Starting phenix.real_space_refine on Tue Apr 9 23:23:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/04_2024/8sxn_40855_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/04_2024/8sxn_40855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/04_2024/8sxn_40855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/04_2024/8sxn_40855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/04_2024/8sxn_40855_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxn_40855/04_2024/8sxn_40855_neut_updated.pdb" } resolution = 4.04 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= 0.002 sd= 0.028 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 6 5.49 5 S 154 5.16 5 C 11278 2.51 5 N 3008 2.21 5 O 3262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17708 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2284 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "B" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2284 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "C" Number of atoms: 6511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6511 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 23, 'TRANS': 792} Chain breaks: 4 Chain: "D" Number of atoms: 6511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6511 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 23, 'TRANS': 792} Chain breaks: 4 Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.09, per 1000 atoms: 0.51 Number of scatterers: 17708 At special positions: 0 Unit cell: (135.616, 172.224, 98.176, 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 154 16.00 P 6 15.00 O 3262 8.00 N 3008 7.00 C 11278 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 - 3.50 Amino acid : False - 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: 6.51 Conformation dependent library (CDL) restraints added in 3.0 seconds 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 10 sheets defined 43.3% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 75 through 88 removed outlier: 4.350A pdb=" N LYS A 81 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 82 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 87 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 135 through 155 removed outlier: 3.661A pdb=" N LYS A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 191 through 195 removed outlier: 4.168A pdb=" N SER A 195 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 208 No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.566A pdb=" N ILE A 219 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 251 Processing helix chain 'A' and resid 265 through 274 Processing helix chain 'A' and resid 285 through 299 removed outlier: 3.668A pdb=" N CYS A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 26 No H-bonds generated for 'chain 'B' and resid 24 through 26' Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 75 through 88 removed outlier: 4.267A pdb=" N LYS B 81 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 82 " --> pdb=" O CYS B 79 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 87 " --> pdb=" O ASP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 128 Processing helix chain 'B' and resid 135 through 155 removed outlier: 3.705A pdb=" N LYS B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLN B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 155 " --> pdb=" O HIS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 191 through 195 removed outlier: 4.190A pdb=" N SER B 195 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 208 No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 215 through 231 removed outlier: 3.573A pdb=" N ILE B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 251 Processing helix chain 'B' and resid 265 through 274 Processing helix chain 'B' and resid 285 through 298 removed outlier: 3.614A pdb=" N CYS B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 147 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 232 through 244 Processing helix chain 'C' and resid 261 through 263 No H-bonds generated for 'chain 'C' and resid 261 through 263' Processing helix chain 'C' and resid 273 through 277 Processing helix chain 'C' and resid 290 through 292 No H-bonds generated for 'chain 'C' and resid 290 through 292' Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.567A pdb=" N GLU C 356 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 361 No H-bonds generated for 'chain 'C' and resid 359 through 361' Processing helix chain 'C' and resid 375 through 385 Processing helix chain 'C' and resid 389 through 401 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.828A pdb=" N PHE C 410 " --> pdb=" O PHE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 439 through 451 Processing helix chain 'C' and resid 463 through 478 removed outlier: 4.090A pdb=" N GLY C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 492 Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.812A pdb=" N TYR C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 removed outlier: 4.806A pdb=" N GLY C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 574 through 583 Processing helix chain 'C' and resid 593 through 595 No H-bonds generated for 'chain 'C' and resid 593 through 595' Processing helix chain 'C' and resid 598 through 615 Processing helix chain 'C' and resid 628 through 636 Processing helix chain 'C' and resid 640 through 649 removed outlier: 3.805A pdb=" N ASP C 648 " --> pdb=" O GLN C 644 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR C 649 " --> pdb=" O ARG C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 731 through 739 removed outlier: 3.748A pdb=" N SER C 738 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 766 Processing helix chain 'C' and resid 784 through 794 Processing helix chain 'C' and resid 812 through 823 removed outlier: 3.679A pdb=" N VAL C 820 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 853 removed outlier: 4.226A pdb=" N ALA C 848 " --> pdb=" O GLN C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 879 removed outlier: 3.562A pdb=" N LYS C 878 " --> pdb=" O