Starting phenix.real_space_refine on Sat Mar 16 11:55:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0n_10356/03_2024/6t0n_10356.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0n_10356/03_2024/6t0n_10356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0n_10356/03_2024/6t0n_10356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0n_10356/03_2024/6t0n_10356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0n_10356/03_2024/6t0n_10356.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0n_10356/03_2024/6t0n_10356.pdb" } resolution = 2.54 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 29 5.49 5 Mg 2 5.21 5 S 92 5.16 5 C 8940 2.51 5 N 2496 2.21 5 O 3039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C GLU 123": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14598 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5741 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 25, 'TRANS': 678} Chain breaks: 2 Chain: "B" Number of atoms: 5972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5972 Classifications: {'peptide': 749} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 718} Chain breaks: 1 Chain: "C" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2016 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain: "V" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 307 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "R" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 292 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 4, 'rna3p': 10} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "B" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "V" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 8.69, per 1000 atoms: 0.60 Number of scatterers: 14598 At special positions: 0 Unit cell: (106.464, 119.467, 118.654, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 92 16.00 P 29 15.00 Mg 2 11.99 O 3039 8.00 N 2496 7.00 C 8940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.37 Conformation dependent library (CDL) restraints added in 2.7 seconds 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3214 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 18 sheets defined 52.4% alpha, 14.0% beta 6 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 4.84 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.645A pdb=" N PHE A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.590A pdb=" N TYR A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 188 through 194 removed outlier: 3.783A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.928A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.648A pdb=" N SER A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 448 through 471 removed outlier: 3.514A pdb=" N GLU A 452 " --> pdb=" O CYS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 533 removed outlier: 3.528A pdb=" N ASN A 527 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 529 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N HIS A 530 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU A 533 " --> pdb=" O HIS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 577 through 599 removed outlier: 3.982A pdb=" N LEU A 581 " --> pdb=" O ARG A 577 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 594 " --> pdb=" O MET A 590 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 609 Processing helix chain 'A' and resid 627 through 645 Processing helix chain 'A' and resid 647 through 669 removed outlier: 4.238A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 687 Processing helix chain 'A' and resid 692 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.695A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 115 removed outlier: 3.504A pdb=" N GLN B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 245 through 264 removed outlier: 3.653A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.504A pdb=" N ASN B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.723A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.805A pdb=" N SER B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.732A pdb=" N TYR B 380 " --> pdb=" O ASN B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.525A pdb=" N VAL B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 removed outlier: 3.515A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.626A pdb=" N MET B 507 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 582 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 removed outlier: 3.519A pdb=" N MET B 616 " --> pdb=" O TRP B 613 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 613 through 616' Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 672 through 679 removed outlier: 3.529A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B 678 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN B 679 " --> pdb=" O ASN B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.070A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 removed outlier: 3.718A pdb=" N THR B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 