Starting phenix.real_space_refine (version: dev) on Wed Apr 6 08:53:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/04_2022/6n9x_0382_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/04_2022/6n9x_0382.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/04_2022/6n9x_0382_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/04_2022/6n9x_0382_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/04_2022/6n9x_0382_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/04_2022/6n9x_0382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/04_2022/6n9x_0382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/04_2022/6n9x_0382_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/04_2022/6n9x_0382_neut_updated.pdb" } resolution = 4.1 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= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "E ARG 363": "NH1" <-> "NH2" Residue "E ARG 370": "NH1" <-> "NH2" Residue "F ARG 274": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "H PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 255": "NH1" <-> "NH2" Residue "H GLU 401": "OE1" <-> "OE2" Residue "H ARG 429": "NH1" <-> "NH2" Residue "H ARG 547": "NH1" <-> "NH2" Residue "H ARG 566": "NH1" <-> "NH2" Residue "H ARG 591": "NH1" <-> "NH2" Residue "H ARG 599": "NH1" <-> "NH2" Residue "H TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 687": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 19658 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2093 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Chain: "B" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3880 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 489} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3680 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 9, 'TRANS': 464} Chain breaks: 3 Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2086 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1861 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 236} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 134 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "H" Number of atoms: 5144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5144 Classifications: {'peptide': 645} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 622, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "P" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {'DOC': 1} Classifications: {'undetermined': 1, 'RNA': 5} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {None: 1, 'rna3p': 4} Not linked: pdbres=" G P 5 " pdbres="DOC P 6 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "T" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 506 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' ZN': 1, ' MG': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'TTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'TTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'TTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'TTP': 1, ' MG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2162 SG CYS B 17 86.829 42.707 47.451 1.00 83.88 S ATOM 2184 SG CYS B 20 84.808 40.498 45.781 1.00 88.35 S ATOM 2297 SG CYS B 36 83.303 42.356 48.342 1.00 63.37 S ATOM 2322 SG CYS B 39 85.429 40.011 49.438 1.00 74.62 S Time building chain proxies: 11.50, per 1000 atoms: 0.59 Number of scatterers: 19658 At special positions: 0 Unit cell: (118.68, 129, 196.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 112 16.00 P 45 15.00 Mg 6 11.99 O 3825 8.00 N 3432 7.00 C 12237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 235 " - pdb=" SG CYS C 241 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.70 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 39 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 20 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 17 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 36 " Number of angles added : 6 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 85 helices and 17 sheets defined 30.3% alpha, 12.3% beta 5 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 6.11 Creating SS restraints... Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 318 through 330 Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 380 through 383 No H-bonds generated for 'chain 'A' and resid 380 through 383' Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 475 through 477 No H-bonds generated for 'chain 'A' and resid 475 through 477' Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'B' and resid 88 through 94 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 188 through 191 No H-bonds generated for 'chain 'B' and resid 188 through 191' Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 239 through 242 No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 247 through 255 removed outlier: 3.668A pdb=" N GLN B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 280 Processing helix chain 'B' and resid 296 through 299 No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 318 through 330 Processing helix chain 'B' and resid 346 through 357 Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 378 through 385 removed outlier: 3.800A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 414 Processing helix chain 'B' and resid 438 through 453 Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'C' and resid 88 through 94 Processing helix chain 'C' and resid 160 through 167 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.926A pdb=" N TRP C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 278 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 366 through 374 removed outlier: 3.896A pdb=" N ARG C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 385 removed outlier: 3.620A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 413 Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 438 through 456 Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'C' and resid 483 through 485 No H-bonds generated for 'chain 'C' and resid 483 through 485' Processing helix chain 'D' and resid 272 through 278 Processing helix chain 'D' and resid 295 through 298 No H-bonds generated for 'chain 'D' and resid 295 through 298' Processing helix chain 'D' and resid 318 through 330 removed outlier: 3.611A pdb=" N GLN D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 357 Processing helix chain 'D' and resid 369 through 375 removed outlier: 3.769A pdb=" N ILE D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 385 removed outlier: 3.890A pdb=" N GLU D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 416 Processing helix chain 'D' and resid 440 through 455 removed outlier: 3.554A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 477 No H-bonds generated for 'chain 'D' and resid 475 through 477' Processing helix chain 'E' and resid 295 through 298 No H-bonds generated for 'chain 'E' and resid 295 through 298' Processing helix chain 'E' and resid 318 through 327 removed outlier: 3.503A pdb=" N GLN E 325 " --> pdb=" O PHE E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 357 removed outlier: 3.811A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 371 removed outlier: 3.604A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 385 removed outlier: 4.143A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 414 Processing helix chain 'E' and resid 440 through 456 removed outlier: 3.637A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 477 No H-bonds generated for 'chain 'E' and resid 475 through 477' Processing helix chain 'E' and resid 491 through 493 No H-bonds generated for 'chain 'E' and resid 491 through 493' Processing helix chain 'F' and resid 274 through 278 Processing helix chain 'H' and resid 39 through 51 Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.508A pdb=" N LYS H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 98 No H-bonds generated for 'chain 'H' and resid 95 through 98' Processing helix chain 'H' and resid 125 through 131 Processing helix chain 'H' and resid 139 through 150 Processing helix chain 'H' and resid 166 through 185 removed outlier: 3.830A pdb=" N LYS H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 230 removed outlier: 3.576A pdb=" N GLU H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS H 218 " --> pdb=" O VAL H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 246 removed outlier: 3.889A pdb=" N LEU H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 258 No H-bonds generated for 'chain 'H' and resid 255 through 258' Processing helix chain 'H' and resid 341 through 347 Processing helix chain 'H' and resid 377 through 399 removed outlier: 3.934A pdb=" N ALA H 381 " --> pdb=" O PRO H 377 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP H 384 " --> pdb=" O GLN H 380 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 408 No H-bonds generated for 'chain 'H' and resid 406 through 408' Processing helix chain 'H' and resid 449 through 452 No H-bonds generated for 'chain 'H' and resid 449 through 452' Processing helix chain 'H' and resid 479 through 487 removed outlier: 3.628A pdb=" N ALA H 485 " --> pdb=" O LEU H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 513 Processing helix chain 'H' and resid 518 through 529 removed outlier: 3.683A pdb=" N TYR H 526 " --> pdb=" O LYS H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 545 through 556 removed outlier: 4.027A pdb=" N LYS H 552 " --> pdb=" O GLY H 548 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 573 Processing helix chain 'H' and resid 609 through 636 removed outlier: 4.088A pdb=" N SER H 616 " --> pdb=" O THR H 612 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA H 617 " --> pdb=" O LEU H 613 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU H 620 " --> pdb=" O SER H 616 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE H 621 " --> pdb=" O ALA H 617 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS H 622 " --> pdb=" O GLY H 618 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE H 627 " --> pdb=" O LYS H 623 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU H 630 " --> pdb=" O ILE H 626 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU H 633 " --> pdb=" O