ILE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 908 Processing helix chain 'C' and resid 925 through 936 Processing helix chain 'C' and resid 955 through 965 removed outlier: 4.290A pdb=" N TRP C 959 " --> pdb=" O HIS C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 993 Processing helix chain 'C' and resid 1012 through 1024 Processing helix chain 'D' and resid 137 through 147 Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 232 through 244 Processing helix chain 'D' and resid 261 through 263 No H-bonds generated for 'chain 'D' and resid 261 through 263' Processing helix chain 'D' and resid 274 through 277 No H-bonds generated for 'chain 'D' and resid 274 through 277' Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 328 through 336 Processing helix chain 'D' and resid 352 through 357 removed outlier: 3.968A pdb=" N GLU D 356 " --> pdb=" O VAL D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 361 No H-bonds generated for 'chain 'D' and resid 359 through 361' Processing helix chain 'D' and resid 375 through 385 Processing helix chain 'D' and resid 389 through 401 Processing helix chain 'D' and resid 403 through 410 removed outlier: 3.799A pdb=" N PHE D 410 " --> pdb=" O PHE D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 427 Processing helix chain 'D' and resid 439 through 451 Processing helix chain 'D' and resid 463 through 478 removed outlier: 4.196A pdb=" N GLY D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 492 Processing helix chain 'D' and resid 497 through 504 Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.942A pdb=" N TYR D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 563 Processing helix chain 'D' and resid 568 through 570 No H-bonds generated for 'chain 'D' and resid 568 through 570' Processing helix chain 'D' and resid 574 through 583 Processing helix chain 'D' and resid 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 through 595' Processing helix chain 'D' and resid 598 through 616 Processing helix chain 'D' and resid 628 through 636 Processing helix chain 'D' and resid 640 through 649 removed outlier: 3.803A pdb=" N ASP D 648 " --> pdb=" O GLN D 644 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYR D 649 " --> pdb=" O ARG D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 731 through 739 removed outlier: 3.862A pdb=" N SER D 738 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 766 Processing helix chain 'D' and resid 784 through 794 Processing helix chain 'D' and resid 812 through 823 removed outlier: 3.693A pdb=" N VAL D 820 " --> pdb=" O ARG D 816 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY D 821 " --> pdb=" O LEU D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 853 removed outlier: 3.667A pdb=" N GLN D 845 " --> pdb=" O ALA D 842 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 848 " --> pdb=" O GLN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 879 removed outlier: 3.534A pdb=" N LYS D 878 " --> pdb=" O ILE D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 910 Processing helix chain 'D' and resid 925 through 936 Processing helix chain 'D' and resid 955 through 965 removed outlier: 4.258A pdb=" N TRP D 959 " --> pdb=" O HIS D 956 " (cutoff:3.500A) Processing helix chain 'D' and resid 983 through 993 Processing helix chain 'D' and resid 1012 through 1024 Processing sheet with id= A, first strand: chain 'A' and resid 97 through 103 removed outlier: 6.666A pdb=" N VAL A 110 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A 100 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A 108 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE A 102 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A 52 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE A 36 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 167 through 169 Processing sheet with id= C, first strand: chain 'B' and resid 97 through 103 removed outlier: 6.696A pdb=" N VAL B 110 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER B 100 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN B 108 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE B 102 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA B 52 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ILE B 36 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 167 through 169 Processing sheet with id= E, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.514A pdb=" N LEU C 346 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE C 224 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE C 348 " --> pdb=" O PHE C 224 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR C 255 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU C 300 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE C 257 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP C 302 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 259 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 652 through 655 removed outlier: 6.554A pdb=" N SER C 678 " --> pdb=" O ILE C 653 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE C 655 " --> pdb=" O SER C 678 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER C 680 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU C 745 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU C 681 " --> pdb=" O GLU C 745 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASP C 747 " --> pdb=" O LEU C 681 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG C 774 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU C 802 " --> pdb=" O LEU C 775 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS C 831 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG C 859 " --> pdb=" O LEU C 832 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 916 through 918 removed outlier: 6.592A pdb=" N VAL C 945 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS C 973 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU C 948 " --> pdb=" O LYS C 973 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER C 975 " --> pdb=" O LEU C 948 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 173 through 175 