Starting phenix.real_space_refine on Thu Mar 14 08:11:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf7_34715/03_2024/8hf7_34715.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf7_34715/03_2024/8hf7_34715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf7_34715/03_2024/8hf7_34715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf7_34715/03_2024/8hf7_34715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf7_34715/03_2024/8hf7_34715.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf7_34715/03_2024/8hf7_34715.pdb" } resolution = 3.8 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 5784 2.51 5 N 1478 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 8978 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4424 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 550} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4424 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 550} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 5.19, per 1000 atoms: 0.58 Number of scatterers: 8978 At special positions: 0 Unit cell: (80.652, 81.51, 140.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1688 8.00 N 1478 7.00 C 5784 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: 3.68 Conformation dependent library (CDL) restraints added in 1.9 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 7 sheets defined 63.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 158 through 163 removed outlier: 4.082A pdb=" N VAL A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 158 through 163' Processing helix chain 'A' and resid 167 through 188 removed outlier: 3.749A pdb=" N VAL A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 250 removed outlier: 4.358A pdb=" N ILE A 239 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 250 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.902A pdb=" N PHE A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 304 removed outlier: 3.836A pdb=" N THR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 313 through 325 removed outlier: 4.013A pdb=" N ILE A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 353 removed outlier: 4.426A pdb=" N GLU A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ARG A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.769A pdb=" N ILE A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 416 removed outlier: 4.446A pdb=" N LYS A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 444 removed outlier: 4.376A pdb=" N VAL A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 444 through 459 Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 528 through 532 removed outlier: 3.622A pdb=" N VAL A 531 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 532 " --> pdb=" O MET A 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 528 through 532' Processing helix chain 'A' and resid 553 through 558 removed outlier: 4.235A pdb=" N GLN A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.728A pdb=" N ASN A 577 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 573 through 579' Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.655A pdb=" N ILE A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 634 removed outlier: 3.707A pdb=" N ILE A 630 " --> pdb=" O GLN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.631A pdb=" N ILE A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 682 removed outlier: 3.865A pdb=" N GLU A 682 " --> pdb=" O THR A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 708 removed outlier: 3.939A pdb=" N GLN A 707 " --> pdb=" O LEU A 704 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY A 708 " --> pdb=" O LEU A 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 704 through 708' Processing helix chain 'A' and resid 710 through 717 removed outlier: 3.529A pdb=" N LEU A 714 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 163 removed outlier: 4.042A pdb=" N VAL B 162 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 through 163' Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.560A pdb=" N LEU B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR B 179 " --> pdb=" O THR B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 202 through 250 removed outlier: 4.478A pdb=" N ILE