THR H 629 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU H 635 " --> pdb=" O GLU H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 663 through 683 removed outlier: 4.573A pdb=" N GLN H 674 " --> pdb=" O ILE H 670 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU H 675 " --> pdb=" O GLU H 671 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 528 through 534 removed outlier: 7.096A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 34 through 36 removed outlier: 3.918A pdb=" N TYR B 13 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.533A pdb=" N SER B 120 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 133 " --> pdb=" O GLN B 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 123 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 175 through 177 removed outlier: 7.885A pdb=" N VAL B 176 " --> pdb=" O LYS B 152 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL B 154 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN B 201 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL B 155 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE B 203 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 528 through 534 removed outlier: 7.141A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 498 " --> pdb=" O VAL B 307 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.561A pdb=" N SER C 120 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 174 through 176 Processing sheet with id= H, first strand: chain 'C' and resid 542 through 544 removed outlier: 6.693A pdb=" N VAL C 516 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR C 532 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 514 " --> pdb=" O TYR C 532 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU C 460 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N VAL C 310 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL C 462 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 528 through 533 removed outlier: 7.071A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR D 498 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU D 460 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL D 310 " --> pdb=" O LEU D 460 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL D 462 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N SER D 312 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N CYS D 464 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 528 through 534 removed outlier: 3.598A pdb=" N GLY E 528 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE E 499 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU E 502 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU E 460 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL E 310 " --> pdb=" O LEU E 460 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL E 462 " --> pdb=" O VAL E 310 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 32 through 34 removed outlier: 4.148A pdb=" N GLY H 21 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA H 7 " --> pdb=" O HIS H 19 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY H 21 " --> pdb=" O ALA H 5 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA H 5 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE H 23 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL H 3 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 56 through 58 Processing sheet with id= M, first strand: chain 'H' and resid 264 through 267 Processing sheet with id= N, first strand: chain 'H' and resid 419 through 421 Processing sheet with id= O, first strand: chain 'H' and resid 692 through 697 removed outlier: 3.618A pdb=" N ALA H 650 " --> pdb=" O GLN H 657 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLY H 659 " --> pdb=" O TYR H 648 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TYR H 648 " --> pdb=" O GLY H 659 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 592 through 594 Processing sheet with id= Q, first strand: chain 'H' and resid 574 through 579 removed outlier: 4.213A pdb=" N GLU H 575 " --> pdb=" O LYS H 587 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LYS H 587 " --> pdb=" O GLU H 575 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N SER H 577 " --> pdb=" O GLN H 585 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN H 585 " --> pdb=" O SER H 577 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q 533 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 8.