start: 0.8354 (tttt) cc_final: 0.8122 (mtmm) REVERT: A 461 LYS cc_start: 0.7904 (mmtp) cc_final: 0.7515 (mtpt) REVERT: A 516 ASP cc_start: 0.8643 (m-30) cc_final: 0.8442 (t70) REVERT: A 518 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7984 (mt-10) REVERT: A 561 MET cc_start: 0.8523 (mmt) cc_final: 0.8210 (mmm) REVERT: A 563 GLU cc_start: 0.8674 (pt0) cc_final: 0.8246 (pm20) REVERT: A 714 ASN cc_start: 0.8494 (m110) cc_final: 0.8224 (m110) REVERT: B 59 ASP cc_start: 0.8732 (p0) cc_final: 0.8471 (p0) REVERT: C 14 MET cc_start: 0.9045 (ttp) cc_final: 0.8790 (ttp) REVERT: C 46 MET cc_start: 0.9319 (mmp) cc_final: 0.8818 (mmp) REVERT: C 80 SER cc_start: 0.9256 (t) cc_final: 0.8897 (p) REVERT: C 105 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7684 (mp10) REVERT: E 51 MET cc_start: 0.8631 (mmm) cc_final: 0.8396 (mmm) REVERT: E 72 ASN cc_start: 0.9230 (m-40) cc_final: 0.8886 (m110) REVERT: E 141 MET cc_start: 0.8884 (ttp) cc_final: 0.8601 (tmm) REVERT: F 1 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6791 (tpp) REVERT: F 38 ASP cc_start: 0.9047 (t70) cc_final: 0.8841 (t70) REVERT: G 79 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8488 (p) outliers start: 25 outliers final: 4 residues processed: 230 average time/residue: 1.5934 time to fit residues: 401.7951 Evaluate side-chains 219 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 211 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 176 optimal weight: 0.6980 chunk 186 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN E 8 ASN E 137 ASN e 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16137 Z= 0.246 Angle : 0.588 7.960 21939 Z= 0.318 Chirality : 0.043 0.235 2633 Planarity : 0.004 0.042 2637 Dihedral : 7.945 75.604 2269 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.08 % Allowed : 11.24 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.25 (0.18), residues: 2010 helix: 2.01 (0.13), residues: 1528 sheet: -0.11 (0.72), residues: 48 loop : -0.12 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 139 HIS 0.008 0.002 HIS A 349 PHE 0.038 0.002 PHE A 352 TYR 0.025 0.002 TYR C 92 ARG 0.010 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 1.794 Fit side-chains revert: symmetry clash REVERT: D 24 LYS cc_start: 0.8610 (mmmm) cc_final: 0.8403 (mppt) REVERT: D 103 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8223 (mm-30) REVERT: D 311 MET cc_start: 0.9251 (mtt) cc_final: 0.8825 (mtt) REVERT: D 439 GLN cc_start: 0.8903 (tt0) cc_final: 0.8232 (pm20) REVERT: D 488 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8798 (mm-30) REVERT: A 207 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8236 (mp0) REVERT: A 459 LYS cc_start: 0.8357 (tttt) cc_final: 0.8144 (mtmm) REVERT: A 461 LYS cc_start: 0.7915 (mmtp) cc_final: 0.7547 (mtpt) REVERT: A 518 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8005 (mt-10) REVERT: A 561 MET cc_start: 0.8510 (mmt) cc_final: 0.8166 (mmm) REVERT: A 563 GLU cc_start: 0.8660 (pt0) cc_final: 0.8147 (pm20) REVERT: A 714 ASN cc_start: 0.8396 (m110) cc_final: 0.8114 (m110) REVERT: B 142 ASP cc_start: 0.8880 (t0) cc_final: 0.8524 (t0) REVERT: C 14 MET cc_start: 0.9042 (ttp) cc_final: 0.8819 (ttp) REVERT: C 80 SER cc_start: 0.9225 (t) cc_final: 0.9012 (p) REVERT: C 105 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7645 (mp10) REVERT: E 51 MET cc_start: 0.8676 (mmm) cc_final: 0.8473 (mmm) REVERT: E 72 ASN cc_start: 0.9203 (m-40) cc_final: 0.8902 (m110) REVERT: E 128 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8917 (tp) REVERT: E 141 MET cc_start: 0.8924 (ttp) cc_final: 0.8651 (tmm) REVERT: F 1 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6781 (tpp) REVERT: G 79 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8445 (p) outliers start: 28 outliers final: 9 residues processed: 229 average time/residue: 1.5532 time to fit residues: 389.9580 Evaluate side-chains 224 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 2 optimal weight: 0.0010 chunk 138 