Starting phenix.real_space_refine on Fri Mar 15 11:12:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t55_25695/03_2024/7t55_25695_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t55_25695/03_2024/7t55_25695.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t55_25695/03_2024/7t55_25695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t55_25695/03_2024/7t55_25695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t55_25695/03_2024/7t55_25695_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t55_25695/03_2024/7t55_25695_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= 0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 7382 2.51 5 N 1870 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B GLU 539": "OE1" <-> "OE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 625": "OE1" <-> "OE2" Residue "B GLU 697": "OE1" <-> "OE2" Residue "B GLU 722": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11460 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5581 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 117 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5581 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "D" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 117 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.18, per 1000 atoms: 0.54 Number of scatterers: 11460 At special positions: 0 Unit cell: (106.09, 111.24, 139.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 6 15.00 Mg 2 11.99 O 2140 8.00 N 1870 7.00 C 7382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.59 Conformation dependent library (CDL) restraints added in 2.2 seconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 8 sheets defined 56.6% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 removed outlier: 3.657A pdb=" N CYS A 25 " --> pdb=" O CYS A 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 26 " --> pdb=" O GLY A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 removed outlier: 3.552A pdb=" N MET A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 65 Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.566A pdb=" N CYS A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 131' Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.791A pdb=" N GLY A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 195 removed outlier: 4.151A pdb=" N PHE A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N TYR A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LYS A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'A' and resid 203 through 251 removed outlier: 3.510A pdb=" N ILE A 208 " --> pdb=" O ASN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 263 through 304 removed outlier: 4.602A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 360 removed outlier: 4.939A pdb=" N LYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix removed outlier: 3.502A pdb=" N SER A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 417 removed outlier: 3.563A pdb=" N THR A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 444 removed outlier: 3.755A pdb=" N LEU A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TYR A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Proline residue: A 438 - end of helix Processing helix chain 'A' and resid 446 through 463 removed outlier: 4.086A pdb=" N VAL A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 576 through 580 Processing helix chain 'A' and resid 589 through 599 Processing helix chain 'A' and resid 602 through 605 No H-bonds generated for 'chain 'A' and resid 602 through 605' Processing helix chain 'A' and resid 625 through 639 removed outlier: 3.595A pdb=" N LYS A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 667 Processing helix chain 'A' and resid 704 through 710 Processing helix chain 'A' and resid 713 through 721 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'B' and resid 21 through 33 removed outlier: 3.677A pdb=" N CYS B 25 " --> pdb=" O CYS B 21 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 26 " --> pdb=" O GLY B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 46 removed outlier: 3.536A pdb=" N MET B 45 " --> pdb=" O LYS B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 65 Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 