removed outlier: 6.527A pdb=" N LEU D 346 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE D 224 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE D 348 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR D 255 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU D 300 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE D 257 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP D 302 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE D 259 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 652 through 655 removed outlier: 6.513A pdb=" N SER D 678 " --> pdb=" O ILE D 653 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE D 655 " --> pdb=" O SER D 678 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER D 680 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU D 745 " --> pdb=" O LEU D 679 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU D 681 " --> pdb=" O GLU D 745 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP D 747 " --> pdb=" O LEU D 681 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG D 774 " --> pdb=" O LEU D 746 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU D 802 " --> pdb=" O LEU D 775 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS D 831 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG D 859 " --> pdb=" O LEU D 832 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LYS D 888 " --> pdb=" O LEU D 860 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 916 through 918 removed outlier: 6.571A pdb=" N VAL D 945 " --> pdb=" O LEU D 917 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS D 973 " --> pdb=" O LEU D 946 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU D 948 " --> pdb=" O LYS D 973 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER D 975 " --> pdb=" O LEU D 948 " (cutoff:3.500A) No H-bonds generated for sheet with id= J 599 hydrogen bonds defined for protein. 1488 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: 5.51 Time building geometry restraints manager: 7.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2968 1.31 - 1.44: 4591 1.44 - 1.56: 10266 1.56 - 1.69: 23 1.69 - 1.82: 216 Bond restraints: 18064 Sorted by residual: bond pdb=" C08 7YN D1101 " pdb=" C09 7YN D1101 " ideal model delta sigma weight residual 1.340 1.521 -0.181 2.00e-02 2.50e+03 8.19e+01 bond pdb=" C08 7YN C1101 " pdb=" C09 7YN C1101 " ideal model delta sigma weight residual 1.340 1.521 -0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" C14 7YN D1101 " pdb=" N13 7YN D1101 " ideal model delta sigma weight residual 1.349 1.469 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C14 7YN C1101 " pdb=" N13 7YN C1101 " ideal model delta sigma weight residual 1.349 1.463 -0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C06 7YN C1101 " pdb=" C09 7YN C1101 " ideal model delta sigma weight residual 1.461 1.544 -0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 18059 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.81: 477 106.81 - 113.91: 10225 113.91 - 121.01: 8783 121.01 - 128.10: 4788 128.10 - 135.20: 117 Bond angle restraints: 24390 Sorted by residual: angle pdb=" PB ATP C1102 " pdb=" O3B ATP C1102 " pdb=" PG ATP C1102 " ideal model delta sigma weight residual 139.87 109.40 30.47 1.00e+00 1.00e+00 9.28e+02 angle pdb=" PB ATP D1102 " pdb=" O3B ATP D1102 " pdb=" PG ATP D1102 " ideal model delta sigma weight residual 139.87 109.46 30.41 1.00e+00 1.00e+00 9.25e+02 angle pdb=" PA ATP D1102 " pdb=" O3A ATP D1102 " pdb=" PB ATP D1102 " ideal model delta sigma weight residual 136.83 111.34 25.49 1.00e+00 1.00e+00 6.50e+02 angle pdb=" PA ATP C1102 " pdb=" O3A ATP C1102 " pdb=" PB ATP C1102 " ideal model delta sigma weight residual 136.83 111.39 25.44 1.00e+00 1.00e+00 6.47e+02 angle pdb=" C5' ATP D1102 " pdb=" O5' ATP D1102 " pdb=" PA ATP D1102 " ideal model delta sigma weight residual 121.27 113.22 8.05 1.00e+00 1.00e+00 6.48e+01 ... (remaining 24385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.04: 10757 27.04 - 54.08: 180 54.08 - 81.12: 61 81.12 - 108.16: 12 108.16 - 135.20: 4 Dihedral angle restraints: 11014 sinusoidal: 4570 harmonic: 6444 Sorted by residual: dihedral pdb=" CA GLN C 624 " pdb=" C GLN C 624 " pdb=" N PRO C 625 " pdb=" CA PRO C 625 " ideal model delta harmonic sigma weight residual 180.00 151.50 28.50 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" C14 7YN C1101 " pdb=" N15 7YN C1101 " pdb=" S17 7YN C1101 " pdb=" O18 7YN C1101 " ideal model delta sinusoidal sigma weight residual 196.22 61.02 135.20 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" C14 7YN D1101 " pdb=" N15 7YN D1101 " pdb=" S17 7YN D1101 " pdb=" O18 7YN D1101 " ideal model delta sinusoidal sigma weight residual 196.22 64.01 132.21 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 11011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1554 0.044 - 0.088: 728 0.088 - 0.131: 332 0.131 - 0.175: 105 0.175 - 0.219: 9 Chirality restraints: 2728 Sorted by residual: chirality pdb=" CA PRO A 134 " pdb=" N PRO A 134 " pdb=" C PRO A 134 " pdb=" CB PRO A 134 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C4' ATP C1102 " pdb=" C3' ATP C1102 " pdb=" C5' ATP C1102 " pdb=" O4' ATP C1102 " both_signs ideal model delta sigma weight residual False -2.49 -2.69 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" C4' ATP D1102 " pdb=" C3' ATP D1102 " pdb=" C5' ATP D1102 " pdb=" O4' ATP D1102 " both_signs ideal model delta sigma weight residual False -2.49 -2.69 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 2725 not shown) Planarity restraints: 3076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 7YN D1101 " -0.077 2.00e-02 2.50e+03 2.02e-01 1.32e+03 pdb=" C02 7YN D1101 " -0.078 2.00e-02 2.50e+03 pdb=" C03 7YN D1101 " -0.103 2.00e-02 2.50e+03 pdb=" C04 7YN D1101 " -0.078 2.00e-02 2.50e+03 pdb=" C05 7YN D1101 " -0.124 2.00e-02 2.50e+03 pdb=" C06 7YN D1101 " -0.093 2.00e-02 2.50e+03 pdb=" C07 7YN D1101 " -0.059 2.00e-02 2.50e+03 pdb=" C08 7YN D1101 " 0.458 2.00e-02 2.50e+03 pdb=" C09 7YN D1101 " -0.096 2.00e-02 2.50e+03 pdb=" C10 7YN D1101 " -0.060 2.00e-02 