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN E 8 ASN E 137 ASN E 146 HIS e 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16137 Z= 0.308 Angle : 0.618 8.259 21939 Z= 0.335 Chirality : 0.045 0.247 2633 Planarity : 0.005 0.043 2637 Dihedral : 7.912 76.771 2269 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.02 % Allowed : 11.77 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.15 (0.18), residues: 2010 helix: 1.92 (0.13), residues: 1526 sheet: -0.07 (0.72), residues: 48 loop : -0.06 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 139 HIS 0.008 0.002 HIS A 345 PHE 0.036 0.002 PHE A 352 TYR 0.026 0.002 TYR C 92 ARG 0.010 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 1.774 Fit side-chains REVERT: D 24 LYS cc_start: 0.8625 (mmmm) cc_final: 0.8417 (mppt) REVERT: D 103 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8267 (mm-30) REVERT: D 311 MET cc_start: 0.9279 (mtt) cc_final: 0.8870 (mtt) REVERT: D 439 GLN cc_start: 0.8915 (tt0) cc_final: 0.8258 (pm20) REVERT: D 488 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8788 (mm-30) REVERT: A 207 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8235 (mp0) REVERT: A 421 MET cc_start: 0.8974 (mtp) cc_final: 0.8772 (mtm) REVERT: A 461 LYS cc_start: 0.7891 (mmtp) cc_final: 0.7511 (mtpt) REVERT: A 518 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7920 (mt-10) REVERT: A 561 MET cc_start: 0.8518 (mmt) cc_final: 0.8213 (mmm) REVERT: A 563 GLU cc_start: 0.8645 (pt0) cc_final: 0.8161 (pm20) REVERT: A 714 ASN cc_start: 0.8390 (m110) cc_final: 0.8124 (m110) REVERT: B 142 ASP cc_start: 0.8884 (t0) cc_final: 0.8473 (t0) REVERT: C 105 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: E 51 MET cc_start: 0.8703 (mmm) cc_final: 0.8489 (mmm) REVERT: E 72 ASN cc_start: 0.9225 (m-40) cc_final: 0.8948 (m110) REVERT: E 124 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8074 (p0) REVERT: E 128 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8921 (tp) REVERT: E 141 MET cc_start: 0.8899 (ttp) cc_final: 0.8620 (tmm) REVERT: F 1 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6818 (tpp) outliers start: 27 outliers final: 15 residues processed: 226 average time/residue: 1.5832 time to fit residues: 391.6275 Evaluate side-chains 227 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 94 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 ASN E 137 ASN E 146 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16137 Z= 0.262 Angle : 0.589 8.306 21939 Z= 0.320 Chirality : 0.044 0.235 2633 Planarity : 0.004 0.043 2637 Dihedral : 7.755 76.389 2268 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.78 % Allowed : 12.19 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.21 (0.18), residues: 2010 helix: 1.96 (0.13), residues: 1527 sheet: -0.02 (0.73), residues: 48 loop : -0.04 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 139 HIS 0.008 0.002 HIS A 349 PHE 0.036 0.002 PHE A 352 TYR 0.025 0.002 TYR C 92 ARG 0.010 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 1.688 Fit side-chains REVERT: D 24 LYS cc_start: 0.8626 (mmmm) cc_final: 0.8414 (mppt) REVERT: D 103 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8252 (mm-30) REVERT: D 311 MET cc_start: 0.9256 (mtt) cc_final: 0.8800 (mtt) REVERT: D 439 GLN cc_start: 0.8900 (tt0) cc_final: 0.8291 (pm20) REVERT: D 488 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8783 (mm-30) REVERT: A 207 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8247 (mp0) REVERT: A 421 MET cc_start: 0.8975 (mtp) cc_final: 0.8765 (mtm) REVERT: A 461 LYS cc_start: 0.7876 (mmtp) cc_final: 0.7517 (mtpt) REVERT: A 518 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7902 (mt-10) REVERT: A 561 MET cc_start: 0.8524 (mmt) cc_final: 0.8221 (mmm) REVERT: A 563 GLU cc_start: 0.8638 (pt0) cc_final: 0.8206 (pm20) REVERT: A 605 MET cc_start: 0.9168 (mtp) cc_final: 0.8943 (mtt) REVERT: A 714 ASN cc_start: 0.8360 (m110) cc_final: 0.8124 (m110) REVERT: B 142 ASP cc_start: 0.8884 (t0) cc_final: 0.8469 (t0) REVERT: C 