Starting phenix.real_space_refine on Mon Mar 18 02:12:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/03_2024/6n9x_0382_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/03_2024/6n9x_0382.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/03_2024/6n9x_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_0382/03_2024/6n9x_0382_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/03_2024/6n9x_0382_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/03_2024/6n9x_0382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/03_2024/6n9x_0382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/03_2024/6n9x_0382_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9x_0382/03_2024/6n9x_0382_neut_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 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. 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-5265/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: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 622} 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: {'RNA': 5, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna3p': 4, None: 1} 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: {' MG': 1, ' ZN': 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: {' MG': 1, 'TTP': 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: {' MG': 1, 'TTP': 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: {' MG': 1, 'TTP': 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: {' MG': 2, 'TTP': 1} 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: 10.19, per 1000 atoms: 0.52 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: 7.19 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal 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: 7.81 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: 5.69 Time building geometry restraints manager: 7.87 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 1.334 1.522 -0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" C4' DOC P 6 " pdb=" O4' DOC P 6 " ideal model delta sigma weight residual 1.609 1.430 0.179 2.00e-02 2.50e+03 7.99e+01 bond pdb=" O4' DOC P 6 " pdb=" C1' DOC P 6 " ideal model delta sigma weight residual 1.268 1.430 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" C2 DOC P 6 " pdb=" N3 DOC P 6 " ideal model delta sigma weight residual 1.492 1.350 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C4 DOC P 6 " pdb=" N4 DOC P 6 " ideal model delta sigma weight residual 1.494 1.356 0.138 2.00e-02 2.50e+03 4.77e+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: 11645 36.00 - 72.00: 192 72.00 - 108.00: 16 108.00 - 144.00: 1 144.00 - 180.00: 8 Dihedral angle restraints: 11862 sinusoidal: 5036 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 11859 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 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: 3.850 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: 13.500 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 57.050 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 0.188 20045 Z= 0.371 Angle : 0.839 12.191 27151 Z= 0.446 Chirality : 0.054 0.377 2995 Planarity : 0.015 0.471 3357 Dihedral : 13.831 179.996 7491 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 % Allowed : 3.62 % Favored : 95.78 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 700 HIS 0.009 0.001 HIS C 145 PHE 0.024 0.002 PHE H 686 TYR 0.013 0.001 TYR H 648 ARG 0.006 0.000 ARG H 96 *********************** 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 : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 GLN cc_start: 0.6865 (mm-40) cc_final: 0.6053 (mm-40) REVERT: A 347 GLU cc_start: 0.7261 (mp0) cc_final: 0.6888 (mt-10) REVERT: A 539 THR cc_start: 0.7350 (p) cc_final: 0.7119 (p) REVERT: B 255 TRP cc_start: 0.7885 (m100) cc_final: 0.7662 (m100) REVERT: B 309 MET cc_start: 0.8748 (tpp) cc_final: 0.8279 (tpp) REVERT: B 329 TRP cc_start: 0.7546 (m-10) cc_final: 0.7258 (m-10) REVERT: B 424 ASP cc_start: 0.8259 (t0) cc_final: 0.8044 (p0) REVERT: B 467 LYS cc_start: 0.7453 (pttt) cc_final: 0.7226 (ptpp) REVERT: C 105 MET cc_start: 0.7782 (mmm) cc_final: 0.7400 (mmp) REVERT: C 117 ASN cc_start: 0.5633 (m110) cc_final: 0.5030 (p0) REVERT: C 236 LYS cc_start: 0.8513 (tmtt) cc_final: 0.8083 (mmmm) REVERT: C 314 SER cc_start: 0.9114 (m) cc_final: 0.8850 (p) REVERT: C 425 HIS cc_start: 0.8299 (t-90) cc_final: 0.8050 (t-90) REVERT: C 476 GLU cc_start: 0.7132 (mp0) cc_final: 0.6829 (mp0) REVERT: D 352 ASP cc_start: 0.8175 (t0) cc_final: 0.7709 (t0) REVERT: D 494 GLN cc_start: 0.7910 (mt0) cc_final: 0.7491 (mt0) REVERT: E 323 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6783 (mtt180) REVERT: E 356 LEU cc_start: 0.8213 (tp) cc_final: 0.7969 (tp) REVERT: H 6 ILE cc_start: 0.8969 (tt) cc_final: 0.8650 (tt) REVERT: H 75 LEU cc_start: 0.8506 (mt) cc_final: 0.8278 (tp) REVERT: H 90 ASP cc_start: 0.9253 (t0) cc_final: 0.8691 (t70) REVERT: H 101 ASN cc_start: 0.7657 (p0) cc_final: 0.7319 (p0) REVERT: H 253 LEU cc_start: 0.8464 (mt) cc_final: 0.7688 (mt) REVERT: H 626 ILE cc_start: 0.9384 (pt) cc_final: 0.8970 (tp) REVERT: H 649 MET cc_start: 0.8077 (mtm) cc_final: 0.7847 (mtt) REVERT: H 669 VAL cc_start: 0.8254 (t) cc_final: 0.8050 (p) outliers start: 12 outliers final: 0 residues processed: 691 average time/residue: 0.3846 time to fit residues: 372.9651 Evaluate side-chains 323 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 322 time to evaluate : 2.294 ------------------------------------------------------------------------------- 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: 3.9990 chunk 101 optimal weight: 0.0870 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: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 507 GLN D 536 ASN E 325 GLN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 ASN H 150 GLN H 173 GLN H 509 ASN H 520 ASN H 615 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 20045 Z= 0.151 Angle : 0.533 8.682 27151 Z= 0.272 Chirality : 0.042 0.154 2995 Planarity : 0.004 0.059 3357 Dihedral : 13.812 175.315 2989 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % 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: -2.73 (0.15), residues: 2367 helix: -1.33 (0.16), residues: 821 sheet: -1.08 (0.26), residues: 396 loop : -2.45 (0.15), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 69 HIS 0.004 0.001 HIS E 475 PHE 0.014 0.001 PHE B 378 TYR 0.026 0.001 TYR C 411 ARG 0.007 0.001 ARG E 323 *********************** 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 438 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 437 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 ASP cc_start: 0.7329 (m-30) cc_final: 0.5766 (t0) REVERT: A 539 THR cc_start: 0.7830 (p) cc_final: 0.7595 (p) REVERT: A 543 GLU cc_start: 0.7854 (mp0) cc_final: 0.7616 (mp0) REVERT: B 195 TYR cc_start: 0.9052 (t80) cc_final: 0.8811 (t80) REVERT: B 205 MET cc_start: 0.9021 (tpp) cc_final: 0.8158 (mtt) REVERT: B 255 TRP cc_start: 0.7975 (m100) cc_final: 0.7569 (m100) REVERT: B 329 TRP cc_start: 0.7607 (m-10) cc_final: 0.7377 (m-10) REVERT: C 105 MET cc_start: 0.7857 (mmm) cc_final: 0.7322 (mmp) REVERT: C 117 ASN cc_start: 0.5692 (m110) cc_final: 0.5097 (p0) REVERT: C 162 MET cc_start: 0.7821 (tmm) cc_final: 0.7474 (tmm) REVERT: C 236 LYS cc_start: 0.8494 (tmtt) cc_final: 0.8106 (mmmm) REVERT: C 314 SER cc_start: 0.9052 (m) cc_final: 0.8786 (p) REVERT: C 333 MET cc_start: 0.8366 (mpp) cc_final: 0.7686 (mpp) REVERT: C 425 HIS cc_start: 0.8347 (t-90) cc_final: 0.8132 (t-90) REVERT: C 476 GLU cc_start: 0.7216 (mp0) cc_final: 0.6814 (mp0) REVERT: D 295 ILE cc_start: 0.8770 (mm) cc_final: 0.8409 (mm) REVERT: D 297 ASP cc_start: 0.8104 (p0) cc_final: 0.7690 (p0) REVERT: D 352 ASP cc_start: 0.8254 (t0) cc_final: 0.7676 (t0) REVERT: D 404 ARG cc_start: 0.7001 (ptt-90) cc_final: 0.6733 (ptt90) REVERT: D 494 GLN cc_start: 0.7824 (mt0) cc_final: 0.7499 (mt0) REVERT: E 356 LEU cc_start: 0.8202 (tp) cc_final: 0.7978 (tp) REVERT: H 6 ILE cc_start: 0.9308 (tt) cc_final: 0.9100 (tt) REVERT: H 75 LEU cc_start: 0.8673 (mt) cc_final: 0.8375 (tp) REVERT: H 101 ASN cc_start: 0.7649 (p0) cc_final: 0.7240 (p0) REVERT: H 253 LEU cc_start: 0.8347 (mt) cc_final: 0.7846 (mt) REVERT: H 335 ASN cc_start: 0.8553 (t0) cc_final: 0.8267 (t0) REVERT: H 626 ILE cc_start: 0.9245 (pt) cc_final: 0.8989 (tp) outliers start: 1 outliers final: 0 residues processed: 438 average time/residue: 0.3441 time to fit residues: 222.9031 Evaluate side-chains 278 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.103 ------------------------------------------------------------------------------- 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: 3.9990 chunk 182 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 220 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS B 136 HIS B 169 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN D 512 ASN D 536 ASN E 358 ASN H 62 HIS H 171 ASN H 173 GLN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 450 GLN H 471 GLN H 509 ASN H 520 ASN ** H 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 657 GLN H 674 GLN H 704 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20045 Z= 0.317 Angle : 0.632 8.020 27151 Z= 0.325 Chirality : 0.045 0.152 2995 Planarity : 0.004 0.050 3357 Dihedral : 13.692 169.636 2989 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: -2.23 (0.16), residues: 2367 helix: -0.72 (0.17), residues: 837 sheet: -1.03 (0.26), residues: 407 loop : -2.25 (0.16), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 700 HIS 0.010 0.001 HIS D 425 PHE 0.015 0.002 PHE B 11 TYR 0.015 0.002 TYR C 96 ARG 0.010 0.001 ARG A 439 *********************** 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 365 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 ASP cc_start: 0.7431 (t0) cc_final: 0.7066 (t0) REVERT: A 448 LYS cc_start: 0.7456 (mmtp) cc_final: 0.7197 (mmtp) REVERT: A 493 ARG cc_start: 0.7943 (ptt180) cc_final: 0.7630 (ptt180) REVERT: A 533 MET cc_start: 0.7360 (mpp) cc_final: 0.6951 (mpp) REVERT: B 309 MET cc_start: 0.8819 (tpp) cc_final: 0.8307 (tpp) REVERT: B 362 LEU cc_start: 0.9163 (tp) cc_final: 0.8180 (tp) REVERT: C 162 MET cc_start: 0.8168 (tmm) cc_final: 0.7932 (tmm) REVERT: C 236 LYS cc_start: 0.8862 (tmtt) cc_final: 0.8116 (mmmm) REVERT: C 314 SER cc_start: 0.9192 (m) cc_final: 0.8898 (p) REVERT: C 333 MET cc_start: 0.8499 (mpp) cc_final: 0.7673 (mpp) REVERT: C 424 ASP cc_start: 0.8463 (t70) cc_final: 0.8214 (t70) REVERT: D 297 ASP cc_start: 0.8469 (p0) cc_final: 0.8092 (p0) REVERT: D 341 MET cc_start: 0.8150 (mmt) cc_final: 0.7920 (mmt) REVERT: D 352 ASP cc_start: 0.8353 (t0) cc_final: 0.7772 (t0) REVERT: D 521 CYS cc_start: 0.8594 (t) cc_final: 0.8314 (m) REVERT: E 295 ILE cc_start: 0.8569 (mm) cc_final: 0.8329 (mm) REVERT: E 356 LEU cc_start: 0.8328 (tp) cc_final: 0.8093 (tp) REVERT: H 75 LEU cc_start: 0.8754 (mt) cc_final: 0.8155 (tp) REVERT: H 90 ASP cc_start: 0.9321 (t0) cc_final: 0.8788 (t0) REVERT: H 101 ASN cc_start: 0.7942 (p0) cc_final: 0.7546 (p0) REVERT: H 136 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7467 (pttm) REVERT: H 253 LEU cc_start: 0.8840 (mt) cc_final: 0.7984 (mp) REVERT: H 495 GLU cc_start: 0.8588 (pp20) cc_final: 0.8283 (pp20) REVERT: H 626 ILE cc_start: 0.9456 (pt) cc_final: 0.9195 (tp) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.3181 time to fit residues: 175.8158 Evaluate side-chains 259 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.841 ------------------------------------------------------------------------------- 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: 1.9990 chunk 165 optimal weight: 0.9990 chunk 114 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 220 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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** A 475 HIS B 169 GLN B 180 HIS B 198 GLN B 358 ASN B 425 HIS C 192 ASN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 558 ASN H 585 GLN ** H 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 653 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20045 Z= 0.153 Angle : 0.511 9.922 27151 Z= 0.262 Chirality : 0.042 0.147 2995 Planarity : 0.003 0.043 3357 Dihedral : 13.249 165.933 2989 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: -1.75 (0.17), residues: 2367 helix: -0.16 (0.18), residues: 835 sheet: -0.89 (0.26), residues: 409 loop : -2.05 (0.17), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 147 HIS 0.004 0.001 HIS A 475 PHE 0.020 0.001 PHE H 120 TYR 0.013 0.001 TYR C 193 ARG 0.004 0.000 ARG D 274 *********************** 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 348 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 ARG cc_start: 0.8043 (ptt180) cc_final: 0.7722 (ptt180) REVERT: A 533 MET cc_start: 0.7396 (mpp) cc_final: 0.6973 (mpp) REVERT: B 271 LEU cc_start: 0.8474 (mt) cc_final: 0.8259 (mt) REVERT: B 309 MET cc_start: 0.8684 (tpp) cc_final: 0.8356 (tpp) REVERT: B 329 TRP cc_start: 0.7791 (m-10) cc_final: 0.7483 (m-10) REVERT: C 90 THR cc_start: 0.7611 (m) cc_final: 0.7360 (m) REVERT: C 126 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6155 (ptmm) REVERT: C 203 ILE cc_start: 0.9438 (mm) cc_final: 0.9151 (mm) REVERT: C 236 LYS cc_start: 0.8823 (tmtt) cc_final: 0.8026 (mmmm) REVERT: C 237 ASP cc_start: 0.9072 (p0) cc_final: 0.8561 (p0) REVERT: C 333 MET cc_start: 0.8533 (mpp) cc_final: 0.7654 (mpp) REVERT: D 297 ASP cc_start: 0.8279 (p0) cc_final: 0.7873 (p0) REVERT: D 352 ASP cc_start: 0.8329 (t0) cc_final: 0.7735 (t0) REVERT: D 395 ASP cc_start: 0.8817 (t0) cc_final: 0.8321 (m-30) REVERT: E 295 ILE cc_start: 0.8505 (mm) cc_final: 0.8295 (mm) REVERT: E 352 ASP cc_start: 0.8488 (t70) cc_final: 0.8284 (t0) REVERT: E 356 LEU cc_start: 0.8224 (tp) cc_final: 0.8006 (tp) REVERT: E 412 MET cc_start: 0.7163 (mmt) cc_final: 0.6819 (mmt) REVERT: E 427 SER cc_start: 0.7918 (m) cc_final: 0.7697 (t) REVERT: H 75 LEU cc_start: 0.8492 (mt) cc_final: 0.8102 (tp) REVERT: H 101 ASN cc_start: 0.7743 (p0) cc_final: 0.7380 (p0) REVERT: H 136 LYS cc_start: 0.7728 (mmmt) cc_final: 0.7356 (pttm) REVERT: H 253 LEU cc_start: 0.8766 (mt) cc_final: 0.8072 (mp) REVERT: H 335 ASN cc_start: 0.8810 (t0) cc_final: 0.8605 (t0) REVERT: H 495 GLU cc_start: 0.8590 (pp20) cc_final: 0.8291 (pp20) REVERT: H 597 ASP cc_start: 0.8561 (p0) cc_final: 0.8145 (p0) REVERT: H 626 ILE cc_start: 0.9458 (pt) cc_final: 0.9177 (tp) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.3044 time to fit residues: 163.7118 Evaluate side-chains 259 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.051 ------------------------------------------------------------------------------- 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: 4.9990 chunk 132 optimal weight: 0.7980 chunk 3 optimal weight: 0.0670 chunk 174 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 chunk 161 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 119 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 475 HIS B 169 GLN B 358 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN H 585 GLN H 615 GLN H 640 HIS H 653 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20045 Z= 0.150 Angle : 0.499 7.200 27151 Z= 0.256 Chirality : 0.042 0.156 2995 Planarity : 0.003 0.041 3357 Dihedral : 12.977 163.973 2989 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.05 % Allowed : 2.23 % Favored : 97.72 % 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: -1.44 (0.17), residues: 2367 helix: 0.22 (0.19), residues: 836 sheet: -0.76 (0.26), residues: 400 loop : -1.95 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 264 HIS 0.010 0.001 HIS C 425 PHE 0.016 0.001 PHE B 378 TYR 0.010 0.001 TYR C 96 ARG 0.005 0.000 ARG D 274 *********************** 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 339 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 MET cc_start: 0.7340 (mpp) cc_final: 0.6971 (mpp) REVERT: B 205 MET cc_start: 0.9152 (tpp) cc_final: 0.8681 (ttm) REVERT: B 207 ASP cc_start: 0.5926 (t0) cc_final: 0.5614 (t70) REVERT: B 309 MET cc_start: 0.8686 (tpp) cc_final: 0.8298 (tpp) REVERT: B 329 TRP cc_start: 0.7837 (m-10) cc_final: 0.7445 (m-10) REVERT: C 90 THR cc_start: 0.7636 (m) cc_final: 0.7356 (m) REVERT: C 126 LYS cc_start: 0.7006 (mmtt) cc_final: 0.6035 (ptmm) REVERT: C 203 ILE cc_start: 0.9458 (mm) cc_final: 0.9186 (mm) REVERT: C 236 LYS cc_start: 0.8829 (tmtt) cc_final: 0.7986 (mmmm) REVERT: C 237 ASP cc_start: 0.9087 (p0) cc_final: 0.8567 (p0) REVERT: C 251 MET cc_start: 0.8027 (mmp) cc_final: 0.7642 (mmp) REVERT: C 333 MET cc_start: 0.8564 (mpp) cc_final: 0.7699 (mpp) REVERT: C 343 GLN cc_start: 0.7938 (pt0) cc_final: 0.7723 (pt0) REVERT: C 404 ARG cc_start: 0.8130 (ptm160) cc_final: 0.7832 (ttt180) REVERT: D 352 ASP cc_start: 0.8324 (t0) cc_final: 0.7743 (t0) REVERT: D 395 ASP cc_start: 0.8795 (t0) cc_final: 0.8291 (m-30) REVERT: E 295 ILE cc_start: 0.8415 (mm) cc_final: 0.8185 (mm) REVERT: E 356 LEU cc_start: 0.8199 (tp) cc_final: 0.7977 (tp) REVERT: E 446 MET cc_start: 0.6907 (tpp) cc_final: 0.6683 (tpp) REVERT: H 75 LEU cc_start: 0.8294 (mt) cc_final: 0.7993 (tp) REVERT: H 101 ASN cc_start: 0.7740 (p0) cc_final: 0.7410 (p0) REVERT: H 155 VAL cc_start: 0.7551 (t) cc_final: 0.7314 (m) REVERT: H 253 LEU cc_start: 0.8792 (mt) cc_final: 0.8299 (mp) REVERT: H 335 ASN cc_start: 0.8785 (t0) cc_final: 0.8565 (t0) REVERT: H 401 GLU cc_start: 0.8596 (tp30) cc_final: 0.8263 (tm-30) REVERT: H 458 GLU cc_start: 0.7955 (pm20) cc_final: 0.7348 (pt0) REVERT: H 495 GLU cc_start: 0.8619 (pp20) cc_final: 0.8416 (pp20) REVERT: H 597 ASP cc_start: 0.8614 (p0) cc_final: 0.8076 (p0) REVERT: H 626 ILE cc_start: 0.9489 (pt) cc_final: 0.9179 (tp) outliers start: 1 outliers final: 0 residues processed: 339 average time/residue: 0.3032 time to fit residues: 158.7093 Evaluate side-chains 252 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.206 ------------------------------------------------------------------------------- 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: 5.9990 chunk 210 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 5.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- 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 475 HIS B 169 GLN B 343 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 ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 558 ASN H 653 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20045 Z= 0.181 Angle : 0.522 8.480 27151 Z= 0.267 Chirality : 0.042 0.151 2995 Planarity : 0.003 0.041 3357 Dihedral : 12.902 164.471 2989 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.67 % 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: -1.30 (0.17), residues: 2367 helix: 0.37 (0.19), residues: 853 sheet: -0.70 (0.26), residues: 400 loop : -1.94 (0.17), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 97 HIS 0.010 0.001 HIS D 425 PHE 0.018 0.001 PHE B 378 TYR 0.010 0.001 TYR C 96 ARG 0.004 0.000 ARG A 439 *********************** 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 329 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 328 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 MET cc_start: 0.7461 (mpp) cc_final: 0.7200 (mpp) REVERT: A 547 TYR cc_start: 0.7036 (t80) cc_final: 0.6776 (t80) REVERT: B 162 MET cc_start: 0.8976 (ttp) cc_final: 0.8562 (tmm) REVERT: B 309 MET cc_start: 0.8716 (tpp) cc_final: 0.8341 (tpp) REVERT: B 329 TRP cc_start: 0.7856 (m-10) cc_final: 0.7439 (m-10) REVERT: B 358 ASN cc_start: 0.7680 (t0) cc_final: 0.7190 (m-40) REVERT: C 90 THR cc_start: 0.7631 (m) cc_final: 0.7335 (m) REVERT: C 126 LYS cc_start: 0.6919 (mmtt) cc_final: 0.5976 (ptmm) REVERT: C 203 ILE cc_start: 0.9477 (mm) cc_final: 0.9207 (mm) REVERT: C 236 LYS cc_start: 0.8904 (tmtt) cc_final: 0.8037 (mmmm) REVERT: C 237 ASP cc_start: 0.9086 (p0) cc_final: 0.8627 (p0) REVERT: C 251 MET cc_start: 0.8046 (mmp) cc_final: 0.7727 (mmp) REVERT: C 333 MET cc_start: 0.8625 (mpp) cc_final: 0.7736 (mpp) REVERT: C 343 GLN cc_start: 0.7958 (pt0) cc_final: 0.7721 (pt0) REVERT: C 404 ARG cc_start: 0.8148 (ptm160) cc_final: 0.7898 (ttt180) REVERT: D 352 ASP cc_start: 0.8352 (t0) cc_final: 0.7732 (t0) REVERT: D 521 CYS cc_start: 0.8652 (t) cc_final: 0.8241 (m) REVERT: E 295 ILE cc_start: 0.8370 (mm) cc_final: 0.8135 (mm) REVERT: E 356 LEU cc_start: 0.8212 (tp) cc_final: 0.7942 (tp) REVERT: H 75 LEU cc_start: 0.8323 (mt) cc_final: 0.7988 (tp) REVERT: H 101 ASN cc_start: 0.7703 (p0) cc_final: 0.7381 (p0) REVERT: H 597 ASP cc_start: 0.8660 (p0) cc_final: 0.8050 (p0) REVERT: H 626 ILE cc_start: 0.9497 (pt) cc_final: 0.9218 (tp) outliers start: 1 outliers final: 0 residues processed: 329 average time/residue: 0.3126 time to fit residues: 157.3605 Evaluate side-chains 244 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.159 ------------------------------------------------------------------------------- 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: 0.9980 chunk 26 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 233 optimal weight: 0.0970 chunk 145 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 107 optimal weight: 0.0870 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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 475 HIS B 169 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 HIS D 343 GLN D 506 GLN ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN H 653 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20045 Z= 0.136 Angle : 0.505 