731 removed outlier: 3.566A pdb=" N GLU B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 757 Processing helix chain 'C' and resid 1 through 13 removed outlier: 3.516A pdb=" N LYS C 5 " --> pdb=" O MET C 1 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.881A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.842A pdb=" N ARG C 121 " --> pdb=" O MET C 117 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 122 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 167 Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 removed outlier: 3.715A pdb=" N VAL C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.700A pdb=" N PHE A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 123 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.700A pdb=" N PHE A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.855A pdb=" N PHE B 447 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 275 removed outlier: 6.480A pdb=" N LYS A 274 " --> pdb=" O LYS A 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.254A pdb=" N TYR A 496 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 552 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU A 544 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS A 554 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP A 542 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A 556 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 537 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY A 541 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N LYS A 319 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N MET A 543 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N TRP A 317 " --> pdb=" O MET A 543 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.364A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 372 through 374 removed outlier: 4.342A pdb=" N GLN B 367 " --> pdb=" O MET A 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 622 through 626 removed outlier: 6.352A pdb=" N GLY A 626 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB2, first strand: chain 'B' and resid 127 through 130 Processing sheet with id=AB3, first strand: chain 'B' and resid 180 through 188 Processing sheet with id=AB4, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.720A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB6, first strand: chain 'B' and resid 642 through 645 Processing sheet with id=AB7, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.457A pdb=" N THR B 667 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR C 81 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.460A pdb=" N GLN C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 141 through 146 700 hydrogen bonds defined for protein. 1929 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 5.20 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3658 1.33 - 1.45: 2874 1.45 - 1.57: 7926 1.57 - 1.69: 56 1.69 - 1.81: 160 Bond restraints: 14674 Sorted by residual: bond pdb=" N ARG B 723 " pdb=" CA ARG B 723 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.11e+00 bond pdb=" CB THR B 141 " pdb=" CG2 THR B 141 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" CB MET A 570 " pdb=" CG MET A 570 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.27e+00 bond pdb=" C GLU A 604 " pdb=" N PRO A 605 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.19e+00 bond pdb=" CB ARG A 561 " pdb=" CG ARG A 561 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.10e+00 ... (remaining 14669 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.15: 484 106.15 - 113.15: 7855 113.15 - 120.14: 5381 120.14 - 127.13: 5996 127.13 - 134.12: 205 Bond angle restraints: 19921 Sorted by residual: angle pdb=" N VAL A 427 " pdb=" CA VAL A 427 " pdb=" C VAL A 427 " ideal model delta sigma weight residual 111.62 108.35 3.27 7.90e-01 1.60e+00 1.72e+01 angle pdb=" N ASP B 295 " pdb=" CA ASP B 295 " pdb=" C ASP B 295 " ideal model delta sigma weight residual 113.97 109.81 4.16 1.28e+00 6.10e-01 1.06e+01 angle pdb=" C ALA B 291 " pdb=" N LYS B 292 " pdb=" CA LYS B 292 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.53e+00 angle pdb=" C2' U R 9 " pdb=" C1' U R 9 " pdb=" N1 U R 9 " ideal model delta sigma weight residual 112.00 116.60 -4.60 1.50e+00 4.44e-01 9.40e+00 angle pdb=" C3' A V 7 " pdb=" C2' A V 7 " pdb=" O2' A V 7 " ideal model delta sigma weight residual 114.60 118.88 -4.28 1.50e+00 4.44e-01 8.15e+00 ... (remaining 19916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8104 17.98 - 35.97: 581 35.97 - 53.95: 190 53.95 - 71.93: 74 71.93 - 89.92: 24 Dihedral angle restraints: 8973 sinusoidal: 4005 harmonic: 4968 Sorted by residual: dihedral pdb=" CA THR C 35 " pdb=" C THR C 35 " pdb=" N SER C 36 " pdb=" CA SER C 36 " ideal model delta harmonic sigma weight residual 180.00 157.09 22.91 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA VAL A 512 " pdb=" C VAL A 512 " pdb=" N VAL A 513 " pdb=" CA VAL A 513 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA TYR A 535 " pdb=" C TYR A 535 " pdb=" N CYS A 536 " pdb=" CA CYS A 536 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 8970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1509 0.044 - 0.087: 541 0.087 - 0.131: 127 0.131 - 0.174: 15 0.174 - 0.218: 4 Chirality restraints: 2196 Sorted by residual: chirality pdb=" C1' U R 9 " pdb=" O4' U R 9 " pdb=" C2' U R 9 " pdb=" N1 U R 9 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CB VAL A 445 " pdb=" CA VAL A 445 " pdb=" CG1 VAL A 445 " pdb=" CG2 VAL A 445 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.32e-01 ... (remaining 2193 not shown) Planarity restraints: 2462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U R 9 " -0.036 2.00e-02 2.50e+03 1.79e-02 7.24e+00 pdb=" N1 U R 9 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U R 9 " 0.006 2.00e-02 2.50e+03 pdb=" O2 U R 9 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U R 9 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U R 9 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U R 9 " -0.011 2.00e-02 2.50e+03 pdb=" C5 U R 9 " 0.004 2.00e-02 2.50e+03 pdb=" C6 U R 9 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 619 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.87e+00 pdb=" N PRO A 620 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 620 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 620 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.031 2.00e-02 2.50e+03 1.44e-02 5.73e+00 pdb=" N9 A V 7 " 0.028 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A V 7 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.017 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.002 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.010 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.010 2.00e-02 2.50e+03 ... (remaining 2459 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 379 2.66 - 3.22: 12487 3.22 - 3.78: 25091 3.78 - 4.34: 35812 4.34 - 4.90: 54945 Nonbonded interactions: 128714 Sorted by model distance: nonbonded pdb=" OP2 A V 4 " pdb="MG MG V 101 " model vdw 2.105 2.170 nonbonded pdb="MG MG V 101 " pdb=" O HOH V 201 " model vdw 2.146 2.170 nonbonded pdb=" OD1 ASP B 446 " pdb="MG MG B 801 " model vdw 2.161 2.170 nonbonded pdb=" OD2 ASP B 522 " pdb=" OH TYR B 559 " model vdw 2.274 2.440 nonbonded pdb=" O ALA B 113 " pdb=" OG1 THR B 117 " model vdw 2.297 2.440 ... (remaining 128709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.470 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 46.920 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 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 : 0.005 0.062 14674 Z= 0.352 Angle : 0.688 7.641 19921 Z= 0.397 Chirality : 0.046 0.218 2196 Planarity : 0.006 0.061 2462 Dihedral : 15.615 89.915 5759 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.32 % Favored : 95.45 % Rotamer: Outliers : 4.90 % Allowed : 6.75 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.16), residues: 1691 helix: -1.63 (0.14), residues: 792 sheet: -1.24 (0.34), residues: 188 loop : -1.50 (0.20), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 438 HIS 0.010 0.002 HIS B 32 PHE 0.021 0.002 PHE A 211 TYR 0.016 0.002 TYR B 380 ARG 0.005 0.001 ARG B 672 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 272 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4684 (OUTLIER) cc_final: 0.4179 (pp20) REVERT: A 258 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8054 (pt0) REVERT: A 356 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8136 (tttt) REVERT: A 372 GLU cc_start: 0.7707 (tt0) cc_final: 0.7481 (tt0) REVERT: A 455 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7253 (mpm) REVERT: A 616 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8704 (pp) REVERT: A 700 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.9005 (p) REVERT: A 713 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7287 (mtp) REVERT: B 108 GLN cc_start: 0.7894 (tp40) cc_final: 0.7470 (tm-30) REVERT: B 135 ARG cc_start: 0.8144 (ptp-170) cc_final: 0.7902 (mtp85) REVERT: B 429 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7306 (mtm180) REVERT: B 534 MET cc_start: 0.9089 (mtp) cc_final: 0.8463 (mtp) REVERT: B 563 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8362 (ttp80) REVERT: B 577 LYS cc_start: 0.8741 (tptt) cc_final: 0.8378 (tppt) REVERT: B 635 MET cc_start: 0.7380 (mtm) cc_final: 0.7042 (mtm) REVERT: B 679 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7383 (mm110) REVERT: B 680 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.6996 (ptp90) REVERT: C 185 ILE cc_start: 0.8527 (mt) cc_final: 0.8230 (mm) outliers start: 74 outliers final: 21 residues processed: 325 average time/residue: 1.6845 time to fit residues: 589.4035 Evaluate side-chains 237 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 206 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 153 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 387 GLN A 425 ASN A 490 GLN A 612 ASN B 115 GLN B 184 HIS B 312 ASN B 413 ASN B 694 GLN C 236 