Starting phenix.real_space_refine on Tue Feb 20 16:07:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btq_30182/02_2024/7btq_30182.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btq_30182/02_2024/7btq_30182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btq_30182/02_2024/7btq_30182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btq_30182/02_2024/7btq_30182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btq_30182/02_2024/7btq_30182.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btq_30182/02_2024/7btq_30182.pdb" } resolution = 4.54 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8103 atoms to isotropic. 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 86 5.49 5 S 37 5.16 5 C 12762 2.51 5 N 3439 2.21 5 O 4095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 925": "NH1" <-> "NH2" Residue "F ARG 989": "NH1" <-> "NH2" Residue "F TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20419 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3740 Classifications: {'peptide': 474} Link IDs: {'CIS': 21, 'PTRANS': 13, 'TRANS': 439} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 906 Classifications: {'DNA': 44} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 43} Chain: "C" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 892 Classifications: {'DNA': 44} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 43} Chain: "D" Number of atoms: 3740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3740 Classifications: {'peptide': 474} Link IDs: {'CIS': 21, 'PTRANS': 13, 'TRANS': 439} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3099 Classifications: {'peptide': 384} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 359} Chain: "F" Number of atoms: 8042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 8042 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 14, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 955} Chain breaks: 4 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Time building chain proxies: 10.77, per 1000 atoms: 0.53 Number of scatterers: 20419 At special positions: 0 Unit cell: (147.15, 166.05, 128.25, 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 37 16.00 P 86 15.00 O 4095 8.00 N 3439 7.00 C 12762 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: 8.30 Conformation dependent library (CDL) restraints added in 3.2 seconds 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 15 sheets defined 45.3% alpha, 6.5% beta 42 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 7.19 Creating SS restraints... Processing helix chain 'A' and resid 13 through 24 Processing helix chain 'A' and resid 28 through 54 removed outlier: 3.891A pdb=" N PHE A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR A 35 " --> pdb=" O ASP A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.818A pdb=" N SER A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 163 Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 202 through 214 removed outlier: 3.677A pdb=" N SER A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 Processing helix chain 'A' and resid 256 through 270 removed outlier: 4.035A pdb=" N HIS A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.878A pdb=" N ASP A 320 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 removed outlier: 4.083A pdb=" N VAL A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 346 " --> pdb=" O HIS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 removed outlier: 4.140A pdb=" N GLU A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 445 removed outlier: 3.921A pdb=" N SER A 445 " --> pdb=" O GLN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 464 Processing helix chain 'A' and resid 482 through 507 removed outlier: 4.230A pdb=" N ILE A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 24 Processing helix chain 'D' and resid 28 through 54 removed outlier: 3.891A pdb=" N PHE D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR D 35 " --> pdb=" O ASP D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 86 Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 115 through 121 removed outlier: 3.817A pdb=" N SER D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 163 Processing helix chain 'D' and resid 178 through 187 Processing helix chain 'D' and resid 202 through 214 removed outlier: 3.677A pdb=" N SER D 206 " --> pdb=" O PRO D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 241 Processing helix chain 'D' and resid 256 through 270 removed outlier: 4.034A pdb=" N HIS D 270 " --> pdb=" O ASN D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 320 removed outlier: 3.878A pdb=" N ASP D 320 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 346 removed outlier: 4.084A pdb=" N VAL D 340 " --> pdb=" O ASP D 336 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR D 346 " --> pdb=" O HIS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 376 removed outlier: 4.141A pdb=" N GLU D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.921A pdb=" N SER D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 464 Processing helix chain 'D' and resid 482 through 507 removed outlier: 4.229A pdb=" N ILE D 499 " --> pdb=" O THR D 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 119 removed outlier: 3.725A pdb=" N ASN E 119 " --> pdb=" O TYR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 141 removed outlier: 4.345A pdb=" N LYS E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 191 removed outlier: 3.996A pdb=" N ILE E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 removed outlier: 3.791A pdb=" N VAL E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 326 removed outlier: 3.551A pdb=" N ILE E 311 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N SER E 320 " --> pdb=" O GLY E 316 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASP E 321 " --> pdb=" O SER E 317 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA E 326 " --> pdb=" O ILE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.672A pdb=" N LEU E 341 " --> pdb=" O ASP E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 369 removed outlier: 3.747A pdb=" N ARG E 356 " --> pdb=" O ASN E 352 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ILE E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 394 removed outlier: 4.163A pdb=" N LEU E 381 " --> pdb=" O ARG E 377 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE E 394 " --> pdb=" O ARG E 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 48 Processing helix chain 'F' and resid 56 through 73 removed outlier: 3.507A pdb=" N MET F 60 " --> pdb=" O SER F 56 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 61 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 88 Processing helix chain 'F' and resid 95 