2.50e+03 pdb=" C11 7YN D1101 " 0.483 2.00e-02 2.50e+03 pdb=" C12 7YN D1101 " -0.118 2.00e-02 2.50e+03 pdb=" N13 7YN D1101 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7YN C1101 " 0.075 2.00e-02 2.50e+03 1.97e-01 1.27e+03 pdb=" C02 7YN C1101 " 0.074 2.00e-02 2.50e+03 pdb=" C03 7YN C1101 " 0.108 2.00e-02 2.50e+03 pdb=" C04 7YN C1101 " 0.079 2.00e-02 2.50e+03 pdb=" C05 7YN C1101 " 0.105 2.00e-02 2.50e+03 pdb=" C06 7YN C1101 " 0.103 2.00e-02 2.50e+03 pdb=" C07 7YN C1101 " 0.065 2.00e-02 2.50e+03 pdb=" C08 7YN C1101 " -0.459 2.00e-02 2.50e+03 pdb=" C09 7YN C1101 " 0.096 2.00e-02 2.50e+03 pdb=" C10 7YN C1101 " 0.058 2.00e-02 2.50e+03 pdb=" C11 7YN C1101 " -0.463 2.00e-02 2.50e+03 pdb=" C12 7YN C1101 " 0.105 2.00e-02 2.50e+03 pdb=" N13 7YN C1101 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP C1102 " 0.222 2.00e-02 2.50e+03 8.84e-02 2.15e+02 pdb=" C2 ATP C1102 " -0.031 2.00e-02 2.50e+03 pdb=" C4 ATP C1102 " -0.062 2.00e-02 2.50e+03 pdb=" C5 ATP C1102 " -0.006 2.00e-02 2.50e+03 pdb=" C6 ATP C1102 " 0.036 2.00e-02 2.50e+03 pdb=" C8 ATP C1102 " -0.090 2.00e-02 2.50e+03 pdb=" N1 ATP C1102 " 0.028 2.00e-02 2.50e+03 pdb=" N3 ATP C1102 " -0.074 2.00e-02 2.50e+03 pdb=" N6 ATP C1102 " 0.089 2.00e-02 2.50e+03 pdb=" N7 ATP C1102 " -0.024 2.00e-02 2.50e+03 pdb=" N9 ATP C1102 " -0.089 2.00e-02 2.50e+03 ... (remaining 3073 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 6737 2.87 - 3.38: 17938 3.38 - 3.89: 30698 3.89 - 4.39: 36800 4.39 - 4.90: 57308 Nonbonded interactions: 149481 Sorted by model distance: nonbonded pdb=" OG SER B 187 " pdb=" OG1 THR B 190 " model vdw 2.369 2.440 nonbonded pdb=" OD2 ASP A 78 " pdb=" NZ LYS A 189 " model vdw 2.382 2.520 nonbonded pdb=" O ASP C 949 " pdb=" C ASN C 950 " model vdw 2.399 3.270 nonbonded pdb=" OD2 ASP B 78 " pdb=" NZ LYS B 189 " model vdw 2.400 2.520 nonbonded pdb=" OG SER D 555 " pdb=" N ARG D 556 " model vdw 2.403 2.520 ... (remaining 149476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.970 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: 10.680 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 46.860 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.012 0.181 18064 Z= 0.816 Angle : 1.263 30.465 24390 Z= 0.904 Chirality : 0.062 0.219 2728 Planarity : 0.007 0.202 3076 Dihedral : 12.199 135.195 6834 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 1.15 % Allowed : 3.03 % Favored : 95.82 % Rotamer: Outliers : 0.05 % Allowed : 0.35 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.17), residues: 2176 helix: -0.18 (0.15), residues: 1024 sheet: -0.51 (0.31), residues: 262 loop : -0.00 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP D 611 HIS 0.006 0.001 HIS C 916 PHE 0.020 0.003 PHE C 502 TYR 0.025 0.004 TYR D 443 ARG 0.004 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 409 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 PHE cc_start: 0.7339 (m-80) cc_final: 0.6926 (m-80) REVERT: A 62 LEU cc_start: 0.7750 (tp) cc_final: 0.3171 (mt) REVERT: A 65 VAL cc_start: 0.8073 (t) cc_final: 0.0643 (t) REVERT: A 109 ILE cc_start: 0.8069 (mt) cc_final: 0.6531 (mt) REVERT: A 140 LYS cc_start: 0.9343 (tttp) cc_final: 0.9104 (ttpt) REVERT: A 142 PHE cc_start: 0.8829 (t80) cc_final: 0.8526 (t80) REVERT: A 158 MET cc_start: 0.6681 (mtm) cc_final: 0.6202 (mtm) REVERT: A 186 PHE cc_start: 0.8800 (m-80) cc_final: 0.8340 (m-80) REVERT: A 226 LEU cc_start: 0.9685 (tp) cc_final: 0.9392 (tp) REVERT: A 236 PHE cc_start: 0.9030 (m-80) cc_final: 0.8773 (m-80) REVERT: A 247 CYS cc_start: 0.8516 (m) cc_final: 0.8229 (t) REVERT: A 286 THR cc_start: 0.9283 (m) cc_final: 0.8879 (t) REVERT: B 34 PHE cc_start: 0.6378 (m-80) cc_final: 0.6048 (m-80) REVERT: B 62 LEU cc_start: 0.7957 (tp) cc_final: 0.3796 (mp) REVERT: B 65 VAL cc_start: 0.8228 (t) cc_final: 0.2226 (t) REVERT: B 104 ASP cc_start: 0.9176 (m-30) cc_final: 0.8963 (t70) REVERT: B 176 LYS cc_start: 0.8552 (mttt) cc_final: 0.8332 (mtpp) REVERT: B 226 LEU cc_start: 0.9642 (tp) cc_final: 0.9356 (tt) REVERT: B 286 THR cc_start: 0.9264 (m) cc_final: 0.8887 (t) REVERT: C 230 ILE cc_start: 0.9210 (mm) cc_final: 0.8900 (mt) REVERT: C 248 LEU cc_start: 0.8082 (tp) cc_final: 0.7391 (mm) REVERT: C 521 ILE cc_start: 0.9156 (pt) cc_final: 0.8635 (mm) REVERT: C 536 LEU cc_start: 0.8468 (mt) cc_final: 0.8192 (pp) REVERT: C 591 TYR cc_start: 0.6877 (m-80) cc_final: 0.6472 (m-10) REVERT: C 637 MET cc_start: 0.8613 (ttm) cc_final: 0.8358 (ttm) REVERT: C 642 PHE cc_start: 0.8475 (t80) cc_final: 0.7625 (t80) REVERT: C 665 VAL cc_start: 0.9590 (t) cc_final: 0.9372 (p) REVERT: C 807 ASP cc_start: 0.8493 (m-30) cc_final: 0.8180 (t70) REVERT: C 846 ASP cc_start: 0.8354 (m-30) cc_final: 0.7831 (t0) REVERT: C 943 LEU cc_start: 0.9266 (tp) cc_final: 0.8958 (tt) REVERT: C 1021 LEU cc_start: 0.9609 (tp) cc_final: 0.9362 (mm) REVERT: C 1025 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8729 (mttp) REVERT: D 230 ILE cc_start: 0.9142 (mm) cc_final: 0.8837 (mt) REVERT: D 240 MET cc_start: 0.8651 (mmm) cc_final: 0.7986 (mmt) REVERT: D 248 LEU cc_start: 0.8089 (tp) cc_final: 0.7723 (mm) REVERT: D 508 PHE cc_start: 0.8130 (m-80) cc_final: 0.7861 (m-10) REVERT: D 521 ILE cc_start: 0.9310 (pt) cc_final: 0.8976 (tp) REVERT: D 591 TYR cc_start: 0.6880 (m-80) cc_final: 0.6650 (m-10) REVERT: D 595 LYS cc_start: 0.8643 (tptt) cc_final: 0.8433 (tptp) REVERT: D 624 GLN cc_start: 0.6675 (mp10) cc_final: 0.6399 (mp10) REVERT: D 807 ASP cc_start: 0.8625 (m-30) cc_final: 0.8235 (t70) REVERT: D 846 ASP cc_start: 0.8290 (m-30) cc_final: 0.7836 (t0) REVERT: D 957 CYS cc_start: 0.8165 (p) cc_final: 0.7551 (p) REVERT: D 961 LEU cc_start: 0.9490 (mt) cc_final: 0.9082 (mt) REVERT: D 1021 LEU cc_start: 0.9592 (tp) cc_final: 0.9361 (mm) outliers start: 1 outliers final: 1 residues processed: 410 average time/residue: 0.3351 time to fit residues: 202.5944 Evaluate side-chains 213 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 91 optimal weight: 0.0980 chunk 56 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 108 ASN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 GLN D 622 GLN ** D1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18064 Z= 0.196 Angle : 0.611 10.197 24390 Z= 0.313 Chirality : 0.040 0.157 2728 Planarity : 0.004 0.029 3076 Dihedral : 9.948 148.001 2474 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.23 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.18), residues: 2176 helix: 0.64 (0.16), residues: 1012 sheet: -0.54 (0.32), residues: 254 loop : -0.04 (0.23), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 478 HIS 0.003 0.001 HIS A 91 PHE 0.028 0.002 PHE C 502 TYR 0.021 0.001 TYR B 141 ARG 0.006 0.000 ARG C 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.7629 (mt) cc_final: 0.4897 (mt) REVERT: A 140 LYS cc_start: 0.9260 (tttp) cc_final: 0.9051 (ttpt) REVERT: A 142 PHE cc_start: 0.8673 (t80) cc_final: 0.8429 (t80) REVERT: A 152 MET cc_start: 0.9208 (ttm) cc_final: 0.8999 (ttm) REVERT: A 158 MET cc_start: 0.6703 (mtm) cc_final: 0.6418 (mtm) REVERT: A 266 GLU cc_start: 0.7862 (pm20) cc_final: 0.7643 (pm20) REVERT: B 104 ASP cc_start: 0.9259 (m-30) cc_final: 0.9004 (t0) REVERT: C 205 MET cc_start: 0.7290 (ttp) cc_final: 0.6887 (tpp) REVERT: C 230 ILE cc_start: 0.9168 (mm) cc_final: 0.8954 (mt) REVERT: C 508 PHE cc_start: 0.8021 (m-80) cc_final: 0.7597 (m-10) REVERT: C 521 ILE cc_start: 0.9133 (pt) cc_final: 0.8696 (mm) REVERT: C 591 TYR cc_start: 0.6768 (m-80) cc_final: 0.6545 (m-10) REVERT: C 636 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8013 (mm-30) REVERT: C 642 PHE cc_start: 0.8375 (t80) cc_final: 0.7416 (t80) REVERT: C 943 LEU cc_start: 0.9245 (tp) cc_final: 0.8916 (tt) REVERT: C 1021 LEU cc_start: 0.9595 (tp) cc_final: 0.9322 (mm) REVERT: D 230 ILE cc_start: 0.9155 (mm) cc_final: 0.8879 (mt) REVERT: D 240 MET cc_start: 0.8497 (mmm) cc_final: 0.8096 (mmt) REVERT: D 508 PHE cc_start: 0.8167 (m-80) cc_final: 0.7849 (m-10) REVERT: D 521 ILE cc_start: 0.9290 (pt) cc_final: 0.8844 (mm) REVERT: D 576 VAL cc_start: 0.9585 (m) cc_final: 0.9340 (p) REVERT: D 595 LYS cc_start: 0.8552 (tptt) cc_final: 0.8317 (tptp) REVERT: D 846 ASP cc_start: 0.8483 (m-30) cc_final: 0.8074 (t0) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.3027 time to fit residues: 125.0576 Evaluate side-chains 171 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 54 optimal weight: 0.0980 chunk 198 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 108 ASN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18064 Z= 0.221 Angle : 0.572 9.569 24390 Z= 0.293 Chirality : 0.039 0.144 2728 Planarity : 0.004 0.034 3076 Dihedral : 9.903 148.904 2474 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.41 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.19), residues: 2176 helix: 0.60 (0.17), residues: 1008 sheet: -0.46 (0.32), residues: 266 loop : -0.19 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 478 HIS 0.004 0.001 HIS D 367 PHE 0.038 0.002 PHE D 502 TYR 0.014 0.001 TYR A 49 ARG 0.005 0.000 ARG C 779 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.6817 (mt) cc_final: 0.6223 (mt) REVERT: A 112 GLU cc_start: 0.7904 (tt0) cc_final: 0.7628 (tm-30) REVERT: A 152 MET cc_start: 0.9265 (ttm) cc_final: 0.9063 (ttm) REVERT: A 158 MET cc_start: 0.6854 (mtm) cc_final: 0.6562 (mtm) REVERT: A 203 MET cc_start: 0.7158 (mtp) cc_final: 0.6861 (mtp) REVERT: B 62 LEU cc_start: 0.6185 (mt) cc_final: 0.5583 (mt) REVERT: B 104 ASP cc_start: 0.9257 (m-30) cc_final: 0.8968 (t0) REVERT: B 142 PHE cc_start: 0.8571 (t80) cc_final: 0.8320 (t80) REVERT: B 158 MET cc_start: 0.6851 (mpp) cc_final: 0.6572 (mmm) REVERT: C 230 ILE cc_start: 0.9276 (mm) cc_final: 0.8974 (mt) REVERT: C 521 ILE cc_start: 0.9164 (pt) cc_final: 0.8700 (mm) REVERT: C 527 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7889 (mm-30) REVERT: C 846 ASP cc_start: 0.8246 (t0) cc_final: 0.7792 (t0) REVERT: C 943 LEU cc_start: 0.9248 (tp) cc_final: 0.8956 (tt) REVERT: C 1009 TYR cc_start: 0.6529 (t80) cc_final: 0.6310 (t80) REVERT: D 140 TYR cc_start: 0.8236 (t80) cc_final: 0.8025 (t80) REVERT: D 230 ILE cc_start: 0.9208 (mm) cc_final: 0.8945 (mt) REVERT: D 240 MET cc_start: 0.8633 (mmm) cc_final: 0.8269 (mmt) REVERT: D 382 PHE cc_start: 0.8212 (m-80) cc_final: 0.7999 (m-80) REVERT: D 484 PHE cc_start: 0.8589 (m-80) cc_final: 0.8377 (m-10) REVERT: D 502 PHE cc_start: 0.7793 (m-80) cc_final: 0.7407 (m-80) REVERT: D 508 PHE cc_start: 0.8275 (m-80) cc_final: 0.8041 (m-10) REVERT: D 521 ILE cc_start: 0.9297 (pt) cc_final: 0.8806 (mm) REVERT: D 595 LYS cc_start: 0.8530 (tptt) cc_final: 0.8268 (tptp) REVERT: D 810 LEU cc_start: 0.8613 (mt) cc_final: 0.8152 (mt) REVERT: D 846 ASP cc_start: 0.8569 (m-30) cc_final: 0.8249 (t0) REVERT: D 957 CYS cc_start: 0.8644 (p) cc_final: 0.8184 (p) REVERT: D 961 LEU cc_start: 0.9409 (mt) cc_final: 0.9082 (mt) REVERT: D 987 MET cc_start: 0.8631 (ppp) cc_final: 0.8112 (mmt) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2742 time to fit residues: 95.7323 Evaluate side-chains 160 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 199 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 HIS C 845 GLN D 215 HIS D 622 GLN D 766 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18064 Z= 0.212 Angle : 0.557 10.133 24390 Z= 0.280 Chirality : 0.039 0.241 2728 Planarity : 0.004 0.033 3076 Dihedral : 9.913 149.809 2474 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.83 % Favored : 94.72 % Rotamer: Outliers : 0.05 % Allowed : 1.26 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.13 (0.19), residues: 2176 helix: 0.61 (0.17), residues: 1000 sheet: -0.67 (0.32), residues: 276 loop : -0.08 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 478 HIS 0.004 0.001 HIS B 159 PHE 0.032 0.002 PHE C 502 TYR 0.013 0.001 TYR B 49 ARG 0.005 0.000 ARG C 779 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.6684 (mt) cc_final: 0.6080 (mt) REVERT: A 112 GLU cc_start: 0.7868 (tt0) cc_final: 0.7653 (tm-30) REVERT: A 152 MET cc_start: 0.9325 (ttm) cc_final: 0.9050 (ttt) REVERT: A 158 MET cc_start: 0.6812 (mtm) cc_final: 0.6151 (mtt) REVERT: A 186 PHE cc_start: 0.8203 (m-80) cc_final: 0.7902 (m-80) REVERT: A 203 MET cc_start: 0.7291 (mtp) cc_final: 