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3278 1.31 - 1.44: 5265 1.44 - 1.56: 11238 1.56 - 1.69: 82 1.69 - 1.82: 182 Bond restraints: 20045 Sorted by residual: bond pdb=" C4' DOC P 6 " pdb=" C3' DOC P 6 " ideal model delta sigma weight residual 1.316 1.522 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C4' DOC P 6 " pdb=" O4' DOC P 6 " ideal model delta sigma weight residual 1.635 1.430 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" O4' DOC P 6 " pdb=" C1' DOC P 6 " ideal model delta sigma weight residual 1.269 1.430 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" C2 DOC P 6 " pdb=" N3 DOC P 6 " ideal model delta sigma weight residual 1.482 1.350 0.132 2.00e-02 2.50e+03 4.32e+01 bond pdb=" N1 DOC P 6 " pdb=" C6 DOC P 6 " ideal model delta sigma weight residual 1.439 1.336 0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 20040 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.81: 399 105.81 - 112.87: 10454 112.87 - 119.93: 7288 119.93 - 126.99: 8725 126.99 - 134.05: 285 Bond angle restraints: 27151 Sorted by residual: angle pdb=" C ASN A 388 " pdb=" N ASP A 389 " pdb=" CA ASP A 389 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" N HIS A 357 " pdb=" CA HIS A 357 " pdb=" C HIS A 357 " ideal model delta sigma weight residual 111.71 116.46 -4.75 1.15e+00 7.56e-01 1.71e+01 angle pdb=" PB TTP H 801 " pdb=" O3B TTP H 801 " pdb=" PG TTP H 801 " ideal model delta sigma weight residual 120.50 132.69 -12.19 3.00e+00 1.11e-01 1.65e+01 angle pdb=" PB TTP E 700 " pdb=" O3B TTP E 700 " pdb=" PG TTP E 700 " ideal model delta sigma weight residual 120.50 132.67 -12.17 3.00e+00 1.11e-01 1.65e+01 angle pdb=" PA TTP H 801 " pdb=" O3A TTP H 801 " pdb=" PB TTP H 801 " ideal model delta sigma weight residual 120.50 132.65 -12.15 3.00e+00 1.11e-01 1.64e+01 ... (remaining 27146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 11627 36.00 - 72.00: 184 72.00 - 108.00: 15 108.00 - 144.00: 1 144.00 - 180.00: 8 Dihedral angle restraints: 11835 sinusoidal: 5009 harmonic: 6826 Sorted by residual: dihedral pdb=" CD ARG H 604 " pdb=" NE ARG H 604 " pdb=" CZ ARG H 604 " pdb=" NH1 ARG H 604 " ideal model delta sinusoidal sigma weight residual 0.00 -73.14 73.14 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CD ARG E 323 " pdb=" NE ARG E 323 " pdb=" CZ ARG E 323 " pdb=" NH1 ARG E 323 " ideal model delta sinusoidal sigma weight residual 0.00 72.85 -72.85 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" C2 TTP C 700 " pdb=" C1' TTP C 700 " pdb=" N1 TTP C 700 " pdb=" O4' TTP C 700 " ideal model delta sinusoidal sigma weight residual 301.68 121.69 180.00 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 11832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2570 0.075 - 0.151: 389 0.151 - 0.226: 25 0.226 - 0.302: 10 0.302 - 0.377: 1 Chirality restraints: 2995 Sorted by residual: chirality pdb=" CB ILE C 261 " pdb=" CA ILE C 261 " pdb=" CG1 ILE C 261 " pdb=" CG2 ILE C 261 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C3' TTP C 700 " pdb=" C2' TTP C 700 " pdb=" C4' TTP C 700 " pdb=" O3' TTP C 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C3' TTP E 700 " pdb=" C2' TTP E 700 " pdb=" C4' TTP E 700 " pdb=" O3' TTP E 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2992 not shown) Planarity restraints: 3357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 604 " 1.051 9.50e-02 1.11e+02 4.71e-01 1.34e+02 pdb=" NE ARG H 604 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG H 604 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 604 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG H 604 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 323 " -1.047 9.50e-02 1.11e+02 4.69e-01 1.33e+02 pdb=" NE ARG E 323 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG E 323 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 323 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG E 323 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 229 " -0.575 9.50e-02 1.11e+02 2.58e-01 4.06e+01 pdb=" NE ARG C 229 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG C 229 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 229 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 229 " -0.019 2.00e-02 2.50e+03 ... (remaining 3354 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 301 2.68 - 3.24: 16735 3.24 - 3.79: 28793 3.79 - 4.35: 38281 4.35 - 4.90: 63038 Nonbonded interactions: 147148 Sorted by model distance: nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.131 2.170 nonbonded pdb=" O2B TTP E 700 " pdb="MG MG E 701 " model vdw 2.184 2.170 nonbonded pdb=" O1G TTP B 602 " pdb="MG MG B 603 " model vdw 2.185 2.170 nonbonded pdb=" OG SER C 319 " pdb="MG MG C 701 " model vdw 2.191 2.170 nonbonded pdb=" OD2 ASP H 654 " pdb="MG MG H 802 " model vdw 2.202 2.170 ... (remaining 147143 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 545)) selection = (chain 'D' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 through 545)) selection = (chain 'E' and resid 285 through 545) } ncs_group { reference = (chain 'B' and (resid 65 through 506 or resid 510 through 547 or resid 602 throu \ gh 603)) selection = (chain 'C' and (resid 65 through 208 or resid 219 through 396 or resid 402 throu \ gh 431 or resid 436 through 547 or resid 700 through 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 45 5.49 5 Mg 6 5.21 5 S 112 5.16 5 C 12237 2.51 5 N 3432 2.21 5 O 3825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.300 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: 0.020 Extract box with map and model: 14.530 Check model and map are aligned: 0.320 Convert atoms to be neutral: 0.200 Process input model: 57.210 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.206 20045 Z= 0.375 Angle : 0.839 12.191 27151 Z= 0.446 Chirality : 0.054 0.377 2995 Planarity : 0.015 0.471 3357 Dihedral : 13.689 179.996 7464 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -4.04 (0.13), residues: 2367 helix: -3.02 (0.12), residues: 838 sheet: -1.22 (0.27), residues: 372 loop : -2.90 (0.14), residues: 1157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 686 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 691 average time/residue: 0.3727 time to fit residues: 371.1362 Evaluate side-chains 315 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 2.