through 105 removed outlier: 3.519A pdb=" N LYS F 99 " --> pdb=" O GLY F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 132 Processing helix chain 'F' and resid 174 through 178 Processing helix chain 'F' and resid 218 through 226 removed outlier: 4.059A pdb=" N SER F 222 " --> pdb=" O ASP F 219 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N PHE F 223 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP F 224 " --> pdb=" O ASN F 221 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR F 226 " --> pdb=" O PHE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 248 Processing helix chain 'F' and resid 249 through 260 removed outlier: 3.739A pdb=" N ASN F 255 " --> pdb=" O HIS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 293 removed outlier: 3.903A pdb=" N ILE F 277 " --> pdb=" O ARG F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 327 removed outlier: 3.969A pdb=" N THR F 316 " --> pdb=" O GLY F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 348 removed outlier: 4.600A pdb=" N TYR F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 373 Processing helix chain 'F' and resid 383 through 393 Processing helix chain 'F' and resid 396 through 401 removed outlier: 3.619A pdb=" N TYR F 399 " --> pdb=" O LEU F 396 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN F 400 " --> pdb=" O PRO F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 425 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 462 through 469 removed outlier: 4.028A pdb=" N ALA F 466 " --> pdb=" O VAL F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 491 Processing helix chain 'F' and resid 494 through 501 Processing helix chain 'F' and resid 509 through 528 removed outlier: 5.214A pdb=" N ARG F 525 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLN F 526 " --> pdb=" O ASN F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 569 removed outlier: 3.572A pdb=" N ALA F 550 " --> pdb=" O SER F 546 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA F 555 " --> pdb=" O LYS F 551 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER F 568 " --> pdb=" O ALA F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 624 removed outlier: 4.434A pdb=" N PHE F 611 " --> pdb=" O SER F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 632 through 647 removed outlier: 3.550A pdb=" N ASN F 636 " --> pdb=" O ASN F 632 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS F 646 " --> pdb=" O ALA F 642 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN F 647 " --> pdb=" O GLN F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 680 through 687 Processing helix chain 'F' and resid 708 through 720 Processing helix chain 'F' and resid 721 through 729 removed outlier: 4.080A pdb=" N LYS F 725 " --> pdb=" O ASP F 721 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN F 726 " --> pdb=" O LYS F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 738 Processing helix chain 'F' and resid 751 through 763 removed outlier: 3.614A pdb=" N PHE F 763 " --> pdb=" O LEU F 759 " (cutoff:3.500A) Processing helix chain 'F' and resid 771 through 793 Processing helix chain 'F' and resid 795 through 804 Processing helix chain 'F' and resid 811 through 822 Processing helix chain 'F' and resid 825 through 835 removed outlier: 3.999A pdb=" N GLU F 831 " --> pdb=" O GLU F 827 " (cutoff:3.500A) Processing helix chain 'F' and resid 839 through 857 Processing helix chain 'F' and resid 879 through 885 removed outlier: 3.545A pdb=" N LEU F 883 " --> pdb=" O GLU F 879 " (cutoff:3.500A) Processing helix chain 'F' and resid 890 through 900 Processing helix chain 'F' and resid 911 through 921 removed outlier: 3.758A pdb=" N LYS F 915 " --> pdb=" O ILE F 911 " (cutoff:3.500A) Processing helix chain 'F' and resid 924 through 926 No H-bonds generated for 'chain 'F' and resid 924 through 926' Processing helix chain 'F' and resid 927 through 936 removed outlier: 3.953A pdb=" N VAL F 931 " --> pdb=" O LYS F 927 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 932 " --> pdb=" O GLU F 928 " (cutoff:3.500A) Processing helix chain 'F' and resid 945 through 972 removed outlier: 3.516A pdb=" N ALA F 967 " --> pdb=" O ARG F 963 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU F 972 " --> pdb=" O LEU F 968 " (cutoff:3.500A) Processing helix chain 'F' and resid 975 through 990 Processing helix chain 'F' and resid 998 through 1002 Processing helix chain 'F' and resid 1016 through 1031 Processing sheet with id=AA1, first strand: chain 'A' and resid 253 through 254 removed outlier: 3.636A pdb=" N GLU A 254 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 357 Processing sheet with id=AA3, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.636A pdb=" N GLU D 254 " --> pdb=" O LYS D 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 353 through 357 Processing sheet with id=AA5, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AA6, first strand: chain 'E' and resid 26 through 28 removed outlier: 4.113A pdb=" N LYS E 99 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 202 through 205 removed outlier: 3.960A pdb=" N GLU E 202 " --> pdb=" O VAL E 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 250 through 251 Processing sheet with id=AA9, first strand: chain 'E' and resid 284 through 287 removed outlier: 3.650A pdb=" N ALA E 285 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 270 " --> pdb=" O ALA E 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 50 through 51 removed outlier: 6.047A pdb=" N GLU F 50 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLN F 138 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL F 162 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL F 156 " --> pdb=" O PRO F 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 109 through 113 Processing sheet with id=AB3, first strand: chain 'F' and resid 261 through 262 Processing sheet with id=AB4, first strand: chain 'F' and resid 379 through 382 removed outlier: 3.999A pdb=" N VAL F 337 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR F 435 " --> pdb=" O ILE F 305 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS F 307 " --> pdb=" O THR F 435 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR F 304 " --> pdb=" O LEU F 458 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER F 460 " --> pdb=" O TYR F 304 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TRP F 306 " --> pdb=" O SER F 460 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 474 through 479 removed outlier: 6.735A pdb=" N LYS F 474 " --> pdb=" O GLY F 700 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE F 702 " --> pdb=" O LYS F 474 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LYS F 476 " --> pdb=" O ILE F 702 