Starting phenix.real_space_refine on Thu Feb 15 20:46:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai5_11791/02_2024/7ai5_11791_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai5_11791/02_2024/7ai5_11791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai5_11791/02_2024/7ai5_11791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai5_11791/02_2024/7ai5_11791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai5_11791/02_2024/7ai5_11791_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai5_11791/02_2024/7ai5_11791_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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: 5 Type Number sf(0) Gaussians P 50 5.49 5 S 58 5.16 5 C 8258 2.51 5 N 2382 2.21 5 O 2628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A TYR 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 693": "OD1" <-> "OD2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 693": "OD1" <-> "OD2" Residue "B GLU 694": "OE1" <-> "OE2" Residue "B ASP 703": "OD1" <-> "OD2" Residue "B PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13376 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6206 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 35, 'TRANS': 752} Chain breaks: 1 Chain: "B" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6206 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 35, 'TRANS': 752} Chain breaks: 1 Chain: "C" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 457 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 445 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.52, per 1000 atoms: 0.56 Number of scatterers: 13376 At special positions: 0 Unit cell: (127.53, 128.7, 115.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 50 15.00 O 2628 8.00 N 2382 7.00 C 8258 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: 5.43 Conformation dependent library (CDL) restraints added in 2.2 seconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 15 sheets defined 45.0% alpha, 11.5% beta 22 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 6.03 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 73 through 85 removed outlier: 5.312A pdb=" N GLU A 77 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 85 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 187 through 190 No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 231 through 248 removed outlier: 3.812A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 318 through 333 removed outlier: 4.693A pdb=" N ASP A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 Proline residue: A 340 - end of helix removed outlier: 3.927A pdb=" N GLN A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 362 through 384 removed outlier: 3.657A pdb=" N ARG A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 376 - end of helix removed outlier: 3.796A pdb=" N THR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 431 through 458 removed outlier: 3.899A pdb=" N LEU A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N THR A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 564 removed outlier: 3.848A pdb=" N PHE A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Proline residue: A 537 - end of helix removed outlier: 4.924A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA A 541 " --> pdb=" O PRO A 537 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 590 No H-bonds generated for 'chain 'A' and resid 588 through 590' Processing helix chain 'A' and resid 622 through 635 removed outlier: 3.848A pdb=" N THR A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 683 removed outlier: 3.730A pdb=" N THR A 675 " --> pdb=" O MET A 671 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 676 " --> pdb=" O VAL A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 717 removed outlier: 4.407A pdb=" N ALA A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 713 " --> pdb=" O TRP A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 738 No H-bonds generated for 'chain 'A' and resid 735 through 738' Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 783 through 799 Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 73 through 85 removed outlier: 5.266A pdb=" N GLU B 77 " --> pdb=" O HIS B 74 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 85 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 231 through 248 removed outlier: 3.822A pdb=" N ALA