0.7072 (mtp) REVERT: B 65 VAL cc_start: 0.8138 (t) cc_final: 0.6798 (t) REVERT: B 158 MET cc_start: 0.6900 (mpp) cc_final: 0.6629 (mmm) REVERT: B 226 LEU cc_start: 0.9671 (tp) cc_final: 0.9415 (tt) REVERT: C 230 ILE cc_start: 0.9298 (mm) cc_final: 0.9024 (mt) REVERT: C 301 MET cc_start: 0.8417 (tpp) cc_final: 0.8202 (mmm) REVERT: C 521 ILE cc_start: 0.9172 (pt) cc_final: 0.8659 (mm) REVERT: C 600 ILE cc_start: 0.9362 (mm) cc_final: 0.8914 (tp) REVERT: C 810 LEU cc_start: 0.8742 (mt) cc_final: 0.8307 (mt) REVERT: C 846 ASP cc_start: 0.8378 (t0) cc_final: 0.7889 (t0) REVERT: C 943 LEU cc_start: 0.9240 (tp) cc_final: 0.8975 (tt) REVERT: D 230 ILE cc_start: 0.9267 (mm) cc_final: 0.8990 (mt) REVERT: D 382 PHE cc_start: 0.8168 (m-80) cc_final: 0.7859 (m-80) REVERT: D 484 PHE cc_start: 0.8654 (m-80) cc_final: 0.8329 (m-10) REVERT: D 502 PHE cc_start: 0.7780 (m-80) cc_final: 0.7405 (m-80) REVERT: D 508 PHE cc_start: 0.8254 (m-80) cc_final: 0.8051 (m-10) REVERT: D 521 ILE cc_start: 0.9265 (pt) cc_final: 0.8740 (mm) REVERT: D 532 MET cc_start: 0.8956 (tpp) cc_final: 0.8599 (tpp) REVERT: D 810 LEU cc_start: 0.8696 (mt) cc_final: 0.8270 (mt) REVERT: D 846 ASP cc_start: 0.8569 (m-30) cc_final: 0.8244 (t0) REVERT: D 957 CYS cc_start: 0.8790 (p) cc_final: 0.8366 (p) REVERT: D 987 MET cc_start: 0.8632 (ppp) cc_final: 0.8097 (mmm) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.2739 time to fit residues: 89.1524 Evaluate side-chains 154 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 179 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 GLN ** C 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 HIS D 995 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18064 Z= 0.284 Angle : 0.602 9.838 24390 Z= 0.302 Chirality : 0.040 0.184 2728 Planarity : 0.004 0.034 3076 Dihedral : 10.096 149.887 2474 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.61 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.09 (0.19), residues: 2176 helix: 0.47 (0.17), residues: 1004 sheet: -0.84 (0.32), residues: 276 loop : -0.22 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 478 HIS 0.005 0.001 HIS B 159 PHE 0.017 0.002 PHE C 148 TYR 0.012 0.002 TYR C 168 ARG 0.005 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.6525 (mt) cc_final: 0.5354 (mt) REVERT: A 112 GLU cc_start: 0.7919 (tt0) cc_final: 0.7628 (tm-30) REVERT: A 152 MET cc_start: 0.9369 (ttm) cc_final: 0.9103 (ttt) REVERT: A 158 MET cc_start: 0.6836 (mtm) cc_final: 0.6481 (mtm) REVERT: A 186 PHE cc_start: 0.8303 (m-80) cc_final: 0.8003 (m-80) REVERT: A 203 MET cc_start: 0.7285 (mtp) cc_final: 0.6742 (ttm) REVERT: B 65 VAL cc_start: 0.8502 (t) cc_final: 0.6981 (t) REVERT: B 152 MET cc_start: 0.9198 (ttm) cc_final: 0.8862 (ttt) REVERT: B 158 MET cc_start: 0.6929 (mpp) cc_final: 0.6590 (mmm) REVERT: B 179 ASP cc_start: 0.6842 (m-30) cc_final: 0.6386 (m-30) REVERT: C 230 ILE cc_start: 0.9332 (mm) cc_final: 0.9038 (mt) REVERT: C 484 PHE cc_start: 0.8781 (m-80) cc_final: 0.8532 (m-10) REVERT: C 521 ILE cc_start: 0.9187 (pt) cc_final: 0.8672 (mm) REVERT: C 636 GLU cc_start: 0.8635 (tp30) cc_final: 0.8385 (tp30) REVERT: C 758 MET cc_start: 0.9246 (tpp) cc_final: 0.8874 (tpp) REVERT: C 846 ASP cc_start: 0.8324 (t0) cc_final: 0.7861 (t0) REVERT: D 230 ILE cc_start: 0.9331 (mm) cc_final: 0.9043 (mt) REVERT: D 484 PHE cc_start: 0.8815 (m-80) cc_final: 0.8410 (m-10) REVERT: D 508 PHE cc_start: 0.8429 (m-80) cc_final: 0.8154 (m-10) REVERT: D 521 ILE cc_start: 0.9275 (pt) cc_final: 0.8721 (mm) REVERT: D 532 MET cc_start: 0.8977 (tpp) cc_final: 0.8635 (tpp) REVERT: D 957 CYS cc_start: 0.8861 (p) cc_final: 0.8508 (p) REVERT: D 987 MET cc_start: 0.8658 (ppp) cc_final: 0.8186 (mmt) REVERT: D 988 MET cc_start: 0.8761 (ppp) cc_final: 0.8537 (ppp) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2784 time to fit residues: 85.1313 Evaluate side-chains 139 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 17 optimal weight: 30.0000 chunk 69 optimal weight: 0.0970 chunk 110 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN ** C 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN D 269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18064 Z= 0.191 Angle : 0.538 8.173 24390 Z= 0.270 Chirality : 0.039 0.147 2728 Planarity : 0.004 0.048 3076 Dihedral : 10.068 150.693 2474 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.51 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.19), residues: 2176 helix: 0.52 (0.17), residues: 1012 sheet: -0.95 (0.32), residues: 274 loop : -0.24 (0.24), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 243 HIS 0.004 0.001 HIS D 492 PHE 0.035 0.002 PHE C 502 TYR 0.012 0.001 TYR C 168 ARG 0.005 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.6133 (mt) cc_final: 0.5146 (mt) REVERT: A 112 GLU cc_start: 0.7824 (tt0) cc_final: 0.7598 (tm-30) REVERT: A 152 MET cc_start: 0.9383 (ttm) cc_final: 0.9121 (ttt) REVERT: A 158 MET cc_start: 0.6771 (mtm) cc_final: 0.6502 (mtm) REVERT: A 186 PHE cc_start: 0.8331 (m-80) cc_final: 0.8054 (m-80) REVERT: A 203 MET cc_start: 0.7055 (mtp) cc_final: 0.6617 (ttm) REVERT: B 28 TYR cc_start: 0.6090 (m-10) cc_final: 0.5690 (m-10) REVERT: B 65 VAL cc_start: 0.8489 (t) cc_final: 0.5386 (p) REVERT: B 152 MET cc_start: 0.9265 (ttm) cc_final: 0.8969 (ttt) REVERT: B 158 MET cc_start: 0.6930 (mpp) cc_final: 0.6505 (mmm) REVERT: B 179 ASP cc_start: 0.6798 (m-30) cc_final: 0.6336 (m-30) REVERT: B 186 PHE cc_start: 0.8296 (m-10) cc_final: 0.7977 (m-10) REVERT: C 230 ILE cc_start: 0.9309 (mm) cc_final: 0.9035 (mt) REVERT: C 277 MET cc_start: 0.8822 (mpp) cc_final: 0.8253 (ttp) REVERT: C 484 PHE cc_start: 0.8810 (m-80) cc_final: 0.8539 (m-10) REVERT: C 521 ILE cc_start: 0.9179 (pt) cc_final: 0.8650 (mm) REVERT: C 758 MET cc_start: 0.9185 (tpp) cc_final: 0.8800 (tpp) REVERT: C 846 ASP cc_start: 0.8363 (t0) cc_final: 0.7891 (t0) REVERT: D 230 ILE cc_start: 0.9310 (mm) cc_final: 0.9027 (mt) REVERT: D 382 PHE cc_start: 0.8118 (m-80) cc_final: 0.7856 (m-80) REVERT: D 484 PHE cc_start: 0.8779 (m-80) cc_final: 0.8409 (m-10) REVERT: D 502 PHE cc_start: 0.8032 (m-80) cc_final: 