Starting phenix.real_space_refine on Fri Dec 8 19:06:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf7_34715/12_2023/8hf7_34715.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf7_34715/12_2023/8hf7_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_34715/12_2023/8hf7_34715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf7_34715/12_2023/8hf7_34715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf7_34715/12_2023/8hf7_34715.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf7_34715/12_2023/8hf7_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-1.21rc1-5172/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: 3.62 Conformation dependent library (CDL) restraints added in 1.7 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: 0.92 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: 2.28 Time building geometry restraints manager: 3.91 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: 1.130 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: 3.960 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.640 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.450 ------------------------------------------------------------------------------- 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 : 0.979 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 177 average time/residue: 0.1711 time to fit residues: 44.6696 Evaluate side-chains 123 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0840 time to fit residues: 1.9174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 0.3980 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 54 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9106 Z= 0.258 Angle : 0.752 9.570 12342 Z= 0.379 Chirality : 0.043 0.220 1514 Planarity : 0.004 0.043 1544 Dihedral : 5.356 29.201 1236 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.72 % Favored : 94.92 % Rotamer: Outliers : 2.23 % Allowed : 13.06 % Favored : 84.72 % 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: -1.01 (0.24), residues: 1122 helix: 0.17 (0.21), residues: 644 sheet: -0.99 (0.76), residues: 34 loop : -1.86 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 408 HIS 0.002 0.001 HIS A 490 PHE 0.016 0.002 PHE B 257 TYR 0.027 0.002 TYR B 188 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 150 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 1.005 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 139 average time/residue: 0.1554 time to fit residues: 32.7042 Evaluate side-chains 131 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0807 time to fit residues: 3.7004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.7525 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9106 Z= 0.160 Angle : 0.656 9.006 12342 Z= 0.319 Chirality : 0.041 0.194 1514 Planarity : 0.003 0.031 1544 Dihedral : 4.896 32.414 1236 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.44 % Favored : 94.21 % Rotamer: Outliers : 0.81 % Allowed : 17.51 % Favored : 81.68 % 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: -0.37 (0.25), residues: 1122 helix: 0.76 (0.22), residues: 644 sheet: -1.14 (0.75), residues: 34 loop : -1.67 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 408 HIS 0.002 0.001 HIS A 676 PHE 0.012 0.001 PHE A 257 TYR 0.030 0.001 TYR B 188 ARG 0.002 0.000 ARG B 593 *********************** 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 138 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 1.089 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 136 average time/residue: 0.1651 time to fit residues: 33.6716 Evaluate side-chains 111 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0841 time to fit residues: 1.9372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 53 optimal weight: 0.0000 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 110 optimal weight: 40.0000 chunk 54 optimal weight: 30.0000 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9106 Z= 0.143 Angle : 0.643 14.039 12342 Z= 0.305 Chirality : 0.041 0.200 1514 Planarity : 0.003 0.029 1544 Dihedral : 4.556 32.114 1236 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.99 % Favored : 94.65 % Rotamer: Outliers : 1.21 % Allowed : 21.05 % Favored : 77.73 % 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: -0.01 (0.26), residues: 1122 helix: 1.07 (0.22), residues: 644 sheet: -1.10 (0.75), residues: 34 loop : -1.55 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 408 HIS 0.002 0.000 HIS A 676 PHE 0.012 0.001 PHE B 257 TYR 0.025 0.001 TYR A 559 ARG 0.002 0.000 ARG B 593 *********************** 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 147 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.117 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 146 average time/residue: 0.1673 time to fit residues: 37.4429 Evaluate side-chains 117 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1091 time to fit residues: 2.3902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** B 273 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9106 Z= 0.199 Angle : 0.697 12.855 12342 Z= 0.336 Chirality : 0.042 0.186 1514 Planarity : 0.003 0.032 1544 Dihedral : 4.648 33.210 1236 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.15 % Favored : 93.49 % Rotamer: Outliers : 1.72 % Allowed : 23.08 % Favored : 75.20 % 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: -0.03 (0.25), residues: 1122 helix: 1.06 (0.21), residues: 644 sheet: -1.12 (0.78), residues: 34 loop : -1.56 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 408 HIS 0.002 0.001 HIS A 490 PHE 0.010 0.001 PHE A 382 TYR 0.025 0.001 TYR A 559 ARG 0.002 0.000 ARG A 497 *********************** 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 130 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.148 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 121 average time/residue: 0.1688 time to fit residues: 30.9483 Evaluate side-chains 116 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0856 time to fit residues: 3.3251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.0170 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 40.0000 chunk 91 optimal weight: 0.0870 chunk 51 optimal weight: 0.3980 chunk 9 optimal weight: 0.0060 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.3012 ------------------------------------------------------------------------------- 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 273 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9106 Z= 0.146 Angle : 0.679 12.995 12342 Z= 0.315 Chirality : 0.041 0.228 1514 Planarity : 0.003 0.028 1544 Dihedral : 4.422 32.686 1236 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.35 % Favored : 94.30 % Rotamer: Outliers : 1.42 % Allowed : 22.67 % Favored : 75.91 % 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: 0.18 (0.26), residues: 1122 helix: 1.27 (0.22), residues: 640 sheet: -1.02 (0.79), residues: 34 loop : -1.51 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 408 HIS 0.002 0.000 HIS B 676 PHE 0.011 0.001 PHE A 256 TYR 0.024 0.001 TYR A 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 138 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 135 average time/residue: 0.1762 time to fit residues: 36.1906 Evaluate side-chains 114 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0836 time to fit residues: 2.5553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 40.0000 chunk 61 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 182 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3487 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= 0.211 Angle : 0.713 13.542 12342 Z= 0.343 Chirality : 0.042 0.247 1514 Planarity : 0.003 0.033 1544 Dihedral : 4.610 33.259 1236 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.70 % Favored : 93.94 % Rotamer: Outliers : 1.01 % Allowed : 25.71 % Favored : 73.28 % 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: 0.28 (0.26), residues: 1122 helix: 1.24 (0.22), residues: 632 sheet: -1.06 (0.80), residues: 34 loop : -1.23 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 408 HIS 0.003 0.001 HIS A 490 PHE 0.010 0.001 PHE A 382 TYR 0.024 0.001 TYR A 568 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 121 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.108 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 117 average time/residue: 0.1701 time to fit residues: 30.3887 Evaluate side-chains 106 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0860 time to fit residues: 2.1627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 86 optimal weight: 0.1980 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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 182 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9106 Z= 0.236 Angle : 0.746 13.030 12342 Z= 0.361 Chirality : 0.043 0.206 1514 Planarity : 0.003 0.033 1544 Dihedral : 4.791 35.326 1236 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.88 % Favored : 93.76 % Rotamer: Outliers : 1.32 % Allowed : 26.11 % Favored : 72.57 % 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: 0.09 (0.25), residues: 1122 helix: 1.07 (0.21), residues: 632 sheet: -1.17 (0.81), residues: 34 loop : -1.28 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 408 HIS 0.002 0.001 HIS A 676 PHE 0.009 0.001 PHE B 434 TYR 0.026 0.002 TYR A 568 ARG 0.008 0.000 ARG B 659 *********************** 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 114 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.110 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 111 average time/residue: 0.1741 time to fit residues: 29.3003 Evaluate side-chains 106 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0802 time to fit residues: 2.5859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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: 0.7611 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9106 Z= 0.220 Angle : 0.744 12.720 12342 Z= 0.353 Chirality : 0.043 0.191 1514 Planarity : 0.003 0.030 1544 Dihedral : 4.742 34.052 1236 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.60 % Favored : 93.05 % Rotamer: Outliers : 0.40 % Allowed : 26.52 % Favored : 73.08 % 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: 0.12 (0.25), residues: 1122 helix: 1.11 (0.21), residues: 618 sheet: -1.16 (0.81), residues: 34 loop : -1.21 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 408 HIS 0.002 0.001 HIS B 490 PHE 0.010 0.001 PHE B 256 TYR 0.025 0.001 TYR A 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 105 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.129 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 105 average time/residue: 0.1839 time to fit residues: 29.5614 Evaluate side-chains 102 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0835 time to fit residues: 1.7807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 8.9990 chunk 113 optimal weight: 30.0000 chunk 104 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 overall best weight: 2.4184 ------------------------------------------------------------------------------- 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: 0.7599 moved from start: 0.4020 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= 0.204 Angle : 0.745 13.223 12342 Z= 0.351 Chirality : 0.043 0.190 1514 Planarity : 0.003 0.032 1544 Dihedral : 4.690 33.784 1236 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.06 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 27.13 % Favored : 72.87 % 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: 0.19 (0.25), residues: 1122 helix: 1.19 (0.21), residues: 620 sheet: -1.21 (0.80), residues: 34 loop : -1.23 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 408 HIS 0.002 0.001 HIS B 490 PHE 0.011 0.001 PHE A 256 TYR 0.026 0.001 TYR A 568 ARG 0.002 0.000 ARG A 627 ********************** 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 103 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1722 time to fit residues: 26.9477 Evaluate side-chains 100 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 11 optimal weight: 0.0030 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 0.0770 overall best weight: 1.2152 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.103702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.080560 restraints weight = 39140.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.082820 restraints weight = 22281.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.084244 restraints weight = 15129.315| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9106 Z= 0.170 Angle : 0.726 13.184 12342 Z= 0.335 Chirality : 0.042 0.187 1514 Planarity : 0.003 0.031 1544 Dihedral : 4.491 33.185 1236 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.51 % Favored : 93.14 % Rotamer: Outliers : 0.30 % Allowed : 27.02 % Favored : 72.67 % 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: 0.25 (0.25), residues: 1122 helix: 1.37 (0.22), residues: 622 sheet: -1.21 (0.62), residues: 54 loop : -1.42 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 408 HIS 0.002 0.001 HIS A 490 PHE 0.012 0.001 PHE A 256 TYR 0.024 0.001 TYR A 559 ARG 0.002 0.000 ARG B 683 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1679.60 seconds wall clock time: 31 minutes 42.41 seconds (1902.41 seconds total)