B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.590A pdb=" N ASN B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 318 through 331 Processing helix chain 'B' and resid 335 through 345 Proline residue: B 340 - end of helix removed outlier: 3.948A pdb=" N GLN B 344 " --> pdb=" O PRO B 340 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 362 through 384 removed outlier: 3.664A pdb=" N ARG B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 376 - end of helix removed outlier: 3.806A pdb=" N THR B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 401 through 410 Processing helix chain 'B' and resid 431 through 458 removed outlier: 3.955A pdb=" N LEU B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 440 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 443 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASP B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR B 446 " --> pdb=" O GLY B 442 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 565 removed outlier: 3.847A pdb=" N PHE B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) Proline residue: B 537 - end of helix removed outlier: 4.816A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ALA B 541 " --> pdb=" O PRO B 537 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 590 No H-bonds generated for 'chain 'B' and resid 588 through 590' Processing helix chain 'B' and resid 622 through 634 removed outlier: 3.659A pdb=" N THR B 627 " --> pdb=" O TYR B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 683 removed outlier: 3.725A pdb=" N THR B 675 " --> pdb=" O MET B 671 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 676 " --> pdb=" O VAL B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 717 removed outlier: 3.850A pdb=" N ALA B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 713 " --> pdb=" O TRP B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 738 removed outlier: 3.661A pdb=" N LEU B 735 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Proline residue: B 736 - end of helix No H-bonds generated for 'chain 'B' and resid 732 through 738' Processing helix chain 'B' and resid 771 through 775 Processing helix chain 'B' and resid 783 through 799 Processing sheet with id= A, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.310A pdb=" N ILE A 66 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 71 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 31 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE A 40 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU A 29 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 32 " --> pdb=" O CYS A 93 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLN A 95 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU A 94 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL A 110 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.630A pdb=" N LEU A 178 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ARG A 199 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A 180 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA A 134 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ALA A 181 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ILE A 136 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 135 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 464 through 468 removed outlier: 3.641A pdb=" N GLY A 466 " --> pdb=" O TYR A 474 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE A 502 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ARG A 491 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 579 through 581 removed outlier: 3.969A pdb=" N LYS A 644 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 609 through 614 removed outlier: 3.737A pdb=" N ASP A 748 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER A 761 " --> pdb=" O ASP A 748 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 652 through 656 removed outlier: 3.864A pdb=" N ARG A 656 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 750 through 752 removed outlier: 3.512A pdb=" N HIS A 752 " --> pdb=" O THR A 755 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 755 " --> pdb=" O HIS A 752 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.273A pdb=" N GLU B 94 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL B 110 " --> pdb=" O GLU B 94 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 56 through 58 