0.7739 (m-80) REVERT: D 505 MET cc_start: 0.7918 (pmm) cc_final: 0.7640 (pmm) REVERT: D 521 ILE cc_start: 0.9236 (pt) cc_final: 0.8649 (mm) REVERT: D 532 MET cc_start: 0.8966 (tpp) cc_final: 0.8636 (tpp) REVERT: D 957 CYS cc_start: 0.8861 (p) cc_final: 0.8474 (p) REVERT: D 987 MET cc_start: 0.8628 (ppp) cc_final: 0.8184 (mmt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2672 time to fit residues: 79.9001 Evaluate side-chains 146 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 120 optimal weight: 0.0770 chunk 154 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18064 Z= 0.147 Angle : 0.523 7.928 24390 Z= 0.261 Chirality : 0.038 0.153 2728 Planarity : 0.003 0.034 3076 Dihedral : 10.028 151.221 2474 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.51 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.19), residues: 2176 helix: 0.53 (0.17), residues: 1012 sheet: -0.99 (0.32), residues: 274 loop : -0.19 (0.23), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 322 HIS 0.005 0.001 HIS C 492 PHE 0.035 0.001 PHE C 382 TYR 0.012 0.001 TYR D 258 ARG 0.005 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.6214 (mt) cc_final: 0.5726 (mt) REVERT: A 152 MET cc_start: 0.9384 (ttm) cc_final: 0.9105 (ttt) REVERT: A 158 MET cc_start: 0.6822 (mtm) cc_final: 0.6554 (mtm) REVERT: A 186 PHE cc_start: 0.8406 (m-80) cc_final: 0.8082 (m-80) REVERT: A 203 MET cc_start: 0.6989 (mtp) cc_final: 0.6577 (ttm) REVERT: A 219 ILE cc_start: 0.9398 (mm) cc_final: 0.9138 (mm) REVERT: B 62 LEU cc_start: 0.5456 (mt) cc_final: 0.4973 (mt) REVERT: B 85 LEU cc_start: 0.9197 (tp) cc_final: 0.8952 (pp) REVERT: B 152 MET cc_start: 0.9330 (ttm) cc_final: 0.9039 (ttt) REVERT: B 158 MET cc_start: 0.6951 (mpp) cc_final: 0.6586 (mmm) REVERT: B 179 ASP cc_start: 0.6737 (m-30) cc_final: 0.6477 (m-30) REVERT: B 263 TYR cc_start: 0.8489 (m-80) cc_final: 0.8245 (m-10) REVERT: C 230 ILE cc_start: 0.9291 (mm) cc_final: 0.9028 (mt) REVERT: C 277 MET cc_start: 0.8792 (mpp) cc_final: 0.8269 (ttp) REVERT: C 287 ILE cc_start: 0.9440 (mp) cc_final: 0.9162 (pt) REVERT: C 484 PHE cc_start: 0.8783 (m-80) cc_final: 0.8548 (m-10) REVERT: C 521 ILE cc_start: 0.9177 (pt) cc_final: 0.8609 (mm) REVERT: C 758 MET cc_start: 0.9171 (tpp) cc_final: 0.8761 (tpp) REVERT: C 846 ASP cc_start: 0.8418 (t0) cc_final: 0.7948 (t0) REVERT: D 230 ILE cc_start: 0.9282 (mm) cc_final: 0.9001 (mt) REVERT: D 484 PHE cc_start: 0.8745 (m-80) cc_final: 0.8406 (m-10) REVERT: D 521 ILE cc_start: 0.9226 (pt) cc_final: 0.8632 (mm) REVERT: D 532 MET cc_start: 0.8923 (tpp) cc_final: 0.8607 (tpp) REVERT: D 957 CYS cc_start: 0.8880 (p) cc_final: 0.8483 (p) REVERT: D 987 MET cc_start: 0.8579 (ppp) cc_final: 0.8190 (mmt) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2584 time to fit residues: 79.3062 Evaluate side-chains 149 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18064 Z= 0.187 Angle : 0.534 7.834 24390 Z= 0.269 Chirality : 0.039 0.142 2728 Planarity : 0.003 0.030 3076 Dihedral : 10.064 151.215 2474 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.65 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.19), residues: 2176 helix: 0.58 (0.17), residues: 1008 sheet: -1.04 (0.32), residues: 276 loop : -0.28 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 243 HIS 0.005 0.001 HIS C 492 PHE 0.040 0.002 PHE D 502 TYR 0.012 0.001 TYR A 237 ARG 0.010 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.9378 (ttm) cc_final: 0.9095 (ttt) REVERT: A 158 MET cc_start: 0.6834 (mtm) cc_final: 0.6556 (mtm) REVERT: A 186 PHE cc_start: 0.8439 (m-80) cc_final: 0.8153 (m-80) REVERT: A 203 MET cc_start: 0.7066 (mtp) cc_final: 0.6620 (ttm) REVERT: A 219 ILE cc_start: 0.9431 (mm) cc_final: 0.9156 (mm) REVERT: B 62 LEU cc_start: 0.5930 (mt) cc_final: 0.5468 (mt) REVERT: B 152 MET cc_start: 0.9290 (ttm) cc_final: 0.8980 (ttt) REVERT: B 158 MET cc_start: 0.6870 (mpp) cc_final: 0.6507 (mmm) REVERT: B 179 ASP cc_start: 0.6737 (m-30) cc_final: 0.5204 (m-30) REVERT: B 263 TYR cc_start: 0.8500 (m-80) cc_final: 0.8247 (m-10) REVERT: C 239 MET cc_start: 0.8995 (ttp) cc_final: 0.8605 (ttp) REVERT: C 277 MET cc_start: 0.8739 (mpp) cc_final: 0.8343 (ttp) REVERT: C 287 ILE cc_start: 0.9444 (mp) cc_final: 0.9199 (pt) REVERT: C 484 PHE cc_start: 0.8853 (m-80) cc_final: 0.8627 (m-10) REVERT: C 521 ILE cc_start: 0.9161 (pt) cc_final: 0.8590 (mm) REVERT: C 758 MET cc_start: 0.9190 (tpp) cc_final: 0.8734 (tpp) REVERT: C 846 ASP cc_start: 0.8384 (t0) cc_final: 0.7901 (t0) REVERT: C 1009 TYR cc_start: 0.6098 (t80) cc_final: 0.5871 (t80) REVERT: D 230 ILE cc_start: 0.9313 (mm) cc_final: 0.9025 (mt) REVERT: D 405 LEU cc_start: 0.9300 (tp) cc_final: 0.8936 (tt) REVERT: D 484 PHE cc_start: 0.8797 (m-80) cc_final: 0.8518 (m-10) REVERT: D 521 ILE cc_start: 0.9235 (pt) cc_final: 0.8645 (mm) REVERT: D 532 MET cc_start: 0.8956 (tpp) cc_final: 0.8631 (tpp) REVERT: D 957 CYS cc_start: 0.8975 (p) cc_final: 0.8555 (p) REVERT: D 987 MET cc_start: 0.8585 (ppp) cc_final: 0.8154 (mmt) REVERT: D 988 MET cc_start: 0.8708 (ppp) cc_final: 0.8445 (ppp) REVERT: D 1008 MET cc_start: 0.7797 (mmm) cc_final: 0.7364 (mmt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2462 time to fit residues: 73.5183 Evaluate side-chains 142 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 195 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 153 optimal weight: 0.0270 chunk 60 optimal weight: 0.0980 chunk 176 optimal weight: 5.9990 chunk 185 optimal weight: 0.0980 chunk 128 optimal weight: 2.