Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 08:55:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0n_10356/04_2023/6t0n_10356.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0n_10356/04_2023/6t0n_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_10356/04_2023/6t0n_10356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0n_10356/04_2023/6t0n_10356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0n_10356/04_2023/6t0n_10356.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0n_10356/04_2023/6t0n_10356.pdb" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 14 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: 8.24, per 1000 atoms: 0.56 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: 6.14 Conformation dependent library (CDL) restraints added in 2.2 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: 4.57 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: 5.55 Time building geometry restraints manager: 6.63 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: 8075 17.98 - 35.97: 571 35.97 - 53.95: 168 53.95 - 71.93: 50 71.93 - 89.92: 17 Dihedral angle restraints: 8881 sinusoidal: 3913 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 8878 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: 1.470 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: 8.020 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 44.820 Find NCS groups from input model: 0.500 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: 0.010 Load rotamer database and sin/cos tables:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.820 ------------------------------------------------------------------------------- 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 : 14.689 89.915 5667 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 % 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 *********************** 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 : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 21 residues processed: 325 average time/residue: 1.6785 time to fit residues: 586.5505 Evaluate side-chains 228 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 1.636 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.4757 time to fit residues: 4.0379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.8602 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 14674 Z= 0.185 Angle : 0.492 8.068 19921 Z= 0.267 Chirality : 0.039 0.208 2196 Planarity : 0.004 0.051 2462 Dihedral : 6.333 73.960 2192 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 3.51 % 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: -0.58 (0.19), residues: 1691 helix: 0.41 (0.17), residues: 806 sheet: -0.90 (0.34), residues: 193 loop : -1.08 (0.22), residues: 692 *********************** 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 258 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 205 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 22 residues processed: 241 average time/residue: 1.6436 time to fit residues: 427.5122 Evaluate side-chains 221 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 199 time to evaluate : 1.770 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 3 average time/residue: 0.8774 time to fit residues: 5.3682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 105 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 425 ASN A 490 GLN B 115 GLN B 413 ASN B 694 GLN C 110 HIS C 243 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 14674 Z= 0.179 Angle : 0.474 7.663 19921 Z= 0.254 Chirality : 0.039 0.204 2196 Planarity : 0.004 0.047 2462 Dihedral : 6.154 73.410 2192 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 3.25 % 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: 0.18 (0.20), residues: 1691 helix: 1.18 (0.18), residues: 804 sheet: -0.65 (0.36), residues: 181 loop : -0.86 (0.22), residues: 706 *********************** 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 257 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 208 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 24 residues processed: 245 average time/residue: 1.6985 time to fit residues: 448.9986 Evaluate side-chains 224 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 200 time to evaluate : 1.739 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 2 average time/residue: 0.8326 time to fit residues: 4.2534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 425 ASN A 490 GLN B 115 GLN B 413 ASN B 678 ASN B 694 GLN C 110 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1828 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= 0.284 Angle : 0.534 8.830 19921 Z= 0.284 Chirality : 0.042 0.216 2196 Planarity : 0.004 0.048 2462 Dihedral : 6.332 73.733 2192 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 3.51 % 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: 0.43 (0.20), residues: 1691 helix: 1.38 (0.18), residues: 797 sheet: -0.54 (0.36), residues: 186 loop : -0.69 (0.22), residues: 708 *********************** 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 256 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 203 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 29 residues processed: 241 average time/residue: 1.6492 time to fit residues: 429.7107 Evaluate side-chains 228 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 199 time to evaluate : 1.874 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 6 average time/residue: 1.0582 time to fit residues: 9.6008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 100 ASN A 239 ASN A 387 GLN A 425 ASN A 490 GLN B 115 GLN B 413 ASN B 694 GLN C 236 GLN C 243 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1954 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= 0.184 Angle : 0.476 7.950 19921 Z= 0.254 Chirality : 0.039 0.206 2196 Planarity : 0.003 0.045 2462 Dihedral : 6.131 73.808 2192 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 2.78 % 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: 0.72 (0.20), residues: 1691 helix: 1.63 (0.18), residues: 798 sheet: -0.27 (0.38), residues: 174 loop : -0.61 (0.22), residues: 719 *********************** 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 