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14674 Z= 0.155 Angle : 0.471 7.855 19921 Z= 0.257 Chirality : 0.039 0.210 2196 Planarity : 0.004 0.050 2462 Dihedral : 11.723 73.496 2356 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.31 % Allowed : 13.18 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.19), residues: 1691 helix: 0.40 (0.17), residues: 806 sheet: -0.91 (0.34), residues: 193 loop : -1.10 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 438 HIS 0.004 0.001 HIS B 32 PHE 0.012 0.001 PHE B 551 TYR 0.016 0.001 TYR B 555 ARG 0.007 0.000 ARG A 608 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 205 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.4593 (OUTLIER) cc_final: 0.4110 (pp20) REVERT: A 356 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8050 (tttt) REVERT: A 419 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: A 594 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7309 (tp30) REVERT: B 108 GLN cc_start: 0.7862 (tp40) cc_final: 0.7405 (tm-30) REVERT: B 290 MET cc_start: 0.7463 (mtp) cc_final: 0.7129 (mmm) REVERT: B 481 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.7641 (mptt) REVERT: B 563 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8288 (mtp85) REVERT: B 635 MET cc_start: 0.7213 (mtm) cc_final: 0.6772 (mtm) REVERT: B 679 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7319 (mm110) REVERT: B 680 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7000 (ptp90) REVERT: C 51 MET cc_start: 0.9062 (mmm) cc_final: 0.8756 (mmm) REVERT: C 243 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.6956 (tm130) outliers start: 50 outliers final: 21 residues processed: 235 average time/residue: 1.6772 time to fit residues: 425.2130 Evaluate side-chains 231 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 129 optimal weight: 0.2980 chunk 105 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 168 optimal weight: 0.4980 chunk 138 optimal weight: 0.7980 chunk 154 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 239 ASN A 387 GLN A 425 ASN A 490 GLN B 115 GLN B 413 ASN B 694 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14674 Z= 0.119 Angle : 0.430 6.720 19921 Z= 0.231 Chirality : 0.037 0.197 2196 Planarity : 0.003 0.045 2462 Dihedral : 11.097 73.481 2331 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.45 % Allowed : 14.70 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1691 helix: 1.27 (0.18), residues: 802 sheet: -0.58 (0.36), residues: 184 loop : -0.82 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 438 HIS 0.004 0.001 HIS B 32 PHE 0.009 0.001 PHE B 696 TYR 0.016 0.001 TYR B 555 ARG 0.008 0.000 ARG A 608 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 212 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4934 (mtp) cc_final: 0.4442 (mtp) REVERT: A 26 GLU cc_start: 0.4664 (OUTLIER) cc_final: 0.4140 (pp20) REVERT: A 356 LYS cc_start: 0.8267 (ttpp) cc_final: 0.8032 (tttt) REVERT: A 419 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: A 594 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7335 (tp30) REVERT: B 290 MET cc_start: 0.7448 (mtp) cc_final: 0.7128 (mmm) REVERT: B 635 MET cc_start: 0.7212 (mtm) cc_final: 0.6934 (mtm) REVERT: B 679 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7256 (mm110) REVERT: B 680 ARG cc_start: 0.7652 (ptp-110) cc_final: 0.6854 (ptp90) REVERT: C 51 MET cc_start: 0.9094 (mmm) cc_final: 0.8855 (mmm) REVERT: C 156 SER cc_start: 0.7149 (m) cc_final: 0.6863 (p) REVERT: C 243 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7005 (tm130) outliers start: 37 outliers final: 18 residues processed: 237 average time/residue: 1.6840 time to fit residues: 431.4183 Evaluate side-chains 225 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 204 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 239 ASN A 387 GLN A 490 GLN B 115 GLN B 413 ASN B 694 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14674 Z= 0.176 Angle : 0.463 7.590 19921 Z= 0.247 Chirality : 0.039 0.198 2196 Planarity : 0.003 0.045 2462 Dihedral : 10.964 73.423 2314 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.85 % Allowed : 14.83 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1691 helix: 1.59 (0.18), residues: 797 sheet: -0.40 (0.36), residues: 184 loop : -0.69 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 438 HIS 0.005 0.001 HIS B 32 PHE 0.014 0.001 PHE B 357 TYR 0.015 0.001 TYR B 555 ARG 0.008 0.000 ARG A 608 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 203 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4903 (mtp) cc_final: 0.4553 (mtp) REVERT: A 26 GLU cc_start: 0.4771 (OUTLIER) cc_final: 0.4157 (pp20) REVERT: A 356 LYS cc_start: 0.8287 (ttpp) cc_final: 0.8035 (tttt) REVERT: A 419 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: A 594 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7354 (tp30) REVERT: B 135 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7366 (ptm-80) REVERT: B 290 MET cc_start: 0.7423 (mtp) cc_final: 0.7076 (mmm) REVERT: B 635 MET cc_start: 0.7232 (mtm) cc_final: 0.6922 (mtm) REVERT: B 679 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7228 (mm110) REVERT: B 680 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6950 (ptp90) REVERT: C 51 MET cc_start: 0.9098 (mmm) cc_final: 0.8846 (mmm) REVERT: C 156 SER cc_start: 0.7126 (m) cc_final: 0.6864 (p) REVERT: C 165 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: C 243 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7036 (tm130) outliers start: 43 outliers final: 19 residues processed: 231 average time/residue: 1.6294 time to fit residues: 406.3450 Evaluate side-chains 226 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 201 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 84 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 239 ASN A 387 GLN A 490 GLN B 115 GLN B 413 ASN B 694 GLN C 110 HIS C 236 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14674 Z= 0.236 Angle : 0.501 8.408 19921 Z= 0.267 Chirality : 0.041 0.212 2196 Planarity : 0.004 0.047 2462 Dihedral : 11.039 74.080 2312 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.05 % Allowed : 15.43 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1691 helix: 1.63 (0.18), residues: 798 sheet: -0.31 (0.37), residues: 186 loop : -0.64 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 438 HIS 0.005 0.001 HIS B 32 PHE 0.015 0.001 PHE B 357 TYR 0.015 0.001 TYR B 555 ARG 0.008 0.000 ARG A 608 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 200 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4856 (mtp) cc_final: 0.4489 (mtp) REVERT: A 26 GLU cc_start: 0.4888 (OUTLIER) cc_final: 0.4190 (pp20) REVERT: A 356 LYS cc_start: 0.8283 (ttpp) cc_final: 0.8009 (tttt) REVERT: A 419 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: B 1 MET cc_start: 0.8318 (tmm) cc_final: 0.8017 (tmm) REVERT: B 135 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7405 (ptm-80) REVERT: B 277 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7274 (mt-10) REVERT: B 290 MET cc_start: 0.7401 (mtp) cc_final: 0.6980 (mmm) REVERT: B 350 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7788 (mtt-85) REVERT: B 480 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8262 (mtpm) REVERT: B 481 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.7731 (mptt) REVERT: B 577 LYS cc_start: 0.8720 (tptt) cc_final: 0.8430 (ttmp) REVERT: B 635 MET cc_start: 0.7235 (mtm) cc_final: 0.6989 (mtm) REVERT: B 674 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8080 (pp) REVERT: B 679 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7224 (mm110) REVERT: B 680 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7017 (ptp90) REVERT: C 156 SER cc_start: 0.7105 (m) cc_final: 0.6816 (p) REVERT: C 165 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7002 (mp0) outliers start: 46 outliers final: 19 residues processed: 235 average time/residue: 1.6820 time to fit residues: 426.8689 Evaluate side-chains 227 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 220 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 54 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 239 ASN A 387 GLN A 490 GLN B 115 GLN B 413 ASN B 694 GLN C 110 HIS C 236 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14674 Z= 0.259 Angle : 0.520 8.922 19921 Z= 0.275 Chirality : 0.041 0.214 2196 Planarity : 0.004 0.047 2462 Dihedral : 11.009 74.048 2306 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.64 % Allowed : 14.90 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1691 helix: 1.62 (0.18), residues: 800 sheet: -0.22 (0.37), residues: 186 loop : -0.59 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 438 HIS 0.007 0.001 HIS B 32 PHE 0.015 0.001 PHE A 211 TYR 0.015 0.001 TYR B 555 ARG 0.007 0.000 ARG A 608 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 197 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4861 (mtp) cc_final: 0.4559 (mtp) REVERT: A 26 GLU cc_start: 0.4844 (OUTLIER) cc_final: 0.4121 (pp20) REVERT: A 356 LYS cc_start: 0.8286 (ttpp) cc_final: 0.8012 (tttt) REVERT: A 419 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: A 491 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7044 (mtt180) REVERT: B 1 MET cc_start: 0.8294 (tmm) cc_final: 0.8086 (tmm) REVERT: B 135 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7410 (ptm-80) REVERT: B 148 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: B 277 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: B 290 MET cc_start: 0.7431 (mtp) cc_final: 0.6981 (mmm) REVERT: B 350 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7736 (mtt-85) REVERT: B 480 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8301 (mtpm) REVERT: B 481 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.7732 (mptt) REVERT: B 674 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8114 (pp) REVERT: B 679 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7253 (mm110) REVERT: B 680 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7037 (ptp90) REVERT: C 156 SER cc_start: 0.7102 (m) cc_final: 0.6803 (p) REVERT: C 165 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7002 (mp0) outliers start: 55 outliers final: 20 residues processed: 236 average time/residue: 1.6464 time to fit residues: 421.6392 Evaluate side-chains 228 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 239 ASN A 387 GLN A 490 GLN B 115 GLN B 413 ASN B 694 GLN C 110 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14674 Z= 0.148 Angle : 0.456 9.324 19921 Z= 0.242 Chirality : 0.038 0.203 2196 Planarity : 0.003 0.044 2462 Dihedral : 10.656 73.500 2303 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.58 % Allowed : 16.03 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1691 helix: 1.86 (0.18), residues: 799 sheet: -0.01 (0.38), residues: 184 loop : -0.48 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 438 HIS 0.006 0.001 HIS B 32 PHE 0.013 0.001 PHE B 357 TYR 0.015 0.001 TYR B 555 ARG 0.010 0.000 ARG A 608 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4936 (mtp) cc_final: 0.4694 (mtp) REVERT: A 26 GLU cc_start: 0.4702 (OUTLIER) cc_final: 0.4038 (pp20) REVERT: A 356 LYS cc_start: 0.8292 (ttpp) cc_final: 0.8032 (tttt) REVERT: A 491 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7073 (mtt180) REVERT: B 118 ARG cc_start: 0.8522 (mtp85) cc_final: 0.8212 (mtp180) REVERT: B 277 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: B 290 MET cc_start: 0.7394 (mtp) cc_final: 0.7021 (mmm) REVERT: B 350 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7701 (mtt-85) REVERT: B 674 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8016 (pp) REVERT: B 679 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7266 (mm110) REVERT: B 680 ARG cc_start: 0.7752 (ptp-110) cc_final: 0.6980 (ptp90) REVERT: C 2 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5957 (mp0) REVERT: C 8 MET cc_start: 0.8281 (tpt) cc_final: 0.7682 (tpt) REVERT: C 156 SER cc_start: 0.7126 (m) cc_final: 0.6911 (p) outliers start: 39 outliers final: 13 residues processed: 225 average time/residue: 1.6226 time to fit residues: 394.8470 Evaluate side-chains 214 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 195 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 129 optimal weight: 0.3980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 239 ASN A 490 GLN B 115 GLN B 394 HIS B 413 ASN B 694 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14674 Z= 0.241 Angle : 0.519 12.032 19921 Z= 0.272 Chirality : 0.041 0.208 2196 Planarity : 0.004 0.047 2462 Dihedral : 10.823 74.121 2303 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.32 % Allowed : 16.42 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1691 helix: 1.76 (0.18), residues: 800 sheet: -0.08 (0.37), residues: 186 loop : -0.47 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 438 HIS 0.006 0.001 HIS B 32 PHE 0.015 0.001 PHE B 357 TYR 0.015 0.001 TYR B 555 ARG 0.008 0.000 ARG A 608 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8302 (ttpp) cc_final: 0.8032 (tttt) REVERT: A 491 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7043 (mtt180) REVERT: A 616 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8599 (pp) REVERT: B 135 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7385 (ptm-80) REVERT: B 277 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: B 290 MET cc_start: 0.7410 (mtp) cc_final: 0.6969 (mmm) REVERT: B 350 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7747 (mtt-85) REVERT: B 481 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.7763 (mptt) REVERT: B 577 LYS cc_start: 0.8742 (tptt) cc_final: 0.8450 (ttmp) REVERT: B 674 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8108 (pp) REVERT: B 679 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7229 (mm110) REVERT: B 680 ARG cc_start: 0.7829 (ptp-110) cc_final: 0.7012 (ptp90) REVERT: B 706 ARG cc_start: 0.7554 (ttm170) cc_final: 0.7164 (ttt180) REVERT: C 2 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5873 (mp0) REVERT: C 8 MET cc_start: 0.8297 (tpt) cc_final: 0.7717 (tpt) REVERT: C 156 SER cc_start: 0.7106 (m) cc_final: 0.6859 (p) REVERT: C 165 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: C 243 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7036 (tm130) outliers start: 35 outliers final: 17 residues processed: 223 average time/residue: 1.6698 time to fit residues: 402.3569 Evaluate side-chains 226 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 199 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 239 ASN A 490 GLN B 115 GLN B 413 ASN B 694 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14674 Z= 0.345 Angle : 0.588 13.137 19921 Z= 0.307 Chirality : 0.044 0.220 2196 Planarity : 0.004 0.048 2462 Dihedral : 11.045 73.863 2300 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.32 % Allowed : 16.69 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.20), residues: 1691 helix: 1.51 (0.18), residues: 805 sheet: -0.19 (0.37), residues: 186 loop : -0.58 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 438 HIS 0.008 0.001 HIS B 32 PHE 0.018 0.002 PHE A 211 TYR 0.015 0.002 TYR B 555 ARG 0.008 0.001 ARG A 608 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 194 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8310 (ttpp) cc_final: 0.8030 (tttt) REVERT: A 491 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7083 (mtt180) REVERT: A 616 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8676 (pp) REVERT: B 135 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7433 (ptm-80) REVERT: B 277 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: B 350 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7839 (mtt-85) REVERT: B 362 MET cc_start: 0.7191 (mpt) cc_final: 0.6980 (mpt) REVERT: B 481 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.7761 (mptt) REVERT: B 577 LYS cc_start: 0.8759 (tptt) cc_final: 0.8470 (ttmp) REVERT: B 674 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8149 (pp) REVERT: B 679 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7266 (mm-40) REVERT: B 680 ARG cc_start: 0.7902 (ptp-110) cc_final: 0.7079 (ptp90) REVERT: B 691 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7784 (ptmt) REVERT: B 706 ARG cc_start: 0.7572 (ttm170) cc_final: 0.7217 (ttt180) REVERT: C 2 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5906 (mp0) REVERT: C 8 MET cc_start: 0.8333 (tpt) cc_final: 0.7724 (tpt) REVERT: C 28 MET cc_start: 0.8865 (ttp) cc_final: 0.8553 (ttp) REVERT: C 156 SER cc_start: 0.7097 (m) cc_final: 0.6783 (p) REVERT: C 165 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: C 243 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7029 (tm130) outliers start: 35 outliers final: 17 residues processed: 218 average time/residue: 1.6782 time to fit residues: 397.4617 Evaluate side-chains 220 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 193 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 135 optimal weight: 0.0470 chunk 14 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 239 ASN A 387 GLN A 490 GLN B 115 GLN B 413 ASN B 694 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14674 Z= 0.146 Angle : 0.480 12.906 19921 Z= 0.250 Chirality : 0.038 0.203 2196 Planarity : 0.003 0.043 2462 Dihedral : 10.667 74.112 2300 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.52 % Allowed : 17.75 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1691 helix: 1.81 (0.18), residues: 804 sheet: 0.04 (0.37), residues: 184 loop : -0.48 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 437 HIS 0.005 0.001 HIS B 32 PHE 0.014 0.001 PHE A 35 TYR 0.013 0.001 TYR B 555 ARG 0.008 0.000 ARG A 608 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 198 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8297 (ttpp) cc_final: 0.8034 (tttt) REVERT: A 491 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7048 (mtt180) REVERT: B 118 ARG cc_start: 0.8522 (mtp85) cc_final: 0.8190 (mtp180) REVERT: B 277 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7236 (mt-10) REVERT: B 290 MET cc_start: 0.7380 (mtp) cc_final: 0.6998 (mmm) REVERT: B 350 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7684 (mtt-85) REVERT: B 674 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8047 (pp) REVERT: B 679 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7269 (mm110) REVERT: B 680 ARG cc_start: 0.7735 (ptp-110) cc_final: 0.6951 (ptp90) REVERT: B 691 LYS cc_start: 0.7966 (ttpp) cc_final: 0.7759 (ptmt) REVERT: C 2 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5910 (mp0) REVERT: C 156 SER cc_start: 0.7095 (m) cc_final: 0.6890 (p) REVERT: C 165 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: C 243 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.6987 (tm130) outliers start: 23 outliers final: 13 residues processed: 214 average time/residue: 1.6680 time to fit residues: 385.4744 Evaluate side-chains 211 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.0010 chunk 119 optimal weight: 0.0570 overall best weight: 0.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 239 ASN A 387 GLN A 490 GLN B 115 GLN B 413 ASN B 694 GLN C 182 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.148674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.108758 restraints weight = 14893.008| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.35 r_work: 0.2825 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14674 Z= 0.120 Angle : 0.454 12.532 19921 Z= 0.235 Chirality : 0.037 0.183 2196 Planarity : 0.003 0.041 2462 Dihedral : 10.409 73.510 2300 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.66 % Allowed : 17.75 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1691 helix: 2.02 (0.19), residues: 803 sheet: 0.18 (0.37), residues: 181 loop : -0.42 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 437 HIS 0.004 0.001 HIS B 32 PHE 0.012 0.001 PHE B 357 TYR 0.013 0.001 TYR B 555 ARG 0.008 0.000 ARG A 608 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6815.11 seconds wall clock time: 120 minutes 38.36 seconds (7238.36 seconds total)