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 219 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN B 198 GLN B 256 ASN B 278 HIS B 296 ASN B 358 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 325 GLN C 358 ASN C 392 HIS ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS C 512 ASN D 278 HIS D 325 GLN D 494 GLN D 507 GLN D 536 ASN E 325 GLN E 512 ASN H 62 HIS ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 GLN H 450 GLN H 509 ASN H 520 ASN H 615 GLN H 704 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 20045 Z= 0.168 Angle : 0.538 8.907 27151 Z= 0.275 Chirality : 0.042 0.164 2995 Planarity : 0.004 0.057 3357 Dihedral : 13.445 177.400 2962 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -2.77 (0.15), residues: 2367 helix: -1.37 (0.16), residues: 820 sheet: -1.09 (0.26), residues: 396 loop : -2.47 (0.15), residues: 1151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 426 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 427 average time/residue: 0.3125 time to fit residues: 201.9859 Evaluate side-chains 272 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 2.255 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 220 optimal weight: 0.8980 chunk 237 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 176 optimal weight: 0.0980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN C 192 ASN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN D 512 ASN D 536 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN H 171 ASN H 173 GLN H 423 ASN H 471 GLN H 520 ASN ** H 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 640 HIS H 657 GLN H 674 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 20045 Z= 0.210 Angle : 0.552 8.357 27151 Z= 0.282 Chirality : 0.043 0.146 2995 Planarity : 0.004 0.049 3357 Dihedral : 13.030 169.449 2962 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.16), residues: 2367 helix: -0.56 (0.18), residues: 835 sheet: -0.94 (0.26), residues: 407 loop : -2.20 (0.16), residues: 1125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.3036 time to fit residues: 175.7323 Evaluate side-chains 252 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.350 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 147 optimal weight: 0.3980 chunk 220 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 209 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS B 169 GLN B 180 HIS B 358 ASN B 425 HIS C 343 GLN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN E 358 ASN ** E 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 558 ASN ** H 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 20045 Z= 0.258 Angle : 0.574 8.851 27151 Z= 0.296 Chirality : 0.044 0.155 2995 Planarity : 0.004 0.060 3357 Dihedral : 12.958 165.353 2962 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.79 (0.17), residues: 2367 helix: -0.18 (0.18), residues: 842 sheet: -0.89 (0.26), residues: 412 loop : -2.11 (0.17), residues: 1113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 350 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 351 average time/residue: 0.3012 time to fit residues: 163.8473 Evaluate side-chains 243 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.315 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN B 358 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 425 HIS D 343 GLN E 325 GLN E 444 ASN ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 HIS ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 558 ASN H 585 GLN H 615 GLN ** H 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 20045 Z= 0.233 Angle : 0.560 9.035 27151 Z= 0.288 Chirality : 0.043 0.152 2995 Planarity : 0.003 0.042 3357 Dihedral : 12.792 163.287 2962 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.55 (0.17), residues: 2367 helix: 0.12 (0.19), residues: 847 sheet: -0.89 (0.26), residues: 406 loop : -2.01 (0.17), residues: 1114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 327 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 328 average time/residue: 0.3146 time to fit residues: 160.3007 Evaluate side-chains 235 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.368 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 137 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS B 169 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 ASN H 171 ASN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 653 HIS ** H 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.106 20045 Z= 0.269 Angle : 0.608 