125 through 131 removed outlier: 3.796A pdb=" N ILE B 131 " --> pdb=" O ASP B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.901A pdb=" N GLY B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 162 " --> pdb=" O PHE B 158 " (cutoff:3.500A) Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 167 through 196 removed outlier: 3.538A pdb=" N LEU B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ILE B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 250 removed outlier: 3.515A pdb=" N LEU B 230 " --> pdb=" O TYR B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 264 through 304 removed outlier: 4.366A pdb=" N ARG B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N MET B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 361 removed outlier: 4.579A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix removed outlier: 3.525A pdb=" N ALA B 342 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N THR B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 417 removed outlier: 3.568A pdb=" N SER B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 444 removed outlier: 4.565A pdb=" N ALA B 433 " --> pdb=" O ASN B 429 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Proline residue: B 438 - end of helix Processing helix chain 'B' and resid 446 through 464 removed outlier: 3.863A pdb=" N VAL B 454 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 471 No H-bonds generated for 'chain 'B' and resid 468 through 471' Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 555 through 561 Processing helix chain 'B' and resid 576 through 579 No H-bonds generated for 'chain 'B' and resid 576 through 579' Processing helix chain 'B' and resid 589 through 598 Processing helix chain 'B' and resid 602 through 604 No H-bonds generated for 'chain 'B' and resid 602 through 604' Processing helix chain 'B' and resid 625 through 638 Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.720A pdb=" N ASN B 659 " --> pdb=" O SER B 655 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 685 No H-bonds generated for 'chain 'B' and resid 683 through 685' Processing helix chain 'B' and resid 704 through 709 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'D' and resid 15 through 20 Processing sheet with id= A, first strand: chain 'A' and resid 67 through 72 Processing sheet with id= B, first strand: chain 'A' and resid 87 through 91 removed outlier: 3.744A pdb=" N VAL A 102 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR A 112 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE A 106 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 506 through 509 removed outlier: 3.860A pdb=" N ARG A 489 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP A 542 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 689 through 693 removed outlier: 6.057A pdb=" N VAL A 674 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE A 517 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A 676 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLY A 519 " --> pdb=" O ILE A 676 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA A 678 " --> pdb=" O GLY A 519 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 70 through 72 Processing sheet with id= F, first strand: chain 'B' and resid 87 through 93 removed outlier: 4.047A pdb=" N LEU B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 102 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 112 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE B 106 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 507 through 509 Processing sheet with id= H, first strand: chain 'B' and resid 697 through 702 removed outlier: 7.687A pdb=" N LEU B 692 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER B 701 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE B 690 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL B 674 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ILE B 517 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE B 676 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLY B 519 " --> pdb=" O ILE B 676 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 678 " --> pdb=" O GLY B 519 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3620 