B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.829A pdb=" N PHE B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 278 through 304 removed outlier: 3.820A pdb=" N THR B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 313 through 325 removed outlier: 4.036A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 353 removed outlier: 4.131A pdb=" N GLU B 330 " --> pdb=" O MET B 326 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ARG B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASP B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.721A pdb=" N ILE B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 416 removed outlier: 4.469A pdb=" N LYS B 369 " --> pdb=" O GLN B 365 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 444 removed outlier: 4.391A pdb=" N VAL B 432 " --> pdb=" O ASN B 428 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR B 433 " --> pdb=" O THR B 429 " (cutoff:3.500A) Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.874A pdb=" N VAL B 464 " --> pdb=" O GLU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 527 Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.889A pdb=" N VAL B 531 " --> pdb=" O LYS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 558 removed outlier: 4.228A pdb=" N GLN B 558 " --> pdb=" O LYS B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 removed outlier: 3.514A pdb=" N LEU B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 574 through 579' Processing helix chain 'B' and resid 587 through 596 removed outlier: 3.741A pdb=" N ILE B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 634 removed outlier: 3.602A pdb=" N ILE B 630 " --> pdb=" O GLN B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 665 removed outlier: 3.586A pdb=" N ARG B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 682 removed outlier: 3.857A pdb=" N GLU B 682 " --> pdb=" O THR B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 708 removed outlier: 3.927A pdb=" N GLN B 707 " --> pdb=" O LEU B 704 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 708 " --> pdb=" O LEU B 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 708' Processing helix chain 'B' and resid 710 through 717 removed outlier: 3.529A pdb=" N LEU B 714 " --> pdb=" O PHE B 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 503 removed outlier: 5.706A pdb=" N VAL A 489 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE A 486 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER A 542 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLN A 488 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU A 540 " --> pdb=" O GLN A 488 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 671 through 674 removed outlier: 3.720A pdb=" N PHE A 673 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS A 512 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 688 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 514 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LEU A 690 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL A 687 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU A 698 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 689 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 696 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 560 through 562 Processing sheet with id=AA4, first strand: chain 'B' and resid 500 through 503 removed outlier: 5.705A pdb=" N VAL B 489 " --> pdb=" O ASP B 502 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE B 486 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N SER B 542 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLN B 488 " --> pdb=" O GLU B 540 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLU B 540 " --> pdb=" O GLN B 488 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 671 through 674 removed outlier: 3.784A pdb=" N PHE B 673 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS B 512 " --> pdb=" O LYS B 686 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL B 688 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA B 514 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU B 690 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL B 687 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLU B 698 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL B 689 " --> pdb=" O VAL B 696 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 696 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 560 through 562 Processing sheet with id=AA7, first strand: chain 'B' and resid 572 through 573 removed outlier: 3.844A pdb=" N GLY B 572 " --> pdb=" O THR B 616 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1338 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: 2.49 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1536 1.32 - 1.45: 2192 1.45 - 1.57: 5322 1.57 - 1.69: 0 1.69 - 1.82: 56 Bond restraints: 9106 Sorted by residual: bond pdb=" CA UNK D 4 " pdb=" C UNK D 4 " ideal model delta sigma weight residual 1.525 1.433 0.092 2.10e-02 2.27e+03 1.92e+01 bond pdb=" CA GLN B 612 " pdb=" C GLN B 612 " ideal model delta sigma weight residual 1.531 1.482 0.049 1.12e-02 7.97e+03 1.89e+01 bond pdb=" CA UNK D 10 " pdb=" C UNK D 10 " ideal model delta sigma weight residual 1.525 1.435 0.090 2.10e-02 2.27e+03 1.84e+01 bond pdb=" CA THR B 613 " pdb=" C THR B 613 " ideal model delta sigma weight residual 1.522 1.473 0.049 1.31e-02 5.83e+03 1.38e+01 bond pdb=" CA UNK C 10 " pdb=" C UNK C 10 " ideal model delta sigma weight residual 1.525 1.452 0.073 2.10e-02 2.27e+03 1.21e+01 ... (remaining 9101 not shown) Histogram of bond angle deviations from ideal: 95.17 - 103.01: 61 103.01 - 110.84: 2779 110.84 - 118.68: 4547 118.68 - 126.52: 4897 126.52 - 134.36: 58 Bond angle restraints: 12342 Sorted by residual: angle pdb=" N ASN B 610 " pdb=" CA ASN B 610 " pdb=" C ASN B 610 " ideal model delta sigma weight residual 111.87 101.49 10.38 1.41e+00 5.03e-01 5.42e+01 angle pdb=" N MET A 607 " pdb=" CA MET A 607 " pdb=" C MET A 607 " ideal model delta sigma weight residual 109.24 99.38 9.86 1.39e+00 5.18e-01 5.03e+01 angle pdb=" C UNK D 12 " pdb=" CA UNK D 12 " pdb=" CB UNK D 12 " ideal model delta sigma weight residual 110.08 121.43 -11.35 1.90e+00 2.77e-01 3.57e+01 angle pdb=" C SER B 501 " pdb=" N ASP B 502 " pdb=" CA ASP B 502 " ideal model delta sigma weight residual 122.46 129.65 -7.19 1.41e+00 5.03e-01 2.60e+01 angle pdb=" C SER A 501 " pdb=" N ASP A 502 " pdb=" CA ASP A 502 " ideal model delta sigma weight residual 122.46 129.62 -7.16 1.41e+00 5.03e-01 2.58e+01 ... (remaining 12337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4991 17.72 - 35.43: 436 35.43 - 53.15: 74 53.15 - 70.86: 15 70.86 - 88.58: 6 Dihedral angle restraints: 5522 sinusoidal: 2152 harmonic: 3370 Sorted by residual: dihedral pdb=" C UNK D 12 " pdb=" N UNK D 12 " pdb=" CA UNK D 12 " pdb=" CB UNK D 12 " ideal model delta harmonic sigma weight residual -122.60 -139.73 17.13 0 2.50e+00 1.60e-01 4.69e+01 dihedral pdb=" N UNK D 12 " pdb=" C UNK D 12 " pdb=" CA UNK D 12 " pdb=" CB UNK D 12 " ideal model delta harmonic sigma weight residual 122.80 137.07 -14.27 0 2.50e+00 1.60e-01 3.26e+01 dihedral pdb=" CA THR B 195 " pdb=" C THR B 195 " pdb=" N TYR B 196 " pdb=" CA TYR B 196 " ideal model delta harmonic sigma weight residual -180.00 -151.96 -28.04 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 5519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1406 0.122 - 0.244: 94 0.244 - 0.366: 11 0.366 - 0.489: 2 0.489 - 0.611: 1 Chirality restraints: 1514 Sorted by residual: chirality pdb=" CA UNK D 12 " pdb=" N UNK D 12 " pdb=" C UNK D 12 " pdb=" CB UNK D 12 " both_signs ideal model delta sigma weight residual False 2.52 1.91 0.61 2.00e-01 2.50e+01 9.33e+00 chirality pdb=" CB VAL A 414 " pdb=" CA VAL A 414 " pdb=" CG1 VAL A 414 " pdb=" CG2 VAL A 414 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CB VAL B 414 " pdb=" CA VAL B 414 " pdb=" CG1 VAL B 414 " pdb=" CG2 VAL B 414 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.72e+00 ... (remaining 1511 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 166 " 0.019 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C GLY A 166 " -0.063 2.00e-02 2.50e+03 pdb=" O GLY A 166 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU A 167 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 197 " 0.056 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO A 198 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 198 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 198 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA UNK D 5 " 0.015 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C UNK D 5 " -0.055 2.00e-02 2.50e+03 pdb=" O UNK D 5 " 0.021 2.00e-02 2.50e+03 pdb=" N UNK D 6 " 0.019 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2573 2.82 - 3.34: 8523 3.34 - 3.86: 14897 3.86 - 4.38: 15743 4.38 - 4.90: 26484 Nonbonded interactions: 68220 Sorted by model distance: nonbonded pdb=" CB ASN B 561 " pdb=" CD2 LEU B 643 " model vdw 2.294 3.860 nonbonded pdb=" CB ASN A 561 " pdb=" CD2 LEU A 643 " model vdw 2.309 3.860 nonbonded pdb=" O LEU A 279 " pdb=" OG1 THR A 282 " model vdw 2.325 2.440 nonbonded pdb=" O LEU B 279 " pdb=" OG1 THR B 282 " model vdw 2.327 2.440 nonbonded pdb=" OG SER A 519 " pdb=" O SER B 651 " model vdw 2.331 2.440 ... (remaining 68215 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: 0.680 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: 3.940 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.890 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 0.092 9106 Z= 0.402 Angle : 1.342 12.566 12342 Z= 0.674 Chirality : 0.069 0.611 1514 Planarity : 0.007 0.087 1544 Dihedral : 14.022 88.580 3346 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.88 % Favored : 93.49 % Rotamer: Outliers : 0.61 % Allowed : 1.92 % Favored : 97.47 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % 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: -3.03 (0.21), residues: 1122 helix: -1.77 (0.17), residues: 634 sheet: -1.21 (0.59), residues: 48 loop : -2.28 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 408 HIS 0.002 0.001 HIS A 676 PHE 0.041 0.002 PHE A 257 TYR 0.023 0.002 TYR A 559 ARG 0.004 0.001 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 172 time to evaluate : 1.132 Fit side-chains REVERT: A 192 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 563 LEU cc_start: 0.8801 (tp) cc_final: 0.8442 (tt) REVERT: A 662 ASP cc_start: 0.9026 (m-30) cc_final: 0.8657 (m-30) REVERT: B 431 LEU cc_start: 0.8845 (tp) cc_final: 0.8636 (mt) REVERT: B 529 MET cc_start: 0.9375 (pmm) cc_final: 0.9061 (pmm) REVERT: B 563 LEU cc_start: 0.8368 (tt) cc_final: 0.8112 (tt) outliers start: 6 outliers final: 3 residues processed: 177 average time/residue: 104.1364 time to fit residues: 18445.7449 Evaluate side-chains 126 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 613 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 30.0000 chunk 54 optimal weight: 30.0000 chunk 66 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 GLN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 GLN ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9106 Z= 0.364 Angle : 0.830 10.415 12342 Z= 0.431 Chirality : 0.046 0.241 1514 Planarity : 0.005 0.038 1544 Dihedral : 6.268 55.565 1242 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.26 % Favored : 94.30 % Rotamer: Outliers : 3.24 % Allowed : 12.55 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.04 (0.24), residues: 1122 helix: 0.05 (0.21), residues: 630 sheet: -1.09 (0.77), residues: 34 loop : -1.66 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 408 HIS 0.004 0.001 HIS A 490 PHE 0.018 0.002 PHE A 257 TYR 0.027 0.003 TYR B 559 ARG 0.004 0.001 ARG B 593 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9070 (mm) REVERT: A 561 ASN cc_start: 0.8932 (t0) cc_final: 0.8395 (t0) REVERT: B 300 LEU cc_start: 0.9292 (mm) cc_final: 0.9030 (mm) REVERT: B 373 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8713 (mp0) REVERT: B 529 MET cc_start: 0.9490 (pmm) cc_final: 0.9213 (pmm) outliers start: 32 outliers final: 25 residues processed: 137 average time/residue: 0.1592 time to fit residues: 33.0285 Evaluate side-chains 130 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 662 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.0970 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9106 Z= 0.249 Angle : 0.697 12.053 12342 Z= 0.354 Chirality : 0.042 0.211 1514 Planarity : 0.004 0.033 1544 Dihedral : 5.718 56.252 1240 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.79 % Favored : 93.76 % Rotamer: Outliers : 3.85 % Allowed : 18.52 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.54 (0.25), residues: 1122 helix: 0.56 (0.21), residues: 640 