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR F 704 " --> pdb=" O LYS F 476 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP F 478 " --> pdb=" O THR F 704 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASN F 669 " --> pdb=" O ASN F 701 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL F 703 " --> pdb=" O ASN F 669 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU F 671 " --> pdb=" O VAL F 703 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN F 539 " --> pdb=" O THR F 670 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N PHE F 672 " --> pdb=" O ASN F 539 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET F 541 " --> pdb=" O PHE F 672 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ASP F 674 " --> pdb=" O MET F 541 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA F 543 " --> pdb=" O ASP F 674 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA F 540 " --> pdb=" O LEU F 653 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL F 655 " --> pdb=" O ALA F 540 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU F 542 " --> pdb=" O VAL F 655 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA F 577 " --> pdb=" O ILE F 654 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 740 through 741 732 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 8.22 Time building geometry restraints manager: 8.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5953 1.34 - 1.46: 5030 1.46 - 1.58: 9793 1.58 - 1.70: 171 1.70 - 1.82: 65 Bond restraints: 21012 Sorted by residual: bond pdb=" O3' DT C -6 " pdb=" P DC C -5 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.50e-02 4.44e+03 6.85e+00 bond pdb=" CA ASN A 429 " pdb=" C ASN A 429 " ideal model delta sigma weight residual 1.525 1.574 -0.049 2.10e-02 2.27e+03 5.49e+00 bond pdb=" CA ASN D 429 " pdb=" C ASN D 429 " ideal model delta sigma weight residual 1.525 1.574 -0.049 2.10e-02 2.27e+03 5.34e+00 bond pdb=" CA LEU F 809 " pdb=" CB LEU F 809 " ideal model delta sigma weight residual 1.526 1.564 -0.038 1.70e-02 3.46e+03 4.97e+00 bond pdb=" C1' DC B 27 " pdb=" N1 DC B 27 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.87e+00 ... (remaining 21007 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.52: 520 104.52 - 111.99: 9784 111.99 - 119.46: 7659 119.46 - 126.93: 10386 126.93 - 134.39: 443 Bond angle restraints: 28792 Sorted by residual: angle pdb=" O3' DT C 12 " pdb=" C3' DT C 12 " pdb=" C2' DT C 12 " ideal model delta sigma weight residual 111.50 100.23 11.27 1.50e+00 4.44e-01 5.64e+01 angle pdb=" C ASN D 427 " pdb=" N ASN D 428 " pdb=" CA ASN D 428 " ideal model delta sigma weight residual 121.70 134.39 -12.69 1.80e+00 3.09e-01 4.97e+01 angle pdb=" C ASN A 427 " pdb=" N ASN A 428 " pdb=" CA ASN A 428 " ideal model delta sigma weight residual 121.70 134.36 -12.66 1.80e+00 3.09e-01 4.95e+01 angle pdb=" C4' DT B 4 " pdb=" C3' DT B 4 " pdb=" O3' DT B 4 " ideal model delta sigma weight residual 110.00 100.25 9.75 1.50e+00 4.44e-01 4.22e+01 angle pdb=" C THR D 395 " pdb=" N THR D 396 " pdb=" CA THR D 396 " ideal model delta sigma weight residual 121.70 133.18 -11.48 1.80e+00 3.09e-01 4.06e+01 ... (remaining 28787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.72: 11773 34.72 - 69.43: 598 69.43 - 104.15: 26 104.15 - 138.86: 1 138.86 - 173.58: 3 Dihedral angle restraints: 12401 sinusoidal: 5560 harmonic: 6841 Sorted by residual: dihedral pdb=" CA ASP F 28 " pdb=" C ASP F 28 " pdb=" N SER F 29 " pdb=" CA SER F 29 " ideal model delta harmonic sigma weight residual 180.00 -137.21 -42.79 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA LEU F 729 " pdb=" C LEU F 729 " pdb=" N GLU F 730 " pdb=" CA GLU F 730 " ideal model delta harmonic sigma weight residual -180.00 -141.99 -38.01 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA HIS E 303 " pdb=" C HIS E 303 " pdb=" N GLU E 304 " pdb=" CA GLU E 304 " ideal model delta harmonic sigma weight residual 180.00 145.60 34.40 0 5.00e+00 4.00e-02 4.73e+01 ... (remaining 12398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2544 0.070 - 0.139: 558 0.139 - 0.209: 84 0.209 - 0.278: 10 0.278 - 0.348: 4 Chirality restraints: 3200 Sorted by residual: chirality pdb=" CB ILE E 277 " pdb=" CA ILE E 277 " pdb=" CG1 ILE E 277 " pdb=" CG2 ILE E 277 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB ILE D 361 " pdb=" CA ILE D 361 " pdb=" CG1 ILE D 361 " pdb=" CG2 ILE D 361 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB ILE A 361 " pdb=" CA ILE A 361 " pdb=" CG1 ILE A 361 " pdb=" CG2 ILE A 361 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 3197 not shown) Planarity restraints: 3412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 117 " 0.026 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP E 117 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP E 117 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP E 117 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 117 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 117 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP E 117 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 117 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 117 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 117 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER F1007 " 0.058 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO F1008 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO F1008 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO F1008 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 46 " -0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO E 47 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 47 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 47 " -0.045 5.00e-02 4.00e+02 ... (remaining 3409 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 1 1.98 - 2.71: 1028 2.71 - 3.44: 29154 3.44 - 4.17: 49655 4.17 - 4.90: 81308 Nonbonded interactions: 161146 Sorted by model distance: nonbonded pdb=" O THR A 395 " pdb=" OP2 DT B 3 " model vdw 1.250 3.040 nonbonded pdb=" O GLY A 131 " pdb=" OH TYR A 274 " model vdw 2.234 2.440 nonbonded pdb=" O GLY D 131 " pdb=" OH TYR D 274 " model vdw 2.234 2.440 nonbonded pdb=" O LYS D 493 " pdb=" OG SER D 497 " model vdw 2.275 2.440 nonbonded pdb=" O LYS A 493 " pdb=" OG SER A 497 " model vdw 2.276 2.440 ... (remaining 161141 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 '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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 2.860 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 59.510 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 0.006 0.082 21012 Z= 0.365 Angle : 1.226 15.389 28792 Z= 0.690 Chirality : 0.059 0.348 3200 Planarity : 0.007 0.086 3412 Dihedral : 17.584 173.577 7967 Min Nonbonded Distance : 1.250 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.59 % Favored : 86.41 % Rotamer: Outliers : 0.85 % Allowed : 4.69 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 2.99 % Twisted General : 0.67 % 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: -4.60 (0.13), residues: 2296 helix: -2.33 (0.12), residues: 979 sheet: -1.60 (0.35), residues: 190 loop : -4.11 (0.14), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP E 117 HIS 0.016 0.002 HIS E 313 PHE 0.033 0.003 PHE A 422 TYR 0.047 0.003 TYR F 553 ARG 0.017 0.001 ARG E 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 416 time to evaluate : 2.286 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: 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 256 ASN cc_start: 0.8907 (t0) cc_final: 0.8688 (t0) REVERT: A 267 MET cc_start: 0.7991 (ptt) cc_final: 0.7619 (ptt) REVERT: A 341 LEU cc_start: 0.9480 (mt) cc_final: 0.9188 (mt) REVERT: A 371 ILE cc_start: 0.9360 (mm) cc_final: 0.9088 (mm) REVERT: A 397 ILE cc_start: 0.8951 (pt) cc_final: 0.8727 (tt) REVERT: A 488 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8433 (pt) REVERT: A 498 LYS cc_start: 0.8833 (mptp) cc_final: 0.8270 (tptt) REVERT: D 43 ARG cc_start: 0.8515 (ttt180) cc_final: 0.7848 (ttt180) REVERT: D 117 GLU cc_start: 0.7822 (pp20) cc_final: 0.7390 (tt0) REVERT: D 150 LYS cc_start: 0.9201 (mttt) cc_final: 0.8882 (pttt) REVERT: D 222 LYS cc_start: 0.7908 (mttt) cc_final: 0.7368 (mttt) REVERT: D 277 PHE cc_start: 0.7133 (t80) cc_final: 0.6850 (t80) REVERT: D 385 ILE cc_start: 0.9368 (mp) cc_final: 0.9076 (mm) REVERT: D 412 ASN cc_start: 0.8965 (m-40) cc_final: 0.8652 (t0) REVERT: D 413 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.7860 (m) REVERT: D 493 LYS cc_start: 0.9241 (mptt) cc_final: 0.8976 (mmtp) REVERT: D 504 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8794 (tptt) REVERT: E 84 ASN cc_start: 0.7835 (t0) cc_final: 0.6971 (t0) REVERT: E 86 TRP cc_start: 0.6971 (m100) cc_final: 0.6599 (m100) REVERT: E 132 ARG cc_start: 0.8203 (tpt170) cc_final: 0.7476 (mmm-85) REVERT: E 134 TRP cc_start: 0.5884 (m100) cc_final: 0.5650 (m100) REVERT: E 175 LEU cc_start: 0.9695 (mt) cc_final: 0.9155 (mt) REVERT: E 297 MET cc_start: 0.9215 (ptm) cc_final: 0.7618 (ptt) REVERT: E 314 MET cc_start: 0.8994 (tpt) cc_final: 0.8686 (tpp) REVERT: E 346 ILE cc_start: 0.9563 (pt) cc_final: 0.9297 (mp) REVERT: E 380 GLU cc_start: 0.8992 (pm20) cc_final: 0.8786 (pm20) REVERT: F 261 SER cc_start: 0.9116 (m) cc_final: 0.8519 (p) REVERT: F 298 LYS cc_start: 0.9161 (mttt) cc_final: 0.8794 (mttp) REVERT: F 332 LYS cc_start: 0.8279 (mmmt) cc_final: 0.8000 (mmtp) REVERT: F 390 MET cc_start: 0.8589 (mmp) cc_final: 0.8266 (tpp) REVERT: F 391 LYS cc_start: 0.8415 (mtpt) cc_final: 0.8178 (mmmt) REVERT: F 511 MET cc_start: 0.8666 (mmm) cc_final: 0.8302 (mmm) REVERT: F 636 ASN cc_start: 0.8945 (m-40) cc_final: 0.8440 (p0) REVERT: F 668 LEU cc_start: 0.9319 (tt) cc_final: 0.9058 (tt) REVERT: F 792 LEU cc_start: 0.9591 (mt) cc_final: 0.9346 (mt) REVERT: F 797 GLU cc_start: 0.9513 (mp0) cc_final: 0.9054 (mp0) outliers start: 17 outliers final: 4 residues processed: 430 average time/residue: 0.3745 time to fit residues: 233.5199 Evaluate side-chains 216 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 210 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 201 optimal weight: 10.0000 chunk 181 optimal weight: 0.0050 chunk 100 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 187 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 217 optimal weight: 0.0270 overall best weight: 1.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 204 HIS ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS D 102 ASN D 106 ASN D 204 HIS D 435 HIS ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 HIS E 313 HIS E 385 GLN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN F 69 GLN F 70 ASN F 72 ASN F 91 ASN F 104 HIS F 178 ASN F 179 GLN F 251 HIS F 522 ASN ** F 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 561 GLN F 622 HIS F 626 ASN F 648 GLN ** F 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 805 GLN F 822 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 21012 Z= 0.198 Angle : 0.759 11.854 28792 Z= 0.405 Chirality : 0.045 0.344 3200 Planarity : 0.005 0.086 3412 Dihedral : 20.820 172.867 3488 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 0.15 % Allowed : 3.49 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.02 (0.16), residues: 2296 helix: -0.49 (0.15), residues: 969 sheet: -0.99 (0.37), residues: 190 loop : -3.73 (0.15), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 17 HIS 0.007 0.001 HIS F 680 PHE 0.027 0.002 PHE F 686 TYR 0.023 0.002 TYR A 188 ARG 0.007 0.001 ARG E 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 290 time to evaluate : 2.305 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: 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 256 ASN cc_start: 0.8863 (t0) cc_final: 0.8394 (t0) REVERT: A 268 PHE cc_start: 0.8365 (t80) cc_final: 0.8065 (t80) REVERT: A 309 TRP cc_start: 0.6929 (p-90) cc_final: 0.6135 (p-90) REVERT: A 337 PHE cc_start: 0.8703 (m-80) cc_final: 0.8463 (m-80) REVERT: A 397 ILE cc_start: 0.9048 (pt) cc_final: 0.8760 (tt) REVERT: A 480 ARG cc_start: 0.8301 (tpp80) cc_final: 0.8012 (tpp80) REVERT: A 488 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8449 (pt) REVERT: D 116 ILE cc_start: 0.8372 (mp) cc_final: 0.7856 (tp) REVERT: D 150 LYS cc_start: 0.9098 (mttt) cc_final: 0.8723 (pttt) REVERT: D 222 LYS cc_start: 0.7923 (mttt) cc_final: 0.7395 (mttt) REVERT: D 412 ASN cc_start: 0.8987 (m-40) cc_final: 0.8663 (t0) REVERT: D 493 LYS cc_start: 0.9312 (mptt) cc_final: 0.9111 (mmtm) REVERT: D 504 LYS cc_start: 0.9155 (ttmt) cc_final: 0.8904 (tptt) REVERT: E 84 ASN cc_start: 0.7246 (t0) cc_final: 0.6360 (t0) REVERT: E 86 TRP cc_start: 0.6776 (m100) cc_final: 0.6338 (m100) REVERT: E 100 MET cc_start: 0.7368 (mpp) cc_final: 0.7051 (mpp) REVERT: E 130 HIS cc_start: 0.8389 (p90) cc_final: 0.7982 (p90) REVERT: E 297 MET cc_start: 0.8851 (ptm) cc_final: 0.7643 (ptp) REVERT: E 314 MET cc_start: 0.8815 (tpt) cc_final: 0.8589 (tpp) REVERT: E 380 GLU cc_start: 0.8916 (pm20) cc_final: 0.8631 (pm20) REVERT: F 60 MET cc_start: 0.8610 (mtm) cc_final: 0.8394 (mtt) REVERT: F 78 ASP cc_start: 0.8305 (m-30) cc_final: 0.8104 (t70) REVERT: F 225 PHE cc_start: 0.8287 (m-10) cc_final: 0.7903 (m-10) REVERT: F 261 SER cc_start: 0.9076 (m) cc_final: 0.8688 (p) REVERT: F 267 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7958 (tm-30) REVERT: F 390 MET cc_start: 0.8531 (mmp) cc_final: 0.8223 (ptp) REVERT: F 391 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8197 (mmmt) REVERT: F 469 ASP cc_start: 0.9260 (t0) cc_final: 0.8802 (m-30) REVERT: F 511 MET cc_start: 0.8714 (mmm) cc_final: 0.8477 (tpp) REVERT: F 708 LEU cc_start: 0.8800 (tp) cc_final: 0.8584 (mt) REVERT: F 1020 VAL cc_start: 0.9421 (p) cc_final: 0.9131 (m) REVERT: F 1029 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8927 (mt-10) outliers start: 3 outliers final: 0 residues processed: 293 average time/residue: 0.3344 time to fit residues: 148.4661 Evaluate side-chains 182 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 GLN F 46 ASN F 370 ASN F 388 ASN F 402 GLN F 518 GLN F 523 ASN ** F 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 643 GLN ** F 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 21012 Z= 0.355 Angle : 0.861 9.930 28792 Z= 0.468 Chirality : 0.047 0.260 3200 Planarity : 0.006 0.082 3412 Dihedral : 21.061 178.841 3488 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 0.20 % Allowed : 4.84 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.16), residues: 2296 helix: -0.27 (0.16), residues: 977 sheet: -1.38 (0.37), residues: 193 loop : -3.61 (0.16), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 17 HIS 0.010 0.002 HIS A 289 PHE 0.037 0.003 PHE D 422 TYR 0.024 0.002 TYR D 188 ARG 0.007 0.001 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 221 time to evaluate : 2.263 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8313 (ppp) cc_final: 0.7986 (ppp) REVERT: A 269 LEU cc_start: 0.9516 (mt) cc_final: 0.9289 (mp) REVERT: A 278 ASP cc_start: 0.7817 (p0) cc_final: 0.7445 (p0) REVERT: A 297 ASP cc_start: 0.6770 (t0) cc_final: 0.5778 (t0) REVERT: A 337 PHE cc_start: 0.8693 (m-80) cc_final: 0.8455 (m-80) REVERT: A 480 ARG cc_start: 0.8536 (tpp80) cc_final: 0.8232 (tpp80) REVERT: A 484 ASP cc_start: 0.8881 (m-30) cc_final: 0.8233 (p0) REVERT: D 43 ARG cc_start: 0.8736 (ttt180) cc_final: 0.8108 (ttt-90) REVERT: D 116 ILE cc_start: 0.8428 (mp) cc_final: 0.7799 (tp) REVERT: D 141 ASN cc_start: 0.8223 (t0) cc_final: 0.7484 (m-40) REVERT: D 222 LYS cc_start: 0.7679 (mttt) cc_final: 0.7250 (mttt) REVERT: D 412 ASN cc_start: 0.8840 (m-40) cc_final: 0.8635 (t0) REVERT: D 493 LYS cc_start: 0.9306 (mptt) cc_final: 0.9074 (mttt) REVERT: E 21 LEU cc_start: 0.9544 (tt) cc_final: 0.9328 (tt) REVERT: E 84 ASN cc_start: 0.7683 (t0) cc_final: 0.6805 (t0) REVERT: E 86 TRP cc_start: 0.7126 (m100) cc_final: 0.6524 (m100) REVERT: E 100 MET cc_start: 0.7724 (mpp) cc_final: 0.7171 (mpp) REVERT: E 130 HIS cc_start: 0.8719 (p90) cc_final: 0.8496 (p90) REVERT: E 132 ARG cc_start: 0.8451 (tpt170) cc_final: 0.7711 (tpt-90) REVERT: E 134 TRP cc_start: 0.6221 (m100) cc_final: 0.5970 (m100) REVERT: E 239 MET cc_start: 0.9182 (mmm) cc_final: 0.8980 (tpt) REVERT: E 297 MET cc_start: 0.8943 (ptm) cc_final: 0.8321 (ptp) REVERT: E 380 GLU cc_start: 0.8967 (pm20) cc_final: 0.8715 (pm20) REVERT: F 60 MET cc_start: 0.8676 (mtm) cc_final: 0.8423 (mtt) REVERT: F 212 PHE cc_start: 0.8052 (t80) cc_final: 0.7779 (t80) REVERT: F 225 PHE cc_start: 0.8394 (m-10) cc_final: 0.7938 (m-10) REVERT: F 267 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7973 (tm-30) REVERT: F 332 LYS cc_start: 0.8659 (mptt) cc_final: 0.8303 (mmtp) REVERT: F 470 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8466 (tm-30) REVERT: F 683 MET cc_start: 0.8666 (tmm) cc_final: 0.8439 (tmm) REVERT: F 737 MET cc_start: 0.8887 (mmp) cc_final: 0.8556 (mmm) REVERT: F 879 GLU cc_start: 0.7831 (tp30) cc_final: 0.7435 (tp30) REVERT: F 1029 GLU cc_start: 0.9267 (mt-10) cc_final: 0.9002 (mt-10) outliers start: 4 outliers final: 2 residues processed: 225 average time/residue: 0.3496 time to fit residues: 119.2678 Evaluate side-chains 149 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 214 optimal weight: 20.0000 chunk 163 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 206 optimal weight: 0.0970 chunk 62 optimal weight: 0.6980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN D 106 ASN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 ASN F 421 ASN F 539 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21012 Z= 0.196 Angle : 0.730 10.981 28792 Z= 0.391 Chirality : 0.044 0.279 3200 Planarity : 0.005 0.087 3412 Dihedral : 20.735 172.633 3488 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.17), residues: 2296 helix: 0.19 (0.16), residues: 982 sheet: -1.10 (0.39), residues: 183 loop : -3.33 (0.16), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 17 HIS 0.006 0.001 HIS F 680 PHE 0.032 0.002 PHE D 277 TYR 0.017 0.002 TYR F 344 ARG 0.005 0.000 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 2.381 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: 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 267 MET cc_start: 0.7891 (ppp) cc_final: 0.7673 (ppp) REVERT: A 269 LEU cc_start: 0.9429 (mt) cc_final: 0.9167 (mp) REVERT: A 480 ARG cc_start: 0.8501 (tpp80) cc_final: 0.8249 (tpp80) REVERT: A 484 ASP cc_start: 0.8808 (m-30) cc_final: 0.8126 (p0) REVERT: D 43 ARG cc_start: 0.8761 (ttt180) cc_final: 0.8102 (ttt-90) REVERT: D 116 ILE cc_start: 0.8341 (mp) cc_final: 0.7971 (tp) REVERT: D 222 LYS cc_start: 0.7602 (mttt) cc_final: 0.7244 (mttt) REVERT: D 412 ASN cc_start: 0.8977 (m-40) cc_final: 0.8678 (t0) REVERT: E 21 LEU cc_start: 0.9560 (tt) cc_final: 0.9359 (tt) REVERT: E 84 ASN cc_start: 0.7493 (t0) cc_final: 0.6505 (t0) REVERT: E 86 TRP cc_start: 0.6950 (m100) cc_final: 0.6533 (m100) REVERT: E 98 MET cc_start: 0.7975 (mpp) cc_final: 0.7328 (mpp) REVERT: E 100 MET cc_start: 0.7812 (mpp) cc_final: 0.7162 (mpp) REVERT: E 130 HIS cc_start: 0.8804 (p90) cc_final: 0.8594 (p90) REVERT: E 239 MET cc_start: 0.9284 (mmm) cc_final: 0.9080 (tmm) REVERT: E 297 MET cc_start: 0.8864 (ptm) cc_final: 0.8145 (ptt) REVERT: F 78 ASP cc_start: 0.8459 (m-30) cc_final: 0.8064 (t0) REVERT: F 212 PHE cc_start: 0.7320 (t80) cc_final: 0.6761 (t80) REVERT: F 225 PHE cc_start: 0.8379 (m-10) cc_final: 0.7877 (m-10) REVERT: F 267 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7943 (tm-30) REVERT: F 332 LYS cc_start: 0.8578 (mptt) cc_final: 0.8199 (mmtp) REVERT: F 390 MET cc_start: 0.8704 (ptp) cc_final: 0.8487 (ptt) REVERT: F 470 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8332 (tm-30) REVERT: F 511 MET cc_start: 0.8365 (tpt) cc_final: 0.8020 (tpp) REVERT: F 683 MET cc_start: 0.8731 (tmm) cc_final: 0.8457 (tmm) REVERT: F 708 LEU cc_start: 0.8651 (mt) cc_final: 0.8392 (mm) REVERT: F 737 MET cc_start: 0.8716 (mmp) cc_final: 0.8375 (mmm) REVERT: F 879 GLU cc_start: 0.7888 (tp30) cc_final: 0.7534 (tm-30) REVERT: F 1029 GLU cc_start: 0.9293 (mt-10) cc_final: 0.9002 (mp0) outliers start: 1 outliers final: 1 residues processed: 231 average time/residue: 0.3373 time to fit residues: 119.9881 Evaluate side-chains 156 