1.34 - 1.46: 2119 1.46 - 1.58: 5783 1.58 - 1.70: 10 1.70 - 1.82: 104 Bond restraints: 11636 Sorted by residual: bond pdb=" O5' ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 1.579 1.604 -0.025 1.10e-02 8.26e+03 5.03e+00 bond pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 1.579 1.603 -0.024 1.10e-02 8.26e+03 4.62e+00 bond pdb=" O2B ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 1.529 1.490 0.039 2.20e-02 2.07e+03 3.20e+00 bond pdb=" O2A ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 1.529 1.491 0.038 2.20e-02 2.07e+03 2.95e+00 bond pdb=" O2B ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 1.529 1.491 0.038 2.20e-02 2.07e+03 2.92e+00 ... (remaining 11631 not shown) Histogram of bond angle deviations from ideal: 98.99 - 105.99: 155 105.99 - 113.00: 6479 113.00 - 120.01: 3964 120.01 - 127.02: 5030 127.02 - 134.03: 68 Bond angle restraints: 15696 Sorted by residual: angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 131.78 8.09 1.00e+00 1.00e+00 6.54e+01 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 131.82 8.05 1.00e+00 1.00e+00 6.49e+01 angle pdb=" C LYS A 640 " pdb=" N PRO A 641 " pdb=" CA PRO A 641 " ideal model delta sigma weight residual 119.85 126.17 -6.32 1.01e+00 9.80e-01 3.91e+01 angle pdb=" N ASP A 126 " pdb=" CA ASP A 126 " pdb=" C ASP A 126 " ideal model delta sigma weight residual 111.28 117.58 -6.30 1.09e+00 8.42e-01 3.34e+01 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 132.18 4.65 1.00e+00 1.00e+00 2.16e+01 ... (remaining 15691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 6377 17.04 - 34.07: 542 34.07 - 51.11: 120 51.11 - 68.14: 19 68.14 - 85.18: 10 Dihedral angle restraints: 7068 sinusoidal: 2846 harmonic: 4222 Sorted by residual: dihedral pdb=" CA LEU A 97 " pdb=" C LEU A 97 " pdb=" N ALA A 98 " pdb=" CA ALA A 98 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER B 130 " pdb=" C SER B 130 " pdb=" N ILE B 131 " pdb=" CA ILE B 131 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ILE B 480 " pdb=" C ILE B 480 " pdb=" N SER B 481 " pdb=" CA SER B 481 " ideal model delta harmonic sigma weight residual -180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 7065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1493 0.052 - 0.103: 296 0.103 - 0.155: 54 0.155 - 0.207: 6 0.207 - 0.259: 3 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CG LEU B 308 " pdb=" CB LEU B 308 " pdb=" CD1 LEU B 308 " pdb=" CD2 LEU B 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE B 643 " pdb=" CA ILE B 643 " pdb=" CG1 ILE B 643 " pdb=" CG2 ILE B 643 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ASP A 127 " pdb=" N ASP A 127 " pdb=" C ASP A 127 " pdb=" CB ASP A 127 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1849 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 498 " 0.238 9.50e-02 1.11e+02 1.07e-01 7.79e+00 pdb=" NE ARG B 498 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 498 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 498 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 498 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 389 " -0.021 2.00e-02 2.50e+03 1.54e-02 4.72e+00 pdb=" CG TYR B 389 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 389 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 389 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 389 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 389 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 389 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 389 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 640 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 641 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 641 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 641 " 0.024 5.00e-02 4.00e+02 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 21 2.37 - 3.01: 6618 3.01 - 3.64: 17448 3.64 - 4.27: 24088 4.27 - 4.90: 39777 Nonbonded interactions: 87952 Sorted by model distance: nonbonded pdb=" O1B ATP B 801 " pdb="MG MG B 802 " model vdw 1.743 2.170 nonbonded pdb=" O2G ATP B 801 " pdb="MG MG B 802 " model vdw 2.029 2.170 nonbonded pdb=" O VAL B 11 " pdb=" OH TYR B 104 " model vdw 2.203 2.440 nonbonded pdb=" OE1 GLN A 336 " pdb=" OG SER A 381 " model vdw 2.237 2.440 nonbonded pdb=" CE2 TYR A 495 " pdb=" N1 ATP A 801 " model vdw 2.242 3.420 ... (remaining 87947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.290 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 34.660 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 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 : 0.004 0.041 11636 Z= 0.238 Angle : 0.710 10.856 15696 Z= 0.424 Chirality : 0.044 0.259 1852 Planarity : 0.004 0.107 1944 Dihedral : 13.628 85.179 4356 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.05 % Rotamer: Outliers : 0.24 % Allowed : 0.88 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.26 (0.22), residues: 1456 helix: 1.17 (0.18), residues: 830 sheet: -0.15 (0.42), residues: 142 loop : -1.45 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 132 HIS 0.006 0.001 HIS B 207 PHE 0.016 0.001 PHE B 270 TYR 0.037 0.001 TYR B 389 ARG 0.016 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ILE cc_start: 0.7639 (tt) cc_final: 0.6613 (tt) REVERT: A 350 GLU cc_start: 0.7199 (tt0) cc_final: 0.5883 (tt0) REVERT: B 25 CYS cc_start: 0.8223 (m) cc_final: 0.7548 (p) REVERT: B 88 ILE cc_start: 0.8220 (mt) cc_final: 0.7786 (mt) REVERT: B 598 MET cc_start: 0.8289 (ptm) cc_final: 0.8059 (ttt) REVERT: D 19 MET cc_start: 0.7801 (mmm) cc_final: 0.7514 (mmm) outliers start: 3 outliers final: 0 residues processed: 193 average time/residue: 0.2340 time to fit residues: 65.0358 Evaluate side-chains 96 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 130 optimal weight: 0.0170 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 60 HIS A 579 ASN A 629 GLN B 534 ASN ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11636 Z= 0.164 Angle : 0.537 6.961 15696 Z= 0.283 Chirality : 0.041 0.159 1852 Planarity : 0.003 0.035 1944 Dihedral : 6.896 77.603 1620 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.24 % Allowed : 3.37 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.81 (0.22), residues: 1456 helix: 1.75 (0.19), residues: 808 sheet: 0.27 (0.43), residues: 140 loop : -1.41 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.004 0.001 HIS B 207 PHE 0.015 0.001 PHE A 493 TYR 0.011 0.001 TYR B 33 ARG 0.006 0.000 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.7313 (ttm) cc_final: 0.5194 (mtt) REVERT: A 528 LEU cc_start: 0.8036 (pt) cc_final: 0.7544 (tp) REVERT: B 25 CYS cc_start: 0.8230 (m) cc_final: 0.7584 (p) outliers start: 3 outliers final: 0 residues processed: 140 average time/residue: 0.2273 time to fit residues: 47.7447 Evaluate side-chains 83 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11636 Z= 0.255 Angle : 0.553 8.151 15696 Z= 0.294 Chirality : 0.040 0.170 1852 Planarity : 0.003 0.037 1944 Dihedral : 6.793 88.952 1620 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.01 (0.23), residues: 1456 helix: 1.85 (0.19), residues: 828 sheet: 0.15 (0.43), residues: 140 loop : -1.27 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 718 HIS 0.003 0.001 HIS B 249 PHE 0.016 0.002 PHE B 493 TYR 0.010 0.001 TYR B 33 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LEU cc_start: 0.8366 (pp) cc_final: 0.7638 (pp) REVERT: A 289 ILE cc_start: 0.7725 (mt) cc_final: 0.6596 (mt) REVERT: A 528 LEU cc_start: 0.7873 (pt) cc_final: 0.7215 (tp) REVERT: B 25 CYS cc_start: 0.8212 (m) cc_final: 0.7534 (p) REVERT: B 88 ILE cc_start: 0.8093 (mt) cc_final: 0.7681 (mt) REVERT: B 155 MET cc_start: 0.8237 (mmm) cc_final: 0.7958 (mmm) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.2187 time to fit residues: 39.3249 Evaluate side-chains 87 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN B 534 ASN ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11636 Z= 0.217 Angle : 0.536 7.188 15696 Z= 0.284 Chirality : 0.040 0.159 1852 Planarity : 0.003 0.037 1944 Dihedral : 6.626 87.953 1620 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.23), residues: 1456 helix: 1.90 (0.19), residues: 828 sheet: 0.24 (0.43), residues: 140 loop : -1.11 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 718 HIS 0.003 0.001 HIS B 660 PHE 0.015 0.001 PHE B 493 TYR 0.011 0.001 TYR B 33 ARG 0.003 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8009 (ttm) cc_final: 0.7758 (ttm) REVERT: A 528 LEU