sheet: -1.28 (0.80), residues: 34 loop : -1.60 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 408 HIS 0.006 0.001 HIS B 490 PHE 0.013 0.002 PHE A 257 TYR 0.025 0.002 TYR A 568 ARG 0.003 0.000 ARG A 659 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 120 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9131 (mm) REVERT: A 409 MET cc_start: 0.7850 (tpp) cc_final: 0.7624 (tpt) REVERT: A 563 LEU cc_start: 0.8789 (tp) cc_final: 0.8577 (tt) REVERT: A 662 ASP cc_start: 0.9137 (m-30) cc_final: 0.8706 (p0) REVERT: B 300 LEU cc_start: 0.9345 (mm) cc_final: 0.9095 (mm) REVERT: B 490 HIS cc_start: 0.9155 (OUTLIER) cc_final: 0.8917 (m-70) outliers start: 38 outliers final: 29 residues processed: 143 average time/residue: 0.1595 time to fit residues: 34.3556 Evaluate side-chains 134 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 490 HIS Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 662 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 0.0270 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 54 optimal weight: 30.0000 chunk 98 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9106 Z= 0.226 Angle : 0.686 11.877 12342 Z= 0.342 Chirality : 0.042 0.189 1514 Planarity : 0.003 0.035 1544 Dihedral : 5.567 56.230 1240 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.70 % Favored : 93.85 % Rotamer: Outliers : 4.86 % Allowed : 20.85 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.21 (0.25), residues: 1122 helix: 0.80 (0.21), residues: 630 sheet: -1.32 (0.80), residues: 34 loop : -1.36 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 408 HIS 0.004 0.001 HIS B 490 PHE 0.011 0.001 PHE B 257 TYR 0.023 0.001 TYR A 568 ARG 0.002 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 106 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.4817 (t80) cc_final: 0.3956 (m-10) REVERT: A 300 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9119 (mm) REVERT: A 409 MET cc_start: 0.7759 (tpp) cc_final: 0.7439 (tpt) REVERT: A 563 LEU cc_start: 0.8758 (tp) cc_final: 0.8508 (tt) REVERT: A 662 ASP cc_start: 0.9115 (m-30) cc_final: 0.8680 (p0) REVERT: A 679 THR cc_start: 0.6504 (OUTLIER) cc_final: 0.6162 (t) REVERT: B 300 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9142 (mm) REVERT: B 679 THR cc_start: 0.6468 (OUTLIER) cc_final: 0.6130 (t) outliers start: 48 outliers final: 31 residues processed: 137 average time/residue: 0.1497 time to fit residues: 31.6246 Evaluate side-chains 137 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 102 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN B 182 ASN B 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9106 Z= 0.157 Angle : 0.658 12.528 12342 Z= 0.312 Chirality : 0.040 0.187 1514 Planarity : 0.003 0.033 1544 Dihedral : 5.117 52.951 1240 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.97 % Favored : 93.67 % Rotamer: Outliers : 3.14 % Allowed : 23.99 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.05 (0.26), residues: 1122 helix: 1.13 (0.22), residues: 642 sheet: -1.21 (0.80), residues: 34 loop : -1.51 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 408 HIS 0.002 0.001 HIS B 676 PHE 0.011 0.001 PHE B 257 TYR 0.013 0.001 TYR A 568 ARG 0.002 0.000 ARG B 593 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.4471 (t80) cc_final: 0.3727 (m-80) REVERT: A 254 MET cc_start: 0.6304 (tmm) cc_final: 0.5939 (tmm) REVERT: A 300 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9063 (mm) REVERT: A 409 MET cc_start: 0.7913 (tpp) cc_final: 0.7653 (tpt) REVERT: A 463 LEU cc_start: 0.8880 (tp) cc_final: 0.8469 (pp) REVERT: A 561 ASN cc_start: 0.8771 (t0) cc_final: 0.8359 (t0) REVERT: A 662 ASP cc_start: 0.9098 (m-30) cc_final: 0.8716 (p0) REVERT: A 679 THR cc_start: 0.6380 (OUTLIER) cc_final: 0.6048 (t) REVERT: B 300 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9086 (mm) REVERT: B 561 ASN cc_start: 0.8888 (t0) cc_final: 0.8470 (t0) outliers start: 31 outliers final: 18 residues processed: 158 average time/residue: 0.1591 time to fit residues: 38.0143 Evaluate side-chains 128 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 644 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 6.9990 chunk 99 optimal weight: 0.0870 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 