removed outlier: 3.909A pdb=" N ILE B 66 " --> pdb=" O ARG B 58 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 196 through 199 removed outlier: 6.619A pdb=" N LEU B 178 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ARG B 199 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR B 180 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA B 134 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N ALA B 181 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ILE B 136 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 135 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP B 137 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 464 through 468 removed outlier: 3.649A pdb=" N GLY B 466 " --> pdb=" O TYR B 474 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE B 502 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ARG B 491 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 579 through 581 removed outlier: 3.959A pdb=" N LYS B 644 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 609 through 614 removed outlier: 3.742A pdb=" N ASP B 748 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER B 761 " --> pdb=" O ASP B 748 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 652 through 657 removed outlier: 3.567A pdb=" N ARG B 656 " --> pdb=" O LEU B 691 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 750 through 752 removed outlier: 3.546A pdb=" N HIS B 752 " --> pdb=" O THR B 755 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 755 " --> pdb=" O HIS B 752 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 5.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2168 1.30 - 1.44: 3618 1.44 - 1.58: 7714 1.58 - 1.72: 96 1.72 - 1.86: 104 Bond restraints: 13700 Sorted by residual: bond pdb=" C ILE A 650 " pdb=" O ILE A 650 " ideal model delta sigma weight residual 1.236 1.317 -0.080 1.04e-02 9.25e+03 5.99e+01 bond pdb=" C ILE A 636 " pdb=" O ILE A 636 " ideal model delta sigma weight residual 1.242 1.309 -0.067 1.13e-02 7.83e+03 3.55e+01 bond pdb=" C THR A 685 " pdb=" O THR A 685 " ideal model delta sigma weight residual 1.238 1.177 0.061 1.06e-02 8.90e+03 3.26e+01 bond pdb=" C PRO A 175 " pdb=" O PRO A 175 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.30e-02 5.92e+03 2.87e+01 bond pdb=" C GLY A 780 " pdb=" O GLY A 780 " ideal model delta sigma weight residual 1.232 1.283 -0.051 1.03e-02 9.43e+03 2.49e+01 ... (remaining 13695 not shown) Histogram of bond angle deviations from ideal: 96.62 - 104.25: 353 104.25 - 111.87: 5856 111.87 - 119.50: 7037 119.50 - 127.13: 5304 127.13 - 134.76: 196 Bond angle restraints: 18746 Sorted by residual: angle pdb=" PB ATP B 901 " pdb=" O3B ATP B 901 " pdb=" PG ATP B 901 " ideal model delta sigma weight residual 139.87 131.11 8.76 1.00e+00 1.00e+00 7.67e+01 angle pdb=" C PRO A 615 " pdb=" CA PRO A 615 " pdb=" CB PRO A 615 " ideal model delta sigma weight residual 110.98 99.55 11.43 1.31e+00 5.83e-01 7.61e+01 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 131.37 8.50 1.00e+00 1.00e+00 7.23e+01 angle pdb=" CA PHE A 155 " pdb=" CB PHE A 155 " pdb=" CG PHE A 155 " ideal model delta sigma weight residual 113.80 121.58 -7.78 1.00e+00 1.00e+00 6.05e+01 angle pdb=" N SER A 621 " pdb=" CA SER A 621 " pdb=" C SER A 621 " ideal model delta sigma weight residual 111.14 119.34 -8.20 1.08e+00 8.57e-01 5.76e+01 ... (remaining 18741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7149 17.99 - 35.97: 713 35.97 - 53.96: 336 53.96 - 71.95: 78 71.95 - 89.93: 22 Dihedral angle restraints: 8298 sinusoidal: 3722 harmonic: 4576 Sorted by residual: dihedral pdb=" C THR A 273 " pdb=" N THR A 273 " pdb=" CA THR A 273 " pdb=" CB THR A 273 " ideal model delta harmonic sigma weight residual -122.00 -109.90 -12.10 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" C PRO A 615 " pdb=" N PRO A 615 " pdb=" CA PRO A 615 " pdb=" CB PRO A 615 " ideal model delta harmonic sigma weight residual -120.70 -108.69 -12.01 0 2.50e+00 1.60e-01 2.31e+01 dihedral pdb=" C ASN B 593 " pdb=" N ASN B 593 " pdb=" CA ASN B 593 " pdb=" CB ASN B 593 " ideal model delta harmonic sigma weight residual -122.60 -111.92 -10.68 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 8295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1228 0.088 - 0.177: 731 0.177 - 0.265: 139 0.265 - 0.353: 21 0.353 - 0.442: 3 Chirality restraints: 2122 Sorted by