cc_start: 0.7841 (pt) cc_final: 0.7167 (tp) REVERT: B 568 ASP cc_start: 0.8635 (t0) cc_final: 0.8402 (t0) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.2097 time to fit residues: 35.9563 Evaluate side-chains 80 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN B 259 ASN ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11636 Z= 0.204 Angle : 0.535 7.870 15696 Z= 0.280 Chirality : 0.040 0.155 1852 Planarity : 0.003 0.033 1944 Dihedral : 6.485 88.490 1620 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.08 % Allowed : 2.65 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.32 (0.23), residues: 1456 helix: 2.08 (0.19), residues: 816 sheet: 0.30 (0.43), residues: 140 loop : -1.03 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 718 HIS 0.003 0.001 HIS A 249 PHE 0.013 0.001 PHE B 493 TYR 0.011 0.001 TYR B 33 ARG 0.004 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8110 (ttm) cc_final: 0.7083 (ttp) REVERT: A 285 LEU cc_start: 0.8455 (pp) cc_final: 0.7814 (pp) REVERT: A 288 MET cc_start: 0.7369 (ppp) cc_final: 0.7120 (ppp) REVERT: A 289 ILE cc_start: 0.7589 (mt) cc_final: 0.6883 (mt) REVERT: A 528 LEU cc_start: 0.7945 (pt) cc_final: 0.7307 (tp) REVERT: B 25 CYS cc_start: 0.7958 (m) cc_final: 0.7661 (p) REVERT: B 88 ILE cc_start: 0.8053 (mt) cc_final: 0.7788 (mt) REVERT: B 236 MET cc_start: 0.7859 (tpp) cc_final: 0.7545 (tpp) REVERT: B 568 ASP cc_start: 0.8662 (t0) cc_final: 0.8417 (t0) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.2118 time to fit residues: 35.2141 Evaluate side-chains 80 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 7.9990 chunk 125 optimal weight: 0.0670 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 534 ASN B 259 ASN B 534 ASN ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11636 Z= 0.161 Angle : 0.515 7.336 15696 Z= 0.270 Chirality : 0.040 0.200 1852 Planarity : 0.002 0.034 1944 Dihedral : 6.337 88.076 1620 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.35 (0.23), residues: 1456 helix: 2.04 (0.19), residues: 840 sheet: 0.39 (0.42), residues: 140 loop : -1.09 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 409 HIS 0.003 0.001 HIS B 207 PHE 0.039 0.001 PHE B 173 TYR 0.011 0.001 TYR B 33 ARG 0.002 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.8184 (ppp) cc_final: 0.7872 (ppp) REVERT: A 528 LEU cc_start: 0.7922 (pt) cc_final: 0.7321 (tp) REVERT: B 25 CYS cc_start: 0.7859 (m) cc_final: 0.7569 (p) REVERT: B 88 ILE cc_start: 0.8040 (mt) cc_final: 0.7777 (mt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2058 time to fit residues: 34.4314 Evaluate side-chains 82 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 138 optimal weight: 0.0470 chunk 86 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 64 optimal weight: 0.0010 chunk 85 optimal weight: 3.9990 overall best weight: 1.5288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 534 ASN ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11636 Z= 0.169 Angle : 0.525 8.436 15696 Z= 0.271 Chirality : 0.040 0.184 1852 Planarity : 0.002 0.034 1944 Dihedral : 6.252 88.468 1620 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.40 (0.23), residues: 1456 helix: 2.13 (0.19), residues: 838 sheet: 0.37 (0.41), residues: 140 loop : -1.13 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 718 HIS 0.003 0.001 HIS B 207 PHE 0.011 0.001 PHE A 258 TYR 0.011 0.001 TYR B 33 ARG 0.002 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.7629 (ttp) cc_final: 0.6639 (tmm) REVERT: A 285 LEU cc_start: 0.8444 (pp) cc_final: 0.7787 (pp) REVERT: A 289 ILE cc_start: 0.7690 (mt) cc_final: 0.6614 (mt) REVERT: A 528 LEU cc_start: 0.8004 (pt) cc_final: 0.7348 (tp) REVERT: B 25 CYS cc_start: 0.7888 (m) cc_final: 0.7573 (p) REVERT: B 88 ILE cc_start: 0.8062 (mt) cc_final: 0.7831 (mt) REVERT: B 379 MET cc_start: 0.6797 (mmp) cc_final: 0.6164 (mmp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2094 time to fit residues: 35.4487 Evaluate side-chains 86 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 109 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 534 ASN ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11636 Z= 0.135 Angle : 0.521 7.715 15696 Z= 0.266 Chirality : 0.040 0.159 1852 Planarity : 0.002 0.034 1944 Dihedral : 6.174 89.267 1620 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.46 (0.23), residues: 1456 helix: 2.19 (0.19), residues: 838 sheet: 0.46 (0.42), residues: 140 loop : -1.15 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.004 0.001 HIS B 207 PHE 0.014 0.001 PHE B 535 TYR 0.009 0.001 TYR A 225 ARG 0.005 0.000 ARG B 680 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.8162 (ppp) cc_final: 0.7770 (ppp) REVERT: A 236 MET cc_start: 0.7558 (ttp) cc_final: 0.6150 (mtt) REVERT: A 288 MET cc_start: 0.7169 (ppp) cc_final: 0.6916 (ppp) REVERT: A 528 LEU cc_start: 0.7967 (pt) cc_final: 0.7330 (tp) REVERT: B 25 CYS cc_start: 0.7809 (m) cc_final: 0.7578 (p) REVERT: B 37 MET cc_start: 0.8333 (tpp) cc_final: 0.8060 (mmm) REVERT: B 568 ASP cc_start: 0.8610 (t0) cc_final: 0.8343 (t0) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2061 time to fit residues: 35.6112 Evaluate side-chains 85 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11636 Z= 0.139 Angle : 0.538 12.383 15696 Z= 0.275 Chirality : 0.040 0.168 1852 Planarity : 0.002 0.035 1944 Dihedral : 6.089 89.754 1620 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.49 (0.23), residues: 1456 helix: 2.20 (0.19), residues: 838 sheet: 0.50 (0.42), residues: 140 loop : -1.11 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 132 HIS 0.004 0.001 HIS B 207 PHE 0.015 0.001 PHE B 535 TYR 0.009 0.001 TYR B 179 ARG 0.003 0.000 ARG B 680 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.8118 (ppp) cc_final: 0.7729 (ppp) REVERT: A 288 MET cc_start: 0.7178 (ppp) cc_final: 0.6525 (ppp) REVERT: A 528 LEU cc_start: 0.7938 (pt) cc_final: 0.7319 (tp) REVERT: B 25 CYS cc_start: 0.7818 (m) cc_final: 0.7575 (p) REVERT: B 37 MET cc_start: 0.8413 (tpp) cc_final: 0.8192 (mmm) REVERT: B 236 MET cc_start: 0.7917 (tpp) cc_final: 0.7695 (tmm) REVERT: B 568 ASP cc_start: 0.8646 (t0) cc_final: 0.8358 (t0) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2059 time to fit residues: 35.3374 Evaluate side-chains 81 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 0.0070 chunk 95 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 114 optimal weight: 0.0670 chunk 11 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 0.0020 chunk 90 optimal weight: 5.9990 overall best weight: 1.3746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11636 Z= 0.158 Angle : 0.528 8.199 15696 Z= 0.271 Chirality : 0.039 0.172 1852 Planarity : 0.002 0.034 1944 Dihedral : 6.069 89.238 1620 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.53 (0.23), residues: 1456 helix: 2.22 (0.19), residues: 836 sheet: 0.46 (0.43), residues: 140 loop : -1.04 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 132 HIS 0.003 0.001 HIS B 207 PHE 0.015 0.001 PHE B 535 TYR 0.009 0.001 TYR B 33 ARG 0.010 0.000 ARG A 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.8135 (ppp) cc_final: 0.7758 (ppp) REVERT: A 528 LEU cc_start: 0.8023 (pt) cc_final: 0.7359 (tp) REVERT: B 25 CYS cc_start: 0.7863 (m) cc_final: 0.7600 (p) REVERT: B 379 MET cc_start: 0.6801 (tpt) cc_final: 0.6278 (tpp) REVERT: B 568 ASP cc_start: 0.8686 (t0) cc_final: 0.8391 (t0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1972 time to fit residues: 33.0364 Evaluate side-chains 83 residues out of total 1252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.046123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.036391 restraints weight = 91104.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.037429 restraints weight = 58120.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.038173 restraints weight = 42113.699| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11636 Z= 0.189 Angle : 0.545 7.733 15696 Z= 0.282 Chirality : 0.039 0.168 1852 Planarity : 0.003 0.041 1944 Dihedral : 6.115 89.283 1620 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.50 (0.23), residues: 1456 helix: 2.18 (0.19), residues: 838 sheet: 0.42 (0.42), residues: 140 loop : -1.01 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 718 HIS 0.003 0.001 HIS B 207 PHE 0.015 0.001 PHE B 326 TYR 0.011 0.001 TYR B 33 ARG 0.008 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2023.87 seconds wall clock time: 37 minutes 42.95 seconds (2262.95 seconds total)