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 192 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN D 90 GLN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21012 Z= 0.184 Angle : 0.712 11.779 28792 Z= 0.380 Chirality : 0.044 0.238 3200 Planarity : 0.005 0.086 3412 Dihedral : 20.562 174.438 3488 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.17), residues: 2296 helix: 0.49 (0.17), residues: 983 sheet: -1.03 (0.38), residues: 186 loop : -3.29 (0.16), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 309 HIS 0.006 0.001 HIS F 680 PHE 0.030 0.002 PHE E 364 TYR 0.017 0.001 TYR E 40 ARG 0.005 0.000 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 2.245 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8442 (tppt) cc_final: 0.8229 (tppt) REVERT: A 254 GLU cc_start: 0.7310 (tm-30) cc_final: 0.7010 (tm-30) REVERT: A 256 ASN cc_start: 0.8801 (t0) cc_final: 0.8451 (t0) REVERT: A 267 MET cc_start: 0.8060 (ppp) cc_final: 0.7803 (ppp) REVERT: A 269 LEU cc_start: 0.9407 (mt) cc_final: 0.9201 (mp) REVERT: A 287 GLU cc_start: 0.8119 (mp0) cc_final: 0.7790 (mp0) REVERT: A 480 ARG cc_start: 0.8547 (tpp80) cc_final: 0.8138 (tpp80) REVERT: A 484 ASP cc_start: 0.8801 (m-30) cc_final: 0.8139 (p0) REVERT: A 504 LYS cc_start: 0.9103 (tptp) cc_final: 0.8737 (tptp) REVERT: D 43 ARG cc_start: 0.8744 (ttt180) cc_final: 0.8047 (ttt-90) REVERT: D 116 ILE cc_start: 0.8312 (mp) cc_final: 0.7923 (tp) REVERT: D 150 LYS cc_start: 0.9179 (mttt) cc_final: 0.8782 (pttt) REVERT: D 222 LYS cc_start: 0.7696 (mttt) cc_final: 0.7272 (mttt) REVERT: D 412 ASN cc_start: 0.8936 (m-40) cc_final: 0.8613 (t0) REVERT: E 84 ASN cc_start: 0.7127 (t0) cc_final: 0.6119 (t0) REVERT: E 86 TRP cc_start: 0.6768 (m100) cc_final: 0.6398 (m100) REVERT: E 98 MET cc_start: 0.7394 (mpp) cc_final: 0.6270 (mpp) REVERT: E 100 MET cc_start: 0.7809 (mpp) cc_final: 0.7189 (mpp) REVERT: E 297 MET cc_start: 0.8634 (ptm) cc_final: 0.7921 (ptt) REVERT: F 78 ASP cc_start: 0.8353 (m-30) cc_final: 0.7884 (t0) REVERT: F 212 PHE cc_start: 0.7489 (t80) cc_final: 0.7026 (t80) REVERT: F 225 PHE cc_start: 0.8367 (m-10) cc_final: 0.7841 (m-10) REVERT: F 267 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7905 (tm-30) REVERT: F 332 LYS cc_start: 0.8583 (mptt) cc_final: 0.8112 (mmtp) REVERT: F 347 MET cc_start: 0.8919 (tmm) cc_final: 0.8647 (tpp) REVERT: F 470 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8288 (tm-30) REVERT: F 683 MET cc_start: 0.8796 (tmm) cc_final: 0.8508 (tmm) REVERT: F 708 LEU cc_start: 0.8659 (mt) cc_final: 0.8452 (mm) REVERT: F 879 GLU cc_start: 0.7891 (tp30) cc_final: 0.7620 (tp30) REVERT: F 1001 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8260 (pt0) REVERT: F 1029 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8893 (mt-10) outliers start: 1 outliers final: 1 residues processed: 235 average time/residue: 0.3088 time to fit residues: 113.3658 Evaluate side-chains 160 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 77 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 135 optimal weight: 0.0040 chunk 57 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 107 optimal weight: 0.0470 chunk 19 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 overall best weight: 1.5694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21012 Z= 0.168 Angle : 0.702 12.312 28792 Z= 0.373 Chirality : 0.044 0.221 3200 Planarity : 0.004 0.087 3412 Dihedral : 20.418 175.071 3488 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.05 % Allowed : 1.85 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.17), residues: 2296 helix: 0.61 (0.17), residues: 989 sheet: -0.81 (0.38), residues: 182 loop : -3.25 (0.16), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 309 HIS 0.006 0.001 HIS F 680 PHE 0.027 0.001 PHE D 422 TYR 0.020 0.001 TYR F 344 ARG 0.003 0.000 ARG F 412 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 2.566 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8526 (tppt) cc_final: 0.8301 (tppt) REVERT: A 256 ASN cc_start: 0.8804 (t0) cc_final: 0.8456 (t0) REVERT: A 267 MET cc_start: 0.8053 (ppp) cc_final: 0.7755 (ppp) REVERT: A 287 GLU cc_start: 0.8258 (mp0) cc_final: 0.7928 (mp0) REVERT: A 480 ARG cc_start: 0.8549 (tpp80) cc_final: 0.8179 (tpp80) REVERT: A 484 ASP cc_start: 0.8816 (m-30) cc_final: 0.8157 (p0) REVERT: A 504 LYS cc_start: 0.9160 (tptp) cc_final: 0.8784 (tptp) REVERT: D 116 ILE cc_start: 0.8259 (mp) cc_final: 0.7865 (tp) REVERT: D 150 LYS cc_start: 0.9236 (mttt) cc_final: 0.8736 (pttt) REVERT: D 222 LYS cc_start: 0.7648 (mttt) cc_final: 0.7230 (mttt) REVERT: D 337 PHE cc_start: 0.8710 (m-10) cc_final: 0.8467 (m-10) REVERT: D 412 ASN cc_start: 0.8858 (m-40) cc_final: 0.8597 (t0) REVERT: E 77 PHE cc_start: 0.6388 (m-10) cc_final: 0.5962 (m-10) REVERT: E 84 ASN cc_start: 0.7039 (t0) cc_final: 0.6163 (t0) REVERT: E 86 TRP cc_start: 0.6714 (m100) cc_final: 0.6424 (m100) REVERT: E 98 MET cc_start: 0.7745 (mpp) cc_final: 0.6746 (mpp) REVERT: E 100 MET cc_start: 0.7728 (mpp) cc_final: 0.7116 (mpp) REVERT: E 132 ARG cc_start: 0.8060 (tpt170) cc_final: 0.6853 (tpt170) REVERT: E 297 MET cc_start: 0.8743 (ptm) cc_final: 0.7899 (ptp) REVERT: F 78 ASP cc_start: 0.8295 (m-30) cc_final: 0.7919 (t0) REVERT: F 212 PHE cc_start: 0.7207 (t80) cc_final: 0.6890 (t80) REVERT: F 225 PHE cc_start: 0.8457 (m-10) cc_final: 0.7911 (m-10) REVERT: F 267 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7706 (tm-30) REVERT: F 332 LYS cc_start: 0.8585 (mptt) cc_final: 0.8035 (mmtp) REVERT: F 347 MET cc_start: 0.8954 (tmm) cc_final: 0.8697 (tpp) REVERT: F 390 MET cc_start: 0.8604 (ptt) cc_final: 0.8350 (ptt) REVERT: F 469 ASP cc_start: 0.9133 (t0) cc_final: 0.8925 (t0) REVERT: F 470 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8333 (tm-30) REVERT: F 676 ASN cc_start: 0.7866 (t0) cc_final: 0.7656 (t0) REVERT: F 683 MET cc_start: 0.8753 (tmm) cc_final: 0.8488 (tmm) REVERT: F 879 GLU cc_start: 0.8059 (tp30) cc_final: 0.7816 (tm-30) REVERT: F 1001 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8242 (pt0) REVERT: F 1029 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8989 (mt-10) outliers start: 1 outliers final: 1 residues processed: 233 average time/residue: 0.3241 time to fit residues: 118.7491 Evaluate side-chains 163 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 222 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 230 optimal weight: 0.0170 chunk 144 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN D 270 HIS ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN ** F 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21012 Z= 0.187 Angle : 0.710 12.178 28792 Z= 0.377 Chirality : 0.044 0.289 3200 Planarity : 0.004 0.089 3412 Dihedral : 20.377 176.930 3488 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 