9.185 27151 Z= 0.256 Chirality : 0.042 0.220 2995 Planarity : 0.003 0.087 3357 Dihedral : 12.724 162.244 2989 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.10 % Allowed : 0.94 % Favored : 98.96 % 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: -1.14 (0.17), residues: 2367 helix: 0.55 (0.19), residues: 850 sheet: -0.57 (0.26), residues: 410 loop : -1.90 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 147 HIS 0.004 0.001 HIS B 278 PHE 0.018 0.001 PHE B 378 TYR 0.009 0.001 TYR H 154 ARG 0.006 0.000 ARG E 323 *********************** 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 342 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 340 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.8307 (tpt-90) cc_final: 0.8035 (tpp80) REVERT: A 533 MET cc_start: 0.7447 (mpp) cc_final: 0.7190 (mpp) REVERT: A 539 THR cc_start: 0.7710 (p) cc_final: 0.7430 (p) REVERT: A 543 GLU cc_start: 0.7686 (mp0) cc_final: 0.7464 (mp0) REVERT: A 547 TYR cc_start: 0.7028 (t80) cc_final: 0.6817 (t80) REVERT: B 162 MET cc_start: 0.8844 (ttp) cc_final: 0.8301 (tmm) REVERT: B 309 MET cc_start: 0.8645 (tpp) cc_final: 0.8335 (tpp) REVERT: B 329 TRP cc_start: 0.7792 (m-10) cc_final: 0.7432 (m-10) REVERT: B 358 ASN cc_start: 0.7609 (t0) cc_final: 0.6764 (m-40) REVERT: C 90 THR cc_start: 0.7632 (m) cc_final: 0.7346 (m) REVERT: C 126 LYS cc_start: 0.6869 (mmtt) cc_final: 0.5970 (ptmm) REVERT: C 203 ILE cc_start: 0.9486 (mm) cc_final: 0.9215 (mm) REVERT: C 236 LYS cc_start: 0.8838 (tmtt) cc_final: 0.8001 (mmmm) REVERT: C 237 ASP cc_start: 0.9038 (p0) cc_final: 0.8572 (p0) REVERT: C 333 MET cc_start: 0.8623 (mpp) cc_final: 0.7765 (mpp) REVERT: C 404 ARG cc_start: 0.8150 (ptm160) cc_final: 0.7784 (ttt180) REVERT: D 352 ASP cc_start: 0.8312 (t0) cc_final: 0.7720 (t0) REVERT: D 521 CYS cc_start: 0.8674 (t) cc_final: 0.8208 (m) REVERT: E 295 ILE cc_start: 0.8366 (mm) cc_final: 0.8095 (mm) REVERT: H 75 LEU cc_start: 0.8250 (mt) cc_final: 0.7978 (tp) REVERT: H 176 VAL cc_start: 0.9018 (t) cc_final: 0.8756 (t) REVERT: H 253 LEU cc_start: 0.8804 (mt) cc_final: 0.8505 (mt) REVERT: H 495 GLU cc_start: 0.8465 (pp20) cc_final: 0.7855 (tp30) REVERT: H 597 ASP cc_start: 0.8652 (p0) cc_final: 0.8015 (p0) REVERT: H 626 ILE cc_start: 0.9471 (pt) cc_final: 0.9221 (tp) outliers start: 2 outliers final: 0 residues processed: 341 average time/residue: 0.3184 time to fit residues: 164.0582 Evaluate side-chains 251 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.114 ------------------------------------------------------------------------------- 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: 0.1980 chunk 93 optimal weight: 0.0370 chunk 139 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN C 343 GLN D 343 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN H 423 ASN H 558 ASN H 653 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20045 Z= 0.149 Angle : 0.509 9.568 27151 Z= 0.257 Chirality : 0.042 0.151 2995 Planarity : 0.003 0.040 3357 Dihedral : 12.600 161.837 2989 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.10 % Allowed : 0.55 % Favored : 99.35 % 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: -1.00 (0.17), residues: 2367 helix: 0.66 (0.19), residues: 850 sheet: -0.53 (0.26), residues: 417 loop : -1.81 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 381 HIS 0.003 0.001 HIS B 357 PHE 0.018 0.001 PHE B 378 TYR 0.009 0.001 TYR H 154 ARG 0.005 0.000 ARG B 274 *********************** 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 321 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 319 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.8308 (tpt-90) cc_final: 0.8042 (tpp80) REVERT: A 533 MET cc_start: 0.7429 (mpp) cc_final: 0.7120 (mpp) REVERT: A 547 TYR cc_start: 0.7052 (t80) cc_final: 0.6844 (t80) REVERT: B 162 MET cc_start: 0.8815 (ttp) cc_final: 0.8380 (tmm) REVERT: B 309 MET cc_start: 0.8664 (tpp) cc_final: 0.8326 (tpp) REVERT: B 329 TRP cc_start: 0.7800 (m-10) cc_final: 0.7352 (m-10) REVERT: B 358 ASN cc_start: 0.7526 (t0) cc_final: 0.6940 (m-40) REVERT: C 90 THR cc_start: 0.7649 (m) cc_final: 0.7379 (m) REVERT: C 203 ILE cc_start: 0.9507 (mm) cc_final: 0.9246 (mm) REVERT: C 236 LYS cc_start: 0.8858 (tmtt) cc_final: 0.7985 (mmmm) REVERT: C 237 ASP cc_start: 0.9039 (p0) cc_final: 0.8629 (p0) REVERT: C 333 MET cc_start: 0.8623 (mpp) cc_final: 0.7737 (mpp) REVERT: C 404 ARG cc_start: 0.8163 (ptm160) cc_final: 0.7800 (ttt180) REVERT: D 352 ASP cc_start: 0.8313 (t0) cc_final: 0.7695 (t0) REVERT: D 521 CYS cc_start: 0.8694 (t) cc_final: 0.8195 (m) REVERT: E 295 ILE cc_start: 0.8515 (mm) cc_final: 0.8165 (mm) REVERT: H 75 LEU cc_start: 0.8308 (mt) cc_final: 0.8042 (tp) REVERT: H 253 LEU cc_start: 0.8783 (mt) cc_final: 0.8480 (mt) REVERT: H 495 GLU cc_start: 0.8521 (pp20) cc_final: 0.7913 (tp30) REVERT: H 597 ASP cc_start: 0.8649 (p0) cc_final: 0.7994 (p0) REVERT: H 626 ILE cc_start: 0.9503 (pt) cc_final: 0.9229 (tp) outliers start: 2 outliers final: 0 residues processed: 320 average time/residue: 0.3058 time to fit residues: 150.8639 Evaluate side-chains 240 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.978 ------------------------------------------------------------------------------- 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: 2.9990 chunk 203 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 205 optimal weight: 0.0870 chunk 216 optimal weight: 0.2980 chunk 142 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN ** E 465 HIS ** 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: 0.7931 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20045 Z= 0.140 Angle : 0.511 9.292 27151 Z= 0.256 Chirality : 0.042 0.152 2995 Planarity : 0.003 0.041 3357 Dihedral : 12.465 159.439 2989 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.10 % Allowed : 0.55 % Favored : 99.35 % 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: -0.88 (0.18), residues: 2367 helix: 0.77 (0.19), residues: 842 sheet: -0.45 (0.26), residues: 416 loop : -1.74 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 147 HIS 0.004 0.001 HIS B 357 PHE 0.017 0.001 PHE B 378 TYR 0.009 0.001 TYR H 203 ARG 0.004 0.000 ARG B 274 *********************** 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 317 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 315 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.8315 (tpt-90) cc_final: 0.8051 (tpp80) REVERT: A 462 VAL cc_start: 0.8147 (t) cc_final: 0.7785 (p) REVERT: A 493 ARG cc_start: 0.8579 (ptt180) cc_final: 0.8267 (ptt180) REVERT: A 533 MET cc_start: 0.7388 (mpp) cc_final: 0.7002 (mpp) REVERT: A 547 TYR cc_start: 0.7030 (t80) cc_final: 0.6830 (t80) REVERT: B 162 MET cc_start: 0.8751 (ttp) cc_final: 0.8253 (tmm) REVERT: B 205 MET cc_start: 0.9022 (tpp) cc_final: 0.8353 (ttm) REVERT: B 309 MET cc_start: 0.8637 (tpp) cc_final: 0.8323 (tpp) REVERT: B 329 TRP cc_start: 0.7771 (m-10) cc_final: 0.7376 (m-10) REVERT: B 358 ASN cc_start: 0.7629 (t0) cc_final: 0.6934 (m-40) REVERT: C 90 THR cc_start: 0.7647 (m) cc_final: 0.7390 (m) REVERT: C 126 LYS cc_start: 0.6897 (mmtt) cc_final: 0.6181 (ptmm) REVERT: C 203 ILE cc_start: 0.9512 (mm) cc_final: 0.9255 (mm) REVERT: C 236 LYS cc_start: 0.8630 (tmtt) cc_final: 0.8083 (mmmm) REVERT: C 333 MET cc_start: 0.8634 (mpp) cc_final: 0.7670 (mpp) REVERT: C 404 ARG cc_start: 0.8181 (ptm160) cc_final: 0.7874 (ttt180) REVERT: D 352 ASP cc_start: 0.8297 (t0) cc_final: 0.7732 (t0) REVERT: D 521 CYS cc_start: 0.8695 (t) cc_final: 0.8208 (m) REVERT: E 295 ILE cc_start: 0.8543 (mm) cc_final: 0.7945 (pt) REVERT: H 75 LEU cc_start: 0.8328 (mt) cc_final: 0.8062 (tp) REVERT: H 253 LEU cc_start: 0.8715 (mt) cc_final: 0.8435 (mt) REVERT: H 458 GLU cc_start: 0.8015 (pm20) cc_final: 0.7564 (pt0) REVERT: H 495 GLU cc_start: 0.8480 (pp20) cc_final: 0.7989 (tp30) REVERT: H 597 ASP cc_start: 0.8654 (p0) cc_final: 0.7987 (p0) REVERT: H 626 ILE cc_start: 0.9507 (pt) cc_final: 0.9234 (tp) outliers start: 2 outliers final: 0 residues processed: 316 average time/residue: 0.2955 time to fit residues: 144.7711 Evaluate side-chains 237 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.180 ------------------------------------------------------------------------------- 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: 1.9990 chunk 140 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 241 optimal weight: 3.9990 chunk 221 optimal weight: 0.5980 chunk 191 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 152 optimal weight: 0.0060 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 HIS D 343 GLN E 325 GLN ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 558 ASN H 653 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20045 Z= 0.177 Angle : 0.542 9.621 27151 Z= 0.272 Chirality : 0.042 0.158 2995 Planarity : 0.003 0.042 3357 Dihedral : 12.320 158.464 2989 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.05 % Allowed : 0.10 % Favored : 99.85 % 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: -0.88 (0.18), residues: 2367 helix: 0.74 (0.19), residues: 852 sheet: -0.48 (0.26), residues: 420 loop : -1.72 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 381 HIS 0.006 0.001 HIS E 465 PHE 0.020 0.001 PHE B 378 TYR 0.009 0.001 TYR C 96 ARG 0.004 0.000 ARG B 274 ********************** 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 298 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 297 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.8296 (tpt-90) cc_final: 0.8044 (tpp80) REVERT: A 462 VAL cc_start: 0.8125 (t) cc_final: 0.7833 (p) REVERT: A 493 ARG cc_start: 0.8651 (ptt180) cc_final: 0.8345 (ptt180) REVERT: A 533 MET cc_start: 0.7347 (mpp) cc_final: 0.6952 (mpp) REVERT: B 162 MET cc_start: 0.8854 (ttp) cc_final: 0.8428 (tmm) REVERT: B 309 MET cc_start: 0.8697 (tpp) cc_final: 0.8308 (tpp) REVERT: B 329 TRP cc_start: 0.7786 (m-10) cc_final: 0.7360 (m-10) REVERT: C 90 THR cc_start: 0.7728 (m) cc_final: 0.7442 (m) REVERT: C 126 LYS cc_start: 0.7113 (mmtt) cc_final: 0.6311 (ptmm) REVERT: C 162 MET cc_start: 0.8364 (tmm) cc_final: 0.7830 (tmm) REVERT: C 203 ILE cc_start: 0.9530 (mm) cc_final: 0.9270 (mm) REVERT: C 236 LYS cc_start: 0.8823 (tmtt) cc_final: 0.7919 (mmmm) REVERT: C 237 ASP cc_start: 0.9107 (p0) cc_final: 0.8618 (p0) REVERT: C 316 MET cc_start: 0.8038 (mtt) cc_final: 0.7727 (mtt) REVERT: C 333 MET cc_start: 0.8615 (mpp) cc_final: 0.7493 (mpp) REVERT: C 404 ARG cc_start: 0.8175 (ptm160) cc_final: 0.7901 (ttt180) REVERT: D 352 ASP cc_start: 0.8336 (t0) cc_final: 0.7731 (t0) REVERT: D 521 CYS cc_start: 0.8778 (t) cc_final: 0.8219 (m) REVERT: E 295 ILE cc_start: 0.8608 (mm) cc_final: 0.8251 (mm) REVERT: E 505 ASN cc_start: 0.8292 (t0) cc_final: 0.7802 (t0) REVERT: E 535 TYR cc_start: 0.8119 (t80) cc_final: 0.7546 (t80) REVERT: H 75 LEU cc_start: 0.8410 (mt) cc_final: 0.8087 (tt) REVERT: H 335 ASN cc_start: 0.8689 (t0) cc_final: 0.7623 (p0) REVERT: H 401 GLU cc_start: 0.8590 (tp30) cc_final: 0.8385 (tp30) REVERT: H 495 GLU cc_start: 0.8481 (pp20) cc_final: 0.7964 (tp30) REVERT: H 597 ASP cc_start: 0.8655 (p0) cc_final: 0.7991 (p0) REVERT: H 626 ILE cc_start: 0.9524 (pt) cc_final: 0.9263 (tp) outliers start: 1 outliers final: 0 residues processed: 298 average time/residue: 0.3078 time to fit residues: 142.9438 Evaluate side-chains 238 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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: 1.9990 chunk 58 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 24 optimal weight: 0.0020 chunk 35 optimal weight: 3.9990 chunk 168 optimal weight: 0.0870 overall best weight: 0.9770 ------------------------------------------------------------------------------- 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 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 558 ASN H 653 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.132625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110194 restraints weight = 42547.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111193 restraints weight = 40500.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112140 restraints weight = 32351.576| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20045 Z= 0.185 Angle : 0.545 8.838 27151 Z= 0.273 Chirality : 0.042 0.152 2995 Planarity : 0.003 0.042 3357 Dihedral : 12.205 157.375 2989 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.05 % Allowed : 0.20 % Favored : 99.75 % 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: -0.79 (0.18), residues: 2367 helix: 0.81 (0.19), residues: 851 sheet: -0.43 (0.26), residues: 416 loop : -1.66 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 97 HIS 0.007 0.001 HIS H 653 PHE 0.017 0.001 PHE B 378 TYR 0.010 0.001 TYR C 96 ARG 0.005 0.000 ARG B 504 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4224.28 seconds wall clock time: 76 minutes 58.60 seconds (4618.60 seconds total)