105 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7549 (mp10) REVERT: E 51 MET cc_start: 0.8689 (mmm) cc_final: 0.8486 (mmm) REVERT: E 72 ASN cc_start: 0.9195 (m-40) cc_final: 0.8918 (m110) REVERT: E 128 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8922 (tp) REVERT: E 141 MET cc_start: 0.8919 (ttp) cc_final: 0.8577 (tmm) REVERT: F 1 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6769 (tpp) outliers start: 24 outliers final: 13 residues processed: 227 average time/residue: 1.5831 time to fit residues: 393.3462 Evaluate side-chains 222 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 94 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 105 optimal weight: 0.2980 chunk 157 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 186 optimal weight: 0.3980 chunk 116 optimal weight: 0.6980 chunk 113 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 ASN E 8 ASN E 137 ASN E 146 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16137 Z= 0.205 Angle : 0.552 8.607 21939 Z= 0.299 Chirality : 0.042 0.218 2633 Planarity : 0.004 0.043 2637 Dihedral : 7.505 73.423 2268 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.61 % Allowed : 12.78 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.39 (0.19), residues: 2010 helix: 2.08 (0.13), residues: 1530 sheet: 0.05 (0.73), residues: 48 loop : 0.05 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 101 HIS 0.008 0.001 HIS D 333 PHE 0.037 0.002 PHE A 352 TYR 0.024 0.002 TYR C 92 ARG 0.010 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 1.820 Fit side-chains REVERT: D 24 LYS cc_start: 0.8635 (mmmm) cc_final: 0.8425 (mppt) REVERT: D 103 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8270 (mm-30) REVERT: D 311 MET cc_start: 0.9225 (mtt) cc_final: 0.8804 (mtt) REVERT: D 439 GLN cc_start: 0.8940 (tt0) cc_final: 0.8290 (pm20) REVERT: D 488 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8784 (mm-30) REVERT: A 207 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8226 (mp0) REVERT: A 296 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8490 (mmtm) REVERT: A 421 MET cc_start: 0.9019 (mtp) cc_final: 0.8778 (mtm) REVERT: A 461 LYS cc_start: 0.7865 (mmtp) cc_final: 0.7509 (mtpt) REVERT: A 518 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7890 (mt-10) REVERT: A 561 MET cc_start: 0.8441 (mmt) cc_final: 0.8071 (mmm) REVERT: A 563 GLU cc_start: 0.8609 (pt0) cc_final: 0.8193 (pm20) REVERT: A 605 MET cc_start: 0.9149 (mtp) cc_final: 0.8937 (mtt) REVERT: A 714 ASN cc_start: 0.8322 (m110) cc_final: 0.8092 (m110) REVERT: B 59 ASP cc_start: 0.8787 (p0) cc_final: 0.8518 (p0) REVERT: B 142 ASP cc_start: 0.8895 (t0) cc_final: 0.8509 (t0) REVERT: C 62 THR cc_start: 0.8750 (p) cc_final: 0.8500 (m) REVERT: C 99 LYS cc_start: 0.8793 (mttm) cc_final: 0.8380 (mmtt) REVERT: C 105 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7632 (mp10) REVERT: E 51 MET cc_start: 0.8659 (mmm) cc_final: 0.8434 (mmm) REVERT: E 72 ASN cc_start: 0.9158 (m-40) cc_final: 0.8853 (m110) REVERT: E 128 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8936 (tp) REVERT: E 141 MET cc_start: 0.8920 (ttp) cc_final: 0.8584 (tmm) REVERT: F 1 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6773 (tpp) outliers start: 21 outliers final: 12 residues processed: 222 average time/residue: 1.5444 time to fit residues: 376.6327 Evaluate side-chains 222 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 0.0870 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 0.0980 chunk 118 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 GLN E 8 ASN E 137 ASN E 146 HIS e 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16137 Z= 0.199 Angle : 0.545 8.479 21939 Z= 0.295 Chirality : 0.041 0.213 2633 Planarity : 0.004 0.045 2637 Dihedral : 7.361 70.834 2268 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.49 % Allowed : 12.96 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.19), residues: 2010 helix: 2.15 (0.13), residues: 1530 sheet: 0.13 (0.73), residues: 48 loop : 0.07 