0.10 % Allowed : 1.65 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.17), residues: 2296 helix: 0.65 (0.17), residues: 997 sheet: -1.02 (0.37), residues: 186 loop : -3.27 (0.16), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 309 HIS 0.006 0.001 HIS F 680 PHE 0.046 0.002 PHE D 422 TYR 0.016 0.001 TYR E 40 ARG 0.003 0.000 ARG E 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 218 time to evaluate : 2.353 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.8862 (t0) cc_final: 0.8654 (t0) REVERT: A 267 MET cc_start: 0.8040 (ppp) cc_final: 0.7649 (ppp) REVERT: A 268 PHE cc_start: 0.8503 (t80) cc_final: 0.8292 (t80) REVERT: A 287 GLU cc_start: 0.8262 (mp0) cc_final: 0.7939 (mp0) REVERT: A 363 TYR cc_start: 0.6291 (p90) cc_final: 0.5794 (p90) REVERT: A 484 ASP cc_start: 0.8847 (m-30) cc_final: 0.8183 (p0) REVERT: D 116 ILE cc_start: 0.8278 (mp) cc_final: 0.7885 (tp) REVERT: D 150 LYS cc_start: 0.9274 (mttt) cc_final: 0.8769 (pttt) REVERT: D 222 LYS cc_start: 0.7668 (mttt) cc_final: 0.7203 (mttt) REVERT: D 337 PHE cc_start: 0.8699 (m-10) cc_final: 0.8420 (m-10) REVERT: D 412 ASN cc_start: 0.8901 (m-40) cc_final: 0.8587 (t0) REVERT: E 84 ASN cc_start: 0.7089 (t0) cc_final: 0.6255 (t0) REVERT: E 86 TRP cc_start: 0.6796 (m100) cc_final: 0.6547 (m100) REVERT: E 100 MET cc_start: 0.7791 (mpp) cc_final: 0.7238 (mpp) REVERT: E 132 ARG cc_start: 0.7647 (tpt170) cc_final: 0.6949 (tpt-90) REVERT: E 239 MET cc_start: 0.9192 (mmm) cc_final: 0.8942 (tpt) REVERT: E 297 MET cc_start: 0.8712 (ptm) cc_final: 0.7419 (ptt) REVERT: E 298 LYS cc_start: 0.8374 (mmpt) cc_final: 0.8143 (mmmt) REVERT: E 380 GLU cc_start: 0.8960 (pm20) cc_final: 0.8699 (pm20) REVERT: F 78 ASP cc_start: 0.8316 (m-30) cc_final: 0.7906 (t0) REVERT: F 212 PHE cc_start: 0.7289 (t80) cc_final: 0.6989 (t80) REVERT: F 225 PHE cc_start: 0.8483 (m-10) cc_final: 0.7903 (m-10) REVERT: F 267 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7790 (tm-30) REVERT: F 332 LYS cc_start: 0.8556 (mptt) cc_final: 0.7943 (mmtp) REVERT: F 347 MET cc_start: 0.8906 (tmm) cc_final: 0.8663 (tpp) REVERT: F 390 MET cc_start: 0.8587 (ptt) cc_final: 0.7967 (ptm) REVERT: F 469 ASP cc_start: 0.9170 (t0) cc_final: 0.8967 (t0) REVERT: F 470 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8312 (tm-30) REVERT: F 683 MET cc_start: 0.8769 (tmm) cc_final: 0.8507 (tmm) REVERT: F 879 GLU cc_start: 0.8107 (tp30) cc_final: 0.7827 (tm-30) REVERT: F 1001 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8255 (pt0) REVERT: F 1029 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8978 (mt-10) outliers start: 2 outliers final: 1 residues processed: 220 average time/residue: 0.3259 time to fit residues: 112.3883 Evaluate side-chains 150 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 142 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 113 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 561 GLN F 857 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21012 Z= 0.222 Angle : 0.736 11.956 28792 Z= 0.394 Chirality : 0.045 0.278 3200 Planarity : 0.005 0.085 3412 Dihedral : 20.402 179.511 3488 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer: Outliers : 0.05 % Allowed : 1.35 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.17), residues: 2296 helix: 0.58 (0.17), residues: 998 sheet: -1.10 (0.37), residues: 188 loop : -3.25 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 17 HIS 0.006 0.001 HIS F 680 PHE 0.046 0.002 PHE D 422 TYR 0.021 0.002 TYR F 344 ARG 0.003 0.000 ARG F 639 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 2.091 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.8955 (t0) cc_final: 0.8700 (t0) REVERT: A 267 MET cc_start: 0.8113 (ppp) cc_final: 0.7743 (ppp) REVERT: A 278 ASP cc_start: 0.7851 (p0) cc_final: 0.7489 (p0) REVERT: A 287 GLU cc_start: 0.8216 (mp0) cc_final: 0.7904 (mp0) REVERT: A 484 ASP cc_start: 0.8944 (m-30) cc_final: 0.8252 (p0) REVERT: D 43 ARG cc_start: 0.8929 (ttt180) cc_final: 0.8351 (ttt-90) REVERT: D 116 ILE cc_start: 0.8329 (mp) cc_final: 0.7947 (tp) REVERT: D 150 LYS cc_start: 0.9309 (mttt) cc_final: 0.8772 (pttt) REVERT: D 337 PHE cc_start: 0.8748 (m-10) cc_final: 0.8418 (m-10) REVERT: D 412 ASN cc_start: 0.8945 (m-40) cc_final: 0.8588 (t0) REVERT: E 84 ASN cc_start: 0.7249 (t0) cc_final: 0.6340 (t0) REVERT: E 86 TRP cc_start: 0.6792 (m100) cc_final: 0.6506 (m100) REVERT: E 98 MET cc_start: 0.7888 (mpp) cc_final: 0.6608 (mpp) REVERT: E 100 MET cc_start: 0.7649 (mpp) cc_final: 0.7138 (mpp) REVERT: E 117 TRP cc_start: 0.7428 (m-10) cc_final: 0.7206 (m-10) REVERT: E 297 MET cc_start: 0.8806 (ptm) cc_final: 0.8049 (ptt) REVERT: E 380 GLU cc_start: 0.8928 (pm20) cc_final: 0.8692 (pm20) REVERT: F 78 ASP cc_start: 0.8362 (m-30) cc_final: 0.7908 (t0) REVERT: F 212 PHE cc_start: 0.7602 (t80) cc_final: 0.7128 (t80) REVERT: F 225 PHE cc_start: 0.8505 (m-10) cc_final: 0.7921 (m-10) REVERT: F 267 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7806 (tm-30) REVERT: F 332 LYS cc_start: 0.8588 (mptt) cc_final: 0.8033 (mmtp) REVERT: F 347 MET cc_start: 0.8941 (tmm) cc_final: 0.8656 (tpp) REVERT: F 390 MET cc_start: 0.8667 (ptt) cc_final: 0.8088 (ptm) REVERT: F 470 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8304 (tm-30) REVERT: F 596 ASP cc_start: 0.7561 (m-30) cc_final: 0.7311 (m-30) REVERT: F 683 MET cc_start: 0.8778 (tmm) cc_final: 0.8564 (tmm) REVERT: F 879 GLU cc_start: 0.8032 (tp30) cc_final: 0.7763 (tm-30) REVERT: F 1001 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8249 (pt0) REVERT: F 1029 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8985 (mt-10) outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 0.3185 time to fit residues: 102.2724 Evaluate side-chains 151 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 209 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 214 optimal weight: 9.9990 chunk 129 optimal weight: 0.0980 chunk 93 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 203 optimal weight: 0.0270 chunk 213 optimal weight: 7.