0.0070 chunk 36 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN B 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9106 Z= 0.150 Angle : 0.652 13.045 12342 Z= 0.307 Chirality : 0.040 0.210 1514 Planarity : 0.003 0.030 1544 Dihedral : 4.777 47.631 1240 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.53 % Favored : 94.12 % Rotamer: Outliers : 2.23 % Allowed : 26.21 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.26), residues: 1122 helix: 1.28 (0.22), residues: 640 sheet: -1.05 (0.80), residues: 34 loop : -1.42 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 408 HIS 0.002 0.000 HIS A 676 PHE 0.017 0.001 PHE B 256 TYR 0.030 0.001 TYR B 559 ARG 0.002 0.000 ARG B 593 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.4437 (t80) cc_final: 0.3726 (m-80) REVERT: A 463 LEU cc_start: 0.8857 (tp) cc_final: 0.8493 (pp) REVERT: A 559 TYR cc_start: 0.8027 (p90) cc_final: 0.7076 (p90) REVERT: A 561 ASN cc_start: 0.8722 (t0) cc_final: 0.8447 (t0) REVERT: A 662 ASP cc_start: 0.9067 (m-30) cc_final: 0.8729 (p0) REVERT: A 679 THR cc_start: 0.6313 (OUTLIER) cc_final: 0.5991 (t) REVERT: B 300 LEU cc_start: 0.9367 (mm) cc_final: 0.9071 (mm) REVERT: B 561 ASN cc_start: 0.8928 (t0) cc_final: 0.8485 (t0) outliers start: 22 outliers final: 17 residues processed: 135 average time/residue: 0.1615 time to fit residues: 32.6381 Evaluate side-chains 121 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 644 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9106 Z= 0.198 Angle : 0.688 13.351 12342 Z= 0.330 Chirality : 0.042 0.266 1514 Planarity : 0.003 0.037 1544 Dihedral : 4.737 43.694 1238 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.97 % Favored : 93.67 % Rotamer: Outliers : 2.73 % Allowed : 26.11 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.41 (0.26), residues: 1122 helix: 1.36 (0.22), residues: 630 sheet: -1.10 (0.80), residues: 34 loop : -1.18 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 408 HIS 0.002 0.001 HIS B 490 PHE 0.010 0.001 PHE A 533 TYR 0.026 0.001 TYR B 559 ARG 0.002 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.128 Fit side-chains REVERT: A 187 TYR cc_start: 0.4521 (t80) cc_final: 0.3831 (m-80) REVERT: A 463 LEU cc_start: 0.8895 (tp) cc_final: 0.8539 (pp) REVERT: A 559 TYR cc_start: 0.8097 (p90) cc_final: 0.7149 (p90) REVERT: A 561 ASN cc_start: 0.8844 (t0) cc_final: 0.8566 (t0) REVERT: A 662 ASP cc_start: 0.9117 (m-30) cc_final: 0.8743 (p0) REVERT: A 679 THR cc_start: 0.6354 (OUTLIER) cc_final: 0.6018 (t) REVERT: B 300 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9175 (mm) REVERT: B 561 ASN cc_start: 0.9032 (t0) cc_final: 0.8614 (t0) REVERT: B 679 THR cc_start: 0.6299 (OUTLIER) cc_final: 0.5958 (t) outliers start: 27 outliers final: 18 residues processed: 126 average time/residue: 0.1590 time to fit residues: 30.6304 Evaluate side-chains 124 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 33 optimal weight: 0.0040 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 86 optimal weight: 0.4980 chunk 99 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 overall best weight: 2.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9106 Z= 0.199 Angle : 0.707 13.637 12342 Z= 0.336 Chirality : 0.042 0.258 1514 Planarity : 0.003 0.039 1544 Dihedral : 4.769 40.747 1237 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.15 % Favored : 93.49 % Rotamer: Outliers : 3.24 % Allowed : 26.01 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.32 (0.26), residues: 1122 helix: 1.28 (0.21), residues: 632 sheet: -1.15 (0.80), residues: 34 loop : -1.22 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 408 HIS 0.002 0.000 HIS B 490 PHE 0.008 0.001 PHE A 533 TYR 0.031 0.001 TYR B 188 ARG 0.003 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.4538 (t80) cc_final: 0.3916 (m-80) REVERT: A 559 TYR cc_start: 0.8082 (p90) cc_final: 0.7145 (p90) REVERT: A 561 ASN cc_start: 0.8887 (t0) cc_final: 0.8585 (t0) REVERT: A 662 ASP cc_start: 0.9135 (m-30) cc_final: 0.8755 (p0) REVERT: A 679 THR cc_start: 0.6304 (OUTLIER) cc_final: 0.5960 (t) REVERT: B 300 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9168 (mm) REVERT: B 561 ASN cc_start: 0.9044 (t0) cc_final: 0.8650 (t0) REVERT: B 679 THR cc_start: 0.6280 (OUTLIER) cc_final: 0.5935 (t) outliers start: 32 outliers final: 22 residues processed: 129 average time/residue: 0.1579 time to fit residues: 31.0745 Evaluate side-chains 129 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9106 Z= 0.205 Angle : 0.717 13.843 12342 Z= 0.341 Chirality : 0.042 0.292 1514 Planarity : 0.003 0.034 1544 Dihedral : 4.765 36.099 1237 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.24 % Favored : 93.40 % Rotamer: Outliers : 2.94 % Allowed : 25.91 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.41 (0.26), residues: 1122 helix: 1.33 (0.22), residues: 622 sheet: -1.37 (0.77), residues: 34 loop : -1.05 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 408 HIS 0.002 0.001 HIS B 490 PHE 0.010 0.001 PHE A 256 TYR 0.027 0.001 TYR B 559 ARG 0.002 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 0.985 Fit side-chains REVERT: A 187 TYR cc_start: 0.4562 (t80) cc_final: 0.3971 (m-80) REVERT: A 463 LEU cc_start: 0.8991 (tp) cc_final: 0.8652 (pp) REVERT: A 559 TYR cc_start: 0.8193 (p90) cc_final: 0.7832 (p90) REVERT: A 561 ASN cc_start: 0.8879 (t0) cc_final: 0.8604 (t0) REVERT: A 662 ASP cc_start: 0.9134 (m-30) cc_final: 0.8754 (p0) REVERT: A 679 THR cc_start: 0.6252 (OUTLIER) cc_final: 0.5897 (t) REVERT: B 300 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9210 (mm) REVERT: B 561 ASN cc_start: 0.9077 (t0) cc_final: 0.8859 (t0) REVERT: B 679 THR cc_start: 0.6147 (OUTLIER) cc_final: 0.5780 (t) outliers start: 29 outliers final: 24 residues processed: 123 average time/residue: 0.1586 time to fit residues: 29.9477 Evaluate side-chains 125 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.0980 chunk 75 optimal weight: 8.9990 chunk 113 optimal weight: 30.0000 chunk 104 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9106 Z= 0.252 Angle : 0.756 13.749 12342 Z= 0.366 Chirality : 0.043 0.290 1514 Planarity : 0.003 0.036 1544 Dihedral : 5.016 35.556 1237 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.15 % Favored : 93.49 % Rotamer: Outliers : 2.94 % Allowed : 26.21 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.22 (0.25), residues: 1122 helix: 1.17 (0.21), residues: 616 sheet: -1.59 (0.74), residues: 34 loop : -1.09 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 408 HIS 0.003 0.001 HIS B 490 PHE 0.017 0.002 PHE B 533 TYR 0.045 0.002 TYR B 188 ARG 0.002 0.000 ARG A 497 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.4655 (t80) cc_final: 0.4143 (m-80) REVERT: A 463 LEU cc_start: 0.9004 (tp) cc_final: 0.8644 (pp) REVERT: A 559 TYR cc_start: 0.8243 (p90) cc_final: 0.7884 (p90) REVERT: A 561 ASN cc_start: 0.8967 (t0) cc_final: 0.8656 (t0) REVERT: A 662 ASP cc_start: 0.9122 (m-30) cc_final: 0.8784 (p0) REVERT: A 679 THR cc_start: 0.6317 (OUTLIER) cc_final: 0.5947 (t) REVERT: B 561 ASN cc_start: 0.9119 (t0) cc_final: 0.8916 (t0) REVERT: B 679 THR cc_start: 0.6161 (OUTLIER) cc_final: 0.5777 (t) outliers start: 29 outliers final: 27 residues processed: 124 average time/residue: 0.1674 time to fit residues: 31.1166 Evaluate side-chains 129 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** 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 = 0.3999 r_free = 0.3999 target = 0.102405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.080263 restraints weight = 39376.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.082541 restraints weight = 22090.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.084013 restraints weight = 14810.914| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9106 Z= 0.179 Angle : 0.711 13.767 12342 Z= 0.336 Chirality : 0.042 0.264 1514 Planarity : 0.003 0.034 1544 Dihedral : 4.797 34.503 1237 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.24 % Favored : 93.40 % Rotamer: Outliers : 2.43 % Allowed : 27.13 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.33 (0.26), residues: 1122 helix: 1.30 (0.21), residues: 644 sheet: -1.46 (0.76), residues: 34 loop : -1.26 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 408 HIS 0.002 0.001 HIS B 676 PHE 0.013 0.001 PHE A 256 TYR 0.034 0.001 TYR B 188 ARG 0.008 0.000 ARG A 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1635.25 seconds wall clock time: 337 minutes 13.67 seconds (20233.67 seconds total)