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18064 Z= 0.132 Angle : 0.534 7.975 24390 Z= 0.264 Chirality : 0.039 0.211 2728 Planarity : 0.003 0.034 3076 Dihedral : 10.009 151.763 2474 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.33 % Favored : 94.26 % Rotamer: Outliers : 0.05 % Allowed : 0.25 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.19), residues: 2176 helix: 0.56 (0.17), residues: 1004 sheet: -1.02 (0.32), residues: 274 loop : -0.20 (0.23), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 243 HIS 0.005 0.001 HIS C 492 PHE 0.044 0.001 PHE C 382 TYR 0.019 0.001 TYR C 565 ARG 0.004 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.5852 (mt) cc_final: 0.5431 (mt) REVERT: A 152 MET cc_start: 0.9395 (ttm) cc_final: 0.9122 (ttt) REVERT: A 158 MET cc_start: 0.6848 (mtm) cc_final: 0.6605 (mtm) REVERT: A 186 PHE cc_start: 0.8499 (m-80) cc_final: 0.8154 (m-80) REVERT: A 203 MET cc_start: 0.7008 (mtp) cc_final: 0.6566 (ttm) REVERT: A 219 ILE cc_start: 0.9363 (mm) cc_final: 0.8833 (mp) REVERT: A 266 GLU cc_start: 0.8292 (pm20) cc_final: 0.7882 (pm20) REVERT: B 152 MET cc_start: 0.9292 (ttm) cc_final: 0.9038 (ttt) REVERT: B 158 MET cc_start: 0.6834 (mpp) cc_final: 0.6413 (mmm) REVERT: B 219 ILE cc_start: 0.9414 (mm) cc_final: 0.9145 (mm) REVERT: B 263 TYR cc_start: 0.8455 (m-80) cc_final: 0.8197 (m-10) REVERT: C 205 MET cc_start: 0.7597 (tpp) cc_final: 0.6249 (tpp) REVERT: C 230 ILE cc_start: 0.9262 (mm) cc_final: 0.8989 (mt) REVERT: C 239 MET cc_start: 0.8896 (ttp) cc_final: 0.8591 (ttp) REVERT: C 277 MET cc_start: 0.8786 (mpp) cc_final: 0.8243 (ttp) REVERT: C 287 ILE cc_start: 0.9440 (mp) cc_final: 0.9193 (pt) REVERT: C 521 ILE cc_start: 0.9171 (pt) cc_final: 0.8564 (mm) REVERT: C 636 GLU cc_start: 0.8588 (tp30) cc_final: 0.7947 (tp30) REVERT: C 669 CYS cc_start: 0.9363 (m) cc_final: 0.8968 (m) REVERT: C 846 ASP cc_start: 0.8371 (t0) cc_final: 0.7861 (t0) REVERT: C 1009 TYR cc_start: 0.5914 (t80) cc_final: 0.5630 (t80) REVERT: D 208 LEU cc_start: 0.9346 (mt) cc_final: 0.9141 (mt) REVERT: D 230 ILE cc_start: 0.9262 (mm) cc_final: 0.8954 (mt) REVERT: D 405 LEU cc_start: 0.9285 (tp) cc_final: 0.8954 (tt) REVERT: D 521 ILE cc_start: 0.9199 (pt) cc_final: 0.8589 (mm) REVERT: D 532 MET cc_start: 0.8914 (tpp) cc_final: 0.8595 (tpp) REVERT: D 669 CYS cc_start: 0.9395 (m) cc_final: 0.9186 (m) REVERT: D 987 MET cc_start: 0.8546 (ppp) cc_final: 0.8094 (mmm) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.2573 time to fit residues: 82.5519 Evaluate side-chains 147 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 17 optimal weight: 30.0000 chunk 133 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 HIS C 602 GLN ** C 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 638 GLN D 883 GLN ** D 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 18064 Z= 0.404 Angle : 0.727 11.552 24390 Z= 0.359 Chirality : 0.043 0.208 2728 Planarity : 0.004 0.043 3076 Dihedral : 10.311 153.944 2474 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.89 % Favored : 92.74 % Rotamer: Outliers : 0.05 % Allowed : 0.20 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.19), residues: 2176 helix: 0.30 (0.17), residues: 1008 sheet: -1.31 (0.31), residues: 276 loop : -0.65 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 243 HIS 0.009 0.001 HIS B 159 PHE 0.042 0.003 PHE D 581 TYR 0.017 0.002 TYR C 565 ARG 0.006 0.001 ARG B 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4352 Ramachandran restraints generated. 2176 Oldfield, 0 Emsley, 2176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.9367 (ttm) cc_final: 0.9106 (ttt) REVERT: A 158 MET cc_start: 0.6840 (mtm) cc_final: 0.6630 (mtm) REVERT: A 186 PHE cc_start: 0.8399 (m-80) cc_final: 0.8027 (m-80) REVERT: A 263 TYR cc_start: 0.8639 (m-80) cc_final: 0.8406 (m-10) REVERT: B 152 MET cc_start: 0.9280 (ttm) cc_final: 0.8971 (ttt) REVERT: B 158 MET cc_start: 0.7064 (mpp) cc_final: 0.6591 (mmm) REVERT: B 179 ASP cc_start: 0.6139 (m-30) cc_final: 0.5549 (m-30) REVERT: B 263 TYR cc_start: 0.8630 (m-80) cc_final: 0.8389 (m-10) REVERT: C 205 MET cc_start: 0.7770 (tpp) cc_final: 0.6964 (tpp) REVERT: C 230 ILE cc_start: 0.9375 (mm) cc_final: 0.9161 (mm) REVERT: C 239 MET cc_start: 0.9215 (ttp) cc_final: 0.8917 (ttp) REVERT: C 277 MET cc_start: 0.8838 (mpp) cc_final: 0.8424 (ttp) REVERT: C 287 ILE cc_start: 0.9454 (mp) cc_final: 0.9236 (pt) REVERT: C 521 ILE cc_start: 0.9183 (pt) cc_final: 0.8622 (mm) REVERT: C 636 GLU cc_start: 0.8632 (tp30) cc_final: 0.7983 (tp30) REVERT: C 647 MET cc_start: 0.8198 (ttm) cc_final: 0.7919 (ttm) REVERT: C 669 CYS cc_start: 0.9486 (m) cc_final: 0.9276 (m) REVERT: C 846 ASP cc_start: 0.8406 (t0) cc_final: 0.7922 (t0) REVERT: C 1008 MET cc_start: 0.6835 (mmt) cc_final: 0.6223 (mmm) REVERT: C 1009 TYR cc_start: 0.6104 (t80) cc_final: 0.5877 (t80) REVERT: D 230 ILE cc_start: 0.9367 (mm) cc_final: 0.9131 (mm) REVERT: D 405 LEU cc_start: 0.9303 (tp) cc_final: 0.8963 (tt) REVERT: D 484 PHE cc_start: 0.8654 (m-10) cc_final: 0.8211 (m-10) REVERT: D 521 ILE cc_start: 0.9212 (pt) cc_final: 0.8629 (mm) REVERT: D 532 MET cc_start: 0.9062 (tpp) cc_final: 0.8681 (tpp) REVERT: D 987 MET cc_start: 0.8717 (ppp) cc_final: 0.8192 (mmt) REVERT: D 988 MET cc_start: 0.8747 (ppp) cc_final: 0.8530 (ppp) REVERT: D 1008 MET cc_start: 0.8120 (mmm) cc_final: 0.7901 (mmm) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.2463 time to fit residues: 65.2873 Evaluate side-chains 125 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 0.0070 chunk 52 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 152 optimal weight: 0.4980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.075248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.058015 restraints weight = 76960.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.059909 restraints weight = 44941.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.061216 restraints weight = 31319.227| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18064 Z= 0.155 Angle : 0.565 13.354 24390 Z= 0.280 Chirality : 0.040 0.172 2728 Planarity : 0.003 0.038 3076 Dihedral : 10.181 154.601 2474 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.97 % Favored : 93.66 % Rotamer: Outliers : 0.05 % Allowed : 0.35 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.19), residues: 2176 helix: 0.59 (0.17), residues: 986 sheet: -1.22 (0.31), residues: 276 loop : -0.44 (0.23), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 467 HIS 0.006 0.001 HIS D 492 PHE 0.024 0.001 PHE D 484 TYR 0.018 0.001 TYR C 565 ARG 0.009 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3385.88 seconds wall clock time: 63 minutes 40.30 seconds (3820.30 seconds total)