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 ASN ** F 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21012 Z= 0.165 Angle : 0.705 12.630 28792 Z= 0.370 Chirality : 0.044 0.288 3200 Planarity : 0.004 0.090 3412 Dihedral : 20.179 178.606 3488 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 0.05 % Allowed : 0.80 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.18), residues: 2296 helix: 0.77 (0.17), residues: 983 sheet: -1.06 (0.36), residues: 194 loop : -3.16 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 17 HIS 0.006 0.001 HIS F 680 PHE 0.034 0.001 PHE D 422 TYR 0.017 0.001 TYR E 40 ARG 0.002 0.000 ARG E 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 2.171 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASN cc_start: 0.8820 (t0) cc_final: 0.8607 (t0) REVERT: A 266 ASN cc_start: 0.9027 (t0) cc_final: 0.8822 (t0) REVERT: A 267 MET cc_start: 0.8112 (ppp) cc_final: 0.7841 (ppp) REVERT: A 287 GLU cc_start: 0.8235 (mp0) cc_final: 0.7900 (mp0) REVERT: A 484 ASP cc_start: 0.8846 (m-30) cc_final: 0.8195 (p0) REVERT: D 116 ILE cc_start: 0.8328 (mp) cc_final: 0.7852 (tp) REVERT: D 150 LYS cc_start: 0.9296 (mttt) cc_final: 0.8708 (pttt) REVERT: D 337 PHE cc_start: 0.8678 (m-10) cc_final: 0.8351 (m-10) REVERT: D 339 PHE cc_start: 0.8730 (m-80) cc_final: 0.8467 (m-80) REVERT: D 412 ASN cc_start: 0.8948 (m-40) cc_final: 0.8607 (t0) REVERT: D 493 LYS cc_start: 0.9215 (mmtm) cc_final: 0.8948 (mmtm) REVERT: E 84 ASN cc_start: 0.7100 (t0) cc_final: 0.6348 (t0) REVERT: E 86 TRP cc_start: 0.6669 (m100) cc_final: 0.6462 (m100) REVERT: E 98 MET cc_start: 0.7351 (mpp) cc_final: 0.5868 (mpp) REVERT: E 100 MET cc_start: 0.7843 (mpp) cc_final: 0.7391 (mpp) REVERT: E 297 MET cc_start: 0.8703 (ptm) cc_final: 0.7976 (ptt) REVERT: F 78 ASP cc_start: 0.8165 (m-30) cc_final: 0.7886 (t0) REVERT: F 212 PHE cc_start: 0.7140 (t80) cc_final: 0.6891 (t80) REVERT: F 225 PHE cc_start: 0.8502 (m-10) cc_final: 0.7885 (m-10) REVERT: F 267 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7633 (tm-30) REVERT: F 332 LYS cc_start: 0.8506 (mptt) cc_final: 0.7957 (mmtp) REVERT: F 347 MET cc_start: 0.8954 (tmm) cc_final: 0.8670 (tpp) REVERT: F 390 MET cc_start: 0.8606 (ptt) cc_final: 0.7908 (ptm) REVERT: F 469 ASP cc_start: 0.9214 (t0) cc_final: 0.8742 (m-30) REVERT: F 470 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8372 (tm-30) REVERT: F 683 MET cc_start: 0.8745 (tmm) cc_final: 0.8464 (tmm) REVERT: F 753 MET cc_start: 0.8926 (mmt) cc_final: 0.8598 (mmt) REVERT: F 882 LEU cc_start: 0.9127 (tp) cc_final: 0.8906 (tp) REVERT: F 1001 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8173 (pt0) REVERT: F 1029 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8855 (mt-10) outliers start: 1 outliers final: 1 residues processed: 224 average time/residue: 0.3194 time to fit residues: 112.3911 Evaluate side-chains 157 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 140 optimal weight: 0.9980 chunk 226 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 238 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN D 106 ASN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 379 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN ** F 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21012 Z= 0.276 Angle : 0.775 12.164 28792 Z= 0.414 Chirality : 0.046 0.268 3200 Planarity : 0.005 0.083 3412 Dihedral : 20.286 177.839 3488 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.07 % Favored : 86.93 % Rotamer: Outliers : 0.05 % Allowed : 0.80 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.17), residues: 2296 helix: 0.51 (0.17), residues: 996 sheet: -1.39 (0.34), residues: 215 loop : -3.25 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 30 HIS 0.008 0.001 HIS D 435 PHE 0.043 0.002 PHE D 422 TYR 0.018 0.002 TYR F 344 ARG 0.004 0.001 ARG F 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 2.243 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: A 256 ASN cc_start: 0.8904 (t0) cc_final: 0.8686 (t0) REVERT: A 267 MET cc_start: 0.8089 (ppp) cc_final: 0.7778 (ppp) REVERT: A 278 ASP cc_start: 0.7930 (p0) cc_final: 0.7542 (p0) REVERT: A 287 GLU cc_start: 0.8275 (mp0) cc_final: 0.8013 (mp0) REVERT: A 484 ASP cc_start: 0.8916 (m-30) cc_final: 0.8325 (p0) REVERT: D 43 ARG cc_start: 0.8951 (ttt180) cc_final: 0.8391 (ttt-90) REVERT: D 116 ILE cc_start: 0.8436 (mp) cc_final: 0.7943 (tp) REVERT: D 150 LYS cc_start: 0.9339 (mttt) cc_final: 0.8790 (pttt) REVERT: D 265 MET cc_start: 0.9152 (ptt) cc_final: 0.8902 (ptm) REVERT: D 337 PHE cc_start: 0.8799 (m-10) cc_final: 0.8454 (m-10) REVERT: D 339 PHE cc_start: 0.8921 (m-80) cc_final: 0.8614 (m-80) REVERT: D 412 ASN cc_start: 0.8968 (m-40) cc_final: 0.8571 (t0) REVERT: E 84 ASN cc_start: 0.7581 (t0) cc_final: 0.6584 (t0) REVERT: E 86 TRP cc_start: 0.6914 (m100) cc_final: 0.6593 (m100) REVERT: E 98 MET cc_start: 0.7798 (mpp) cc_final: 0.6347 (mpp) REVERT: E 100 MET cc_start: 0.7678 (mpp) cc_final: 0.7120 (mpp) REVERT: E 297 MET cc_start: 0.8883 (ptm) cc_final: 0.8158 (ptt) REVERT: E 380 GLU cc_start: 0.9055 (pm20) cc_final: 0.8751 (pm20) REVERT: F 212 PHE cc_start: 0.7599 (t80) cc_final: 0.7170 (t80) REVERT: F 225 PHE cc_start: 0.8538 (m-10) cc_final: 0.7863 (m-10) REVERT: F 267 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7480 (tm-30) REVERT: F 332 LYS cc_start: 0.8588 (mptt) cc_final: 0.8052 (mmtp) REVERT: F 347 MET cc_start: 0.8913 (tmm) cc_final: 0.8631 (mmp) REVERT: F 470 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8320 (tm-30) REVERT: F 683 MET cc_start: 0.8818 (tmm) cc_final: 0.8557 (tmm) REVERT: F 1001 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8215 (pt0) REVERT: F 1029 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8934 (mt-10) outliers start: 1 outliers final: 1 residues processed: 199 average time/residue: 0.3119 time to fit residues: 98.0392 Evaluate side-chains 146 residues out of total 2032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 150 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 174 optimal weight: 9.9990 chunk 27 optimal weight: 0.1980 chunk 52 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN D 253 GLN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN F 234 ASN ** F 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 GLN F 620 ASN F 626 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.067286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.054248 restraints weight = 117467.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.055732 restraints weight = 75894.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.056780 restraints weight = 55334.594| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21012 Z= 0.169 Angle : 0.725 13.528 28792 Z= 0.380 Chirality : 0.045 0.279 3200 Planarity : 0.004 0.090 3412 Dihedral : 20.088 179.731 3488 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.05 % Allowed : 0.40 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 2.72 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.18), residues: 2296 helix: 0.73 (0.17), residues: 981 sheet: -1.12 (0.35), residues: 198 loop : -3.13 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 17 HIS 0.005 0.001 HIS F 680 PHE 0.032 0.001 PHE D 422 TYR 0.024 0.001 TYR D 181 ARG 0.003 0.000 ARG E 132 =============================================================================== Job complete usr+sys time: 3561.64 seconds wall clock time: 66 minutes 27.08 seconds (3987.08 seconds total)