243 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 201 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 25 residues processed: 235 average time/residue: 1.6474 time to fit residues: 419.6833 Evaluate side-chains 226 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 201 time to evaluate : 1.804 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 3 average time/residue: 0.9011 time to fit residues: 5.4091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 54 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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: 0.8624 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 14674 Z= 0.214 Angle : 0.495 8.442 19921 Z= 0.263 Chirality : 0.040 0.206 2196 Planarity : 0.004 0.046 2462 Dihedral : 6.163 73.952 2192 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 2.65 % 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: 0.79 (0.20), residues: 1691 helix: 1.66 (0.18), residues: 799 sheet: -0.22 (0.37), residues: 186 loop : -0.56 (0.22), residues: 706 *********************** 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 240 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 200 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 24 residues processed: 232 average time/residue: 1.6471 time to fit residues: 413.7028 Evaluate side-chains 216 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 192 time to evaluate : 1.840 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 3 average time/residue: 1.1442 time to fit residues: 6.3460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 94 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 243 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 14674 Z= 0.148 Angle : 0.465 9.386 19921 Z= 0.246 Chirality : 0.038 0.200 2196 Planarity : 0.003 0.043 2462 Dihedral : 5.987 73.357 2192 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 2.58 % 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: 0.96 (0.20), residues: 1691 helix: 1.84 (0.18), residues: 798 sheet: -0.03 (0.39), residues: 174 loop : -0.53 (0.22), residues: 719 *********************** 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 236 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 23 residues processed: 230 average time/residue: 1.5748 time to fit residues: 392.1025 Evaluate side-chains 222 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 199 time to evaluate : 1.734 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 3 average time/residue: 0.5788 time to fit residues: 4.5286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 129 optimal weight: 0.5980 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 14674 Z= 0.166 Angle : 0.479 11.008 19921 Z= 0.251 Chirality : 0.039 0.198 2196 Planarity : 0.003 0.044 2462 Dihedral : 5.986 73.191 2192 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 1.99 % 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: 0.97 (0.20), residues: 1691 helix: 1.83 (0.18), residues: 804 sheet: -0.02 (0.38), residues: 174 loop : -0.53 (0.22), residues: 713 *********************** 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 226 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 23 residues processed: 222 average time/residue: 1.6086 time to fit residues: 386.8521 Evaluate side-chains 215 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 1.790 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 3 average time/residue: 0.5930 time to fit residues: 4.5892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.5075 > 50: distance: 101 - 106: 4.507 distance: 106 - 107: 3.848 distance: 107 - 108: 12.951 distance: 107 - 110: 5.701 distance: 108 - 109: 8.770 distance: 108 - 115: 9.672 distance: 110 - 111: 8.498 distance: 111 - 112: 5.563 distance: 112 - 113: 3.105 distance: 115 - 116: 5.679 distance: 116 - 117: 25.182 distance: 116 - 119: 7.256 distance: 117 - 118: 18.072 distance: 117 - 129: 22.119 distance: 119 - 120: 6.120 distance: 120 - 121: 7.059 distance: 120 - 122: 11.517 distance: 121 - 123: 9.424 distance: 122 - 124: 26.618 distance: 122 - 125: 17.919 distance: 123 - 124: 16.519 distance: 124 - 126: 18.788 distance: 125 - 127: 7.030 distance: 126 - 128: 8.810 distance: 127 - 128: 5.752 distance: 129 - 130: 7.090 distance: 130 - 131: 12.568 distance: 130 - 133: 8.646 distance: 131 - 132: 8.798 distance: 131 - 137: 14.526 distance: 133 - 134: 11.025 distance: 134 - 135: 11.420 distance: 134 - 136: 7.987 distance: 137 - 138: 9.825 distance: 138 - 139: 26.794 distance: 138 - 141: 16.331 distance: 139 - 140: 20.149 distance: 139 - 146: 41.868 distance: 141 - 142: 25.968 distance: 142 - 143: 6.449 distance: 143 - 144: 12.750 distance: 143 - 145: 8.057 distance: 146 - 147: 32.021 distance: 147 - 148: 23.983 distance: 147 - 150: 26.516 distance: 148 - 149: 11.181 distance: 148 - 154: 8.942 distance: 150 - 151: 20.963 distance: 151 - 152: 15.073 distance: 151 - 153: 15.300 distance: 154 - 155: 25.558 distance: 155 - 156: 23.309 distance: 155 - 158: 31.429 distance: 156 - 157: 15.123 distance: 158 - 159: 11.521 distance: 159 - 160: 14.358 distance: 160 - 161: 12.128 distance: 160 - 162: 10.564 distance: 164 - 165: 16.923 distance: 164 - 167: 5.013 distance: 165 - 166: 18.611 distance: 165 - 171: 27.701 distance: 166 - 197: 13.046 distance: 167 - 168: 6.171 distance: 168 - 169: 13.045 distance: 168 - 170: 5.777 distance: 171 - 172: 15.582 distance: 171 - 177: 12.132 distance: 172 - 173: 5.989 distance: 172 - 175: 14.298 distance: 173 - 174: 7.403 distance: 173 - 178: 13.086 distance: 174 - 207: 5.778 distance: 175 - 176: 10.219 distance: 176 - 177: 5.048 distance: 178 - 179: 10.129 distance: 179 - 180: 11.843 distance: 179 - 182: 9.531 distance: 180 - 181: 8.601 distance: 180 - 189: 12.671 distance: 181 - 214: 4.773 distance: 182 - 183: 9.928 distance: 183 - 184: 3.568 distance: 184 - 185: 6.834 distance: 185 - 186: 6.412 distance: 186 - 187: 3.387 distance: 189 - 190: 16.510 distance: 190 - 191: 31.790 distance: 190 - 193: 15.502 distance: 191 - 192: 22.830 distance: 191 - 197: 22.753 distance: 192 - 219: 5.196 distance: 193 - 194: 7.683 distance: 193 - 195: 5.366 distance: 194 - 196: 10.046