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 101 HIS 0.008 0.001 HIS D 333 PHE 0.036 0.002 PHE A 352 TYR 0.024 0.002 TYR C 92 ARG 0.006 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 1.857 Fit side-chains REVERT: D 24 LYS cc_start: 0.8637 (mmmm) cc_final: 0.8430 (mppt) REVERT: D 103 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8285 (mm-30) REVERT: D 311 MET cc_start: 0.9217 (mtt) cc_final: 0.8807 (mtt) REVERT: D 439 GLN cc_start: 0.8942 (tt0) cc_final: 0.8300 (pm20) REVERT: D 488 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8791 (mm-30) REVERT: A 207 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8232 (mp0) REVERT: A 296 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8480 (mmtm) REVERT: A 421 MET cc_start: 0.9000 (mtp) cc_final: 0.8750 (mtm) REVERT: A 461 LYS cc_start: 0.7830 (mmtp) cc_final: 0.7472 (mtpt) REVERT: A 518 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7872 (mt-10) REVERT: A 561 MET cc_start: 0.8439 (mmt) cc_final: 0.8117 (mmm) REVERT: A 563 GLU cc_start: 0.8609 (pt0) cc_final: 0.8189 (pm20) REVERT: A 605 MET cc_start: 0.9140 (mtp) cc_final: 0.8924 (mtt) REVERT: B 59 ASP cc_start: 0.8781 (p0) cc_final: 0.8507 (p0) REVERT: B 142 ASP cc_start: 0.8857 (t0) cc_final: 0.8449 (t0) REVERT: C 62 THR cc_start: 0.8842 (p) cc_final: 0.8598 (m) REVERT: C 99 LYS cc_start: 0.8789 (mttm) cc_final: 0.8392 (mmtt) REVERT: C 105 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: E 51 MET cc_start: 0.8650 (mmm) cc_final: 0.8439 (mmm) REVERT: E 72 ASN cc_start: 0.9138 (m-40) cc_final: 0.8839 (m110) REVERT: E 128 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8939 (tp) REVERT: E 141 MET cc_start: 0.8919 (ttp) cc_final: 0.8580 (tmm) outliers start: 19 outliers final: 12 residues processed: 220 average time/residue: 1.5642 time to fit residues: 377.5493 Evaluate side-chains 221 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 136 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 113 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 GLN C 50 GLN E 8 ASN E 137 ASN E 146 HIS e 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16137 Z= 0.201 Angle : 0.544 8.291 21939 Z= 0.295 Chirality : 0.041 0.211 2633 Planarity : 0.004 0.044 2637 Dihedral : 7.292 68.214 2268 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.43 % Allowed : 13.02 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.51 (0.19), residues: 2010 helix: 2.16 (0.13), residues: 1530 sheet: 0.15 (0.72), residues: 48 loop : 0.08 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 101 HIS 0.007 0.001 HIS D 333 PHE 0.036 0.002 PHE A 352 TYR 0.023 0.002 TYR C 92 ARG 0.009 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 1.657 Fit side-chains REVERT: D 24 LYS cc_start: 0.8634 (mmmm) cc_final: 0.8422 (mppt) REVERT: D 103 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8263 (mm-30) REVERT: D 311 MET cc_start: 0.9223 (mtt) cc_final: 0.8814 (mtt) REVERT: D 439 GLN cc_start: 0.8962 (tt0) cc_final: 0.8334 (pm20) REVERT: D 488 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8789 (mm-30) REVERT: D 489 SER cc_start: 0.9122 (m) cc_final: 0.8919 (m) REVERT: A 207 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8237 (mp0) REVERT: A 296 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8417 (mmtm) REVERT: A 421 MET cc_start: 0.9000 (mtp) cc_final: 0.8744 (mtm) REVERT: A 461 LYS cc_start: 0.7824 (mmtp) cc_final: 0.7469 (mtpt) REVERT: A 518 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7839 (mt-10) REVERT: A 561 MET cc_start: 0.8358 (mmt) cc_final: 0.8032 (mmm) REVERT: A 563 GLU cc_start: 0.8610 (pt0) cc_final: 0.8189 (pm20) REVERT: A 605 MET cc_start: 0.9143 (mtp) cc_final: 0.8925 (mtt) REVERT: B 59 ASP cc_start: 0.8800 (p0) cc_final: 0.8536 (p0) REVERT: B 142 ASP cc_start: 0.8857 (t0) cc_final: 0.8443 (t0) REVERT: C 62 THR cc_start: 0.8843 (p) cc_final: 0.8601 (m) REVERT: C 99 LYS cc_start: 0.8775 (mttm) cc_final: 0.8389 (mmtt) REVERT: C 102 ASP cc_start: 0.9002 (t0) cc_final: 0.8713 (t0) REVERT: C 105 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: E 51 MET cc_start: 0.8628 (mmm) cc_final: 0.8413 (mmm) REVERT: E 72 ASN cc_start: 0.9134 (m-40) cc_final: 0.8837 (m110) REVERT: E 128 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8952 (tp) REVERT: E 141 MET cc_start: 0.8921 (ttp) cc_final: 0.8585 (tmm) outliers start: 18 outliers final: 12 residues processed: 218 average time/residue: 1.5666 time to fit residues: 373.9519 Evaluate side-chains 221 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 118 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 GLN E 8 ASN E 137 ASN E 146 HIS e 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16137 Z= 0.243 Angle : 0.571 8.992 21939 Z= 0.310 Chirality : 0.043 0.221 2633 Planarity : 0.004 0.044 2637 Dihedral : 7.384 67.751 2268 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.43 % Allowed : 13.14 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.39 (0.18), residues: 2010 helix: 2.08 (0.13), residues: 1527 sheet: 0.12 (0.72), residues: 48 loop : 0.05 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 101 HIS 0.007 0.001 HIS A 349 PHE 0.035 0.002 PHE A 352 TYR 0.025 0.002 TYR C 92 ARG 0.009 0.001 ARG E 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 1.719 Fit side-chains REVERT: D 103 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8288 (mm-30) REVERT: D 311 MET cc_start: 0.9267 (mtt) cc_final: 0.8826 (mtt) REVERT: D 422 MET cc_start: 0.9278 (mmp) cc_final: 0.8987 (mmp) REVERT: D 439 GLN cc_start: 0.8955 (tt0) cc_final: 0.8310 (pm20) REVERT: D 488 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8794 (mm-30) REVERT: A 207 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8234 (mp0) REVERT: A 296 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8446 (mmtm) REVERT: A 421 MET cc_start: 0.8997 (mtp) cc_final: 0.8768 (mtm) REVERT: A 461 LYS cc_start: 0.7824 (mmtp) cc_final: 0.7466 (mtpt) REVERT: A 518 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7825 (mt-10) REVERT: A 561 MET cc_start: 0.8363 (mmt) cc_final: 0.8065 (mmm) REVERT: A 563 GLU cc_start: 0.8631 (pt0) cc_final: 0.8204 (pm20) REVERT: A 605 MET cc_start: 0.9157 (mtp) cc_final: 0.8927 (mtt) REVERT: B 142 ASP cc_start: 0.8831 (t0) cc_final: 0.8427 (t0) REVERT: C 62 THR cc_start: 0.8844 (p) cc_final: 0.8604 (m) REVERT: C 99 LYS cc_start: 0.8787 (mttm) cc_final: 0.8384 (mmtt) REVERT: C 102 ASP cc_start: 0.9038 (t0) cc_final: 0.8789 (t0) REVERT: C 105 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: E 51 MET cc_start: 0.8715 (mmm) cc_final: 0.8466 (mmm) REVERT: E 72 ASN cc_start: 0.9173 (m-40) cc_final: 0.8880 (m110) REVERT: E 128 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8947 (tp) REVERT: E 141 MET cc_start: 0.8917 (ttp) cc_final: 0.8577 (tmm) outliers start: 18 outliers final: 12 residues processed: 216 average time/residue: 1.6050 time to fit residues: 379.8928 Evaluate side-chains 218 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 134 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 ASN E 137 ASN E 146 HIS e 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.103325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.074994 restraints weight = 96728.238| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.76 r_work: 0.2635 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16137 Z= 0.260 Angle : 0.583 9.019 21939 Z= 0.316 Chirality : 0.043 0.223 2633 Planarity : 0.004 0.043 2637 Dihedral : 7.406 68.410 2268 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.37 % Allowed : 13.44 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.35 (0.18), residues: 2010 helix: 2.05 (0.13), residues: 1527 sheet: 0.12 (0.72), residues: 48 loop : 0.05 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 101 HIS 0.008 0.002 HIS A 349 PHE 0.034 0.002 PHE A 352 TYR 0.025 0.002 TYR C 92 ARG 0.008 0.001 ARG E 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6613.11 seconds wall clock time: 119 minutes 19.88 seconds (7159.88 seconds total)