12.882 27151 Z= 0.313 Chirality : 0.044 0.162 2995 Planarity : 0.004 0.048 3357 Dihedral : 12.802 161.518 2962 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.48 (0.17), residues: 2367 helix: 0.25 (0.19), residues: 844 sheet: -0.88 (0.26), residues: 406 loop : -2.00 (0.17), residues: 1117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 312 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 313 average time/residue: 0.3458 time to fit residues: 167.4872 Evaluate side-chains 226 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.662 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 133 optimal weight: 0.3980 chunk 170 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 233 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN B 198 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN C 343 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.248 20045 Z= 0.205 Angle : 0.572 20.439 27151 Z= 0.296 Chirality : 0.042 0.150 2995 Planarity : 0.003 0.040 3357 Dihedral : 12.515 158.530 2962 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.21 (0.17), residues: 2367 helix: 0.47 (0.19), residues: 843 sheet: -0.74 (0.26), residues: 399 loop : -1.84 (0.17), residues: 1125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 315 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 315 average time/residue: 0.3099 time to fit residues: 151.7572 Evaluate side-chains 223 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 2.448 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 115 optimal weight: 0.0770 chunk 21 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 212 optimal weight: 0.0970 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN H 653 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.699 20045 Z= 0.524 Angle : 0.788 73.899 27151 Z= 0.363 Chirality : 0.043 0.277 2995 Planarity : 0.003 0.081 3357 Dihedral : 12.507 158.715 2962 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.18 (0.17), residues: 2367 helix: 0.50 (0.19), residues: 843 sheet: -0.74 (0.26), residues: 399 loop : -1.82 (0.17), residues: 1125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 292 average time/residue: 0.3068 time to fit residues: 139.8320 Evaluate side-chains 222 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.592 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 217 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 196 optimal weight: 0.9980 chunk 205 optimal weight: 0.0570 chunk 216 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS B 169 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN ** H 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 653 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.699 20045 Z= 0.529 Angle : 0.792 73.899 27151 Z= 0.368 Chirality : 0.043 0.277 2995 Planarity : 0.004 0.140 3357 Dihedral : 12.507 158.715 2962 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.18 (0.17), residues: 2367 helix: 0.50 (0.19), residues: 843 sheet: -0.74 (0.26), residues: 399 loop : -1.82 (0.17), residues: 1125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 289 average time/residue: 0.3127 time to fit residues: 142.1333 Evaluate side-chains 222 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.579 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 159 optimal weight: 0.0000 chunk 241 optimal weight: 3.9990 chunk 221 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 148 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN ** H 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 653 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.699 20045 Z= 0.529 Angle : 0.792 73.899 27151 Z= 0.368 Chirality : 0.043 0.277 2995 Planarity : 0.004 0.140 3357 Dihedral : 12.507 158.715 2962 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.18 (0.17), residues: 2367 helix: 0.50 (0.19), residues: 843 sheet: -0.74 (0.26), residues: 399 loop : -1.82 (0.17), residues: 1125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 289 average time/residue: 0.3031 time to fit residues: 137.8661 Evaluate side-chains 222 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 0.0570 chunk 58 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN ** H 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 653 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105711 restraints weight = 41142.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.105475 restraints weight = 33704.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106340 restraints weight = 31608.470| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.699 20045 Z= 0.529 Angle : 0.792 73.899 27151 Z= 0.368 Chirality : 0.043 0.277 2995 Planarity : 0.004 0.140 3357 Dihedral : 12.507 158.715 2962 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.18 (0.17), residues: 2367 helix: 0.50 (0.19), residues: 843 sheet: -0.74 (0.26), residues: 399 loop : -1.82 (0.17), residues: 1125 =============================================================================== Job complete usr+sys time: 3965.24 seconds wall clock time: 73 minutes 0.46 seconds (4380.46 seconds total)