residual: chirality pdb=" CB VAL A 640 " pdb=" CA VAL A 640 " pdb=" CG1 VAL A 640 " pdb=" CG2 VAL A 640 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CA ALA A 766 " pdb=" N ALA A 766 " pdb=" C ALA A 766 " pdb=" CB ALA A 766 " both_signs ideal model delta sigma weight residual False 2.48 2.87 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA VAL B 657 " pdb=" N VAL B 657 " pdb=" C VAL B 657 " pdb=" CB VAL B 657 " both_signs ideal model delta sigma weight residual False 2.44 2.81 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 2119 not shown) Planarity restraints: 2288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 635 " 0.021 2.00e-02 2.50e+03 3.60e-02 2.59e+01 pdb=" CG TYR A 635 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 635 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 635 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR A 635 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR A 635 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 635 " 0.041 2.00e-02 2.50e+03 pdb=" OH TYR A 635 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 132 " 0.022 2.00e-02 2.50e+03 4.59e-02 2.10e+01 pdb=" C LEU A 132 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU A 132 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU A 133 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 309 " -0.020 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C ARG A 309 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG A 309 " -0.027 2.00e-02 2.50e+03 pdb=" N TRP A 310 " -0.025 2.00e-02 2.50e+03 ... (remaining 2285 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 5580 2.96 - 3.44: 13355 3.44 - 3.93: 23039 3.93 - 4.41: 26104 4.41 - 4.90: 40778 Nonbonded interactions: 108856 Sorted by model distance: nonbonded pdb=" N ASN B 616 " pdb=" O ASN B 616 " model vdw 2.472 2.496 nonbonded pdb=" OD1 ASP B 296 " pdb=" OG1 THR B 298 " model vdw 2.479 2.440 nonbonded pdb=" O ASP B 98 " pdb=" OG1 THR B 101 " model vdw 2.484 2.440 nonbonded pdb=" O LYS A 245 " pdb=" N ARG A 249 " model vdw 2.506 2.520 nonbonded pdb=" N GLU A 731 " pdb=" OE1 GLU A 731 " model vdw 2.511 2.520 ... (remaining 108851 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' } 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: 1.030 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: 3.650 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 40.770 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 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 : 0.014 0.080 13700 Z= 0.921 Angle : 1.846 11.431 18746 Z= 1.375 Chirality : 0.104 0.442 2122 Planarity : 0.008 0.054 2288 Dihedral : 18.260 89.933 5346 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.14 % Allowed : 9.60 % Favored : 89.25 % Cbeta Deviations : 0.34 % 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: -2.02 (0.18), residues: 1568 helix: -0.83 (0.18), residues: 665 sheet: -1.88 (0.36), residues: 137 loop : -1.65 (0.19), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP A 310 HIS 0.040 0.006 HIS A 728 PHE 0.070 0.006 PHE A 36 TYR 0.072 0.007 TYR A 635 ARG 0.032 0.002 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 289 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.8196 (mmm) cc_final: 0.7995 (mmm) REVERT: A 187 MET cc_start: 0.8972 (mmm) cc_final: 0.8043 (mmt) REVERT: A 269 MET cc_start: 0.7066 (mtm) cc_final: 0.6796 (mmm) REVERT: A 365 LEU cc_start: 0.9282 (mt) cc_final: 0.8913 (mm) REVERT: A 574 ASP cc_start: 0.8482 (m-30) cc_final: 0.7958 (p0) REVERT: A 674 MET cc_start: 0.8911 (mmm) cc_final: 0.8247 (mmt) REVERT: A 686 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8191 (tp30) REVERT: A 730 PHE cc_start: 0.8007 (t80) cc_final: 0.7600 (t80) REVERT: B 88 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8122 (mm-30) REVERT: B 171 GLN cc_start: 0.9430 (tt0) cc_final: 0.9137 (tt0) REVERT: B 173 THR cc_start: 0.8876 (p) cc_final: 0.8181 (p) REVERT: B 258 ILE cc_start: 0.9151 (tt) cc_final: 0.8771 (tt) REVERT: B 441 ASP cc_start: 0.7806 (m-30) cc_final: 0.7556 (p0) REVERT: B 603 LEU cc_start: 0.8852 (mt) cc_final: 0.8558 (mm) REVERT: B 616 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8520 (m-40) REVERT: B 633 MET cc_start: 0.8694 (mtm) cc_final: 0.8270 (mtm) REVERT: B 703 ASP cc_start: 0.8564 (t70) cc_final: 0.7946 (t70) REVERT: B 730 PHE cc_start: 0.7229 (t80) cc_final: 0.6938 (t80) REVERT: B 732 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8237 (mt) outliers start: 15 outliers final: 3 residues processed: 300 average time/residue: 0.3235 time to fit residues: 131.1497 Evaluate side-chains 160 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 155 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 248 GLN A 276 ASN A 557 ASN A 599 ASN A 606 GLN A 683 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 683 ASN B 763 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13700 Z= 0.213 Angle : 0.634 6.672 18746 Z= 0.342 Chirality : 0.043 0.216 2122 Planarity : 0.005 0.072 2288 Dihedral : 18.271 87.907 2292 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.30 % Allowed : 2.29 % Favored : 97.41 % 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: -0.67 (0.20), residues: 1568 helix: 0.56 (0.19), residues: 700 sheet: -1.18 (0.33), residues: 174 loop : -1.24 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 137 HIS 0.006 0.001 HIS B 370 PHE 0.025 0.002 PHE A 372 TYR 0.018 0.002 TYR B 623 ARG 0.018 0.001 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.8417 (m-30) cc_final: 0.7682 (p0) REVERT: A 674 MET cc_start: 0.9000 (mmm) cc_final: 0.8093 (mmt) REVERT: A 771 TYR cc_start: 0.8152 (p90) cc_final: 0.7752 (p90) REVERT: B 68 MET cc_start: 0.4021 (tmm) cc_final: 0.3699 (tmm) REVERT: B 128 ARG cc_start: 0.6299 (mtt180) cc_final: 0.6019 (ptp-110) REVERT: B 629 LEU cc_start: 0.8308 (mt) cc_final: 0.7843 (mt) REVERT: B 633 MET cc_start: 0.8777 (mtm) cc_final: 0.8483 (mtm) outliers start: 4 outliers final: 0 residues processed: 188 average time/residue: 0.2921 time to fit residues: 76.9288 Evaluate side-chains 108 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 116 optimal weight: 0.5980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN B 78 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13700 Z= 0.243 Angle : 0.617 6.821 18746 Z= 0.328 Chirality : 0.041 0.171 2122 Planarity : 0.005 0.056 2288 Dihedral : 18.322 89.758 2292 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: -0.49 (0.20), residues: 1568 helix: 0.61 (0.19), residues: 708 sheet: -0.70 (0.34), residues: 194 loop : -1.16 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS B 24 PHE 0.018 0.002 PHE A 372 TYR 0.018 0.002 TYR A 702 ARG 0.005 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.8577 (m-80) cc_final: 0.8317 (m-80) REVERT: A 739 MET cc_start: 0.8167 (mtp) cc_final: 0.7873 (mtt) REVERT: A 771 TYR cc_start: 0.8249 (p90) cc_final: 0.7759 (p90) REVERT: B 68 MET cc_start: 0.4375 (tmm) cc_final: 0.3877 (tmm) REVERT: B 609 MET cc_start: 0.8441 (tpp) cc_final: 0.8198 (tpp) REVERT: B 633 MET cc_start: 0.8810 (mtm) cc_final: 0.8530 (mtm) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2686 time to fit residues: 56.7842 Evaluate side-chains 110 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13700 Z= 0.172 Angle : 0.557 6.859 18746 Z= 0.298 Chirality : 0.040 0.183 2122 Planarity : 0.004 0.049 2288 Dihedral : 18.166 89.808 2292 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.08 % Allowed : 2.21 % Favored : 97.71 % 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: -0.22 (0.20), residues: 1568 helix: 0.88 (0.19), residues: 708 sheet: -0.70 (0.33), residues: 194 loop : -1.05 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 436 HIS 0.005 0.001 HIS B 24 PHE 0.023 0.001 PHE B 155 TYR 0.018 0.001 TYR A 528 ARG 0.004 0.000 ARG A 788 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.8666 (m-80) cc_final: 0.8378 (m-80) REVERT: A 671 MET cc_start: 0.8482 (mmm) cc_final: 0.8122 (tpp) REVERT: A 674 MET cc_start: 0.8490 (tpp) cc_final: 0.7905 (mmt) REVERT: A 739 MET cc_start: 0.8114 (mtp) cc_final: 0.7866 (mtt) REVERT: A 771 TYR cc_start: 0.8284 (p90) cc_final: 0.7747 (p90) REVERT: B 68 MET cc_start: 0.4281 (tmm) cc_final: 0.3774 (tmm) REVERT: B 441 ASP cc_start: 0.8105 (m-30) cc_final: 0.7669 (p0) REVERT: B 609 MET cc_start: 0.8450 (tpp) cc_final: 0.8182 (tpp) REVERT: B 633 MET cc_start: 0.8837 (mtm) cc_final: 0.8351 (mtm) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.2805 time to fit residues: 58.8838 Evaluate side-chains 116 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 0.0570 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13700 Z= 0.324 Angle : 0.695 7.483 18746 Z= 0.362 Chirality : 0.043 0.172 2122 Planarity : 0.005 0.048 2288 Dihedral : 18.298 88.712 2292 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: -0.49 (0.20), residues: 1568 helix: 0.58 (0.19), residues: 704 sheet: -0.93 (0.31), residues: 216 loop : -1.03 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 137 HIS 0.006 0.001 HIS B 24 PHE 0.024 0.003 PHE B 36 TYR 0.024 0.002 TYR A 702 ARG 0.006 0.001 ARG A 697 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.8681 (m-80) cc_final: 0.8460 (m-80) REVERT: A 574 ASP cc_start: 0.8599 (m-30) cc_final: 0.7955 (p0) REVERT: A 671 MET cc_start: 0.8601 (mmm) cc_final: 0.8203 (tpp) REVERT: B 13 MET cc_start: 0.7984 (ppp) cc_final: 0.7687 (ppp) REVERT: B 68 MET cc_start: 0.4996 (tmm) cc_final: 0.4651 (tmm) REVERT: B 397 MET cc_start: 0.8615 (mtm) cc_final: 0.8324 (mmm) REVERT: B 441 ASP cc_start: 0.8133 (m-30) cc_final: 0.7670 (p0) REVERT: B 609 MET cc_start: 0.8420 (tpp) cc_final: 0.8152 (tpp) REVERT: B 633 MET cc_start: 0.8903 (mtm) cc_final: 0.8614 (mtm) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2823 time to fit residues: 55.5443 Evaluate side-chains 96 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.0040 chunk 154 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13700 Z= 0.166 Angle : 0.591 10.363 18746 Z= 0.304 Chirality : 0.041 0.256 2122 Planarity : 0.004 0.047 2288 Dihedral : 18.147 88.907 2292 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -0.12 (0.20), residues: 1568 helix: 0.94 (0.19), residues: 704 sheet: -0.60 (0.34), residues: 199 loop : -0.96 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.005 0.001 HIS B 24 PHE 0.020 0.002 PHE A 143 TYR 0.020 0.001 TYR A 446 ARG 0.003 0.000 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8058 (tpp) cc_final: 0.7775 (tpt) REVERT: A 372 PHE cc_start: 0.8738 (m-10) cc_final: 0.8429 (m-80) REVERT: A 574 ASP cc_start: 0.8572 (m-30) cc_final: 0.7919 (p0) REVERT: A 624 MET cc_start: 0.6211 (mtt) cc_final: 0.5896 (mtt) REVERT: A 671 MET cc_start: 0.8464 (mmm) cc_final: 0.8039 (tpp) REVERT: B 68 MET cc_start: 0.4985 (tmm) cc_final: 0.4683 (tmm) REVERT: B 441 ASP cc_start: 0.8113 (m-30) cc_final: 0.7677 (p0) REVERT: B 543 GLN cc_start: 0.8592 (mt0) cc_final: 0.8121 (mt0) REVERT: B 617 MET cc_start: 0.8300 (mmt) cc_final: 0.7805 (ttm) REVERT: B 633 MET cc_start: 0.8749 (mtm) cc_final: 0.8345 (mtm) REVERT: B 717 ASN cc_start: 0.9085 (m-40) cc_final: 0.8798 (m-40) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2739 time to fit residues: 56.8673 Evaluate side-chains 103 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 88 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13700 Z= 0.250 Angle : 0.644 7.841 18746 Z= 0.333 Chirality : 0.042 0.233 2122 Planarity : 0.005 0.060 2288 Dihedral : 18.102 88.338 2292 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -0.22 (0.20), residues: 1568 helix: 0.84 (0.19), residues: 704 sheet: -0.74 (0.32), residues: 211 loop : -0.97 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 137 HIS 0.006 0.001 HIS B 24 PHE 0.018 0.002 PHE B 36 TYR 0.018 0.002 TYR A 702 ARG 0.004 0.001 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8478 (mm) cc_final: 0.8228 (tp) REVERT: A 372 PHE cc_start: 0.8748 (m-10) cc_final: 0.8506 (m-80) REVERT: A 574 ASP cc_start: 0.8655 (m-30) cc_final: 0.7927 (p0) REVERT: A 671 MET cc_start: 0.8590 (mmm) cc_final: 0.8226 (tpp) REVERT: A 692 MET cc_start: 0.7608 (tpp) cc_final: 0.7375 (mmm) REVERT: B 68 MET cc_start: 0.5217 (tmm) cc_final: 0.4790 (tmm) REVERT: B 441 ASP cc_start: 0.8173 (m-30) cc_final: 0.7749 (p0) REVERT: B 617 MET cc_start: 0.8303 (mmt) cc_final: 0.7914 (ttm) REVERT: B 633 MET cc_start: 0.8905 (mtm) cc_final: 0.8588 (mtm) REVERT: B 717 ASN cc_start: 0.9172 (m-40) cc_final: 0.8876 (m-40) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2704 time to fit residues: 53.4604 Evaluate side-chains 96 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13700 Z= 0.211 Angle : 0.595 8.255 18746 Z= 0.308 Chirality : 0.041 0.211 2122 Planarity : 0.004 0.058 2288 Dihedral : 18.104 89.803 2292 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -0.14 (0.20), residues: 1568 helix: 0.89 (0.19), residues: 702 sheet: -0.71 (0.33), residues: 213 loop : -0.89 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 137 HIS 0.006 0.001 HIS B 24 PHE 0.012 0.001 PHE B 155 TYR 0.016 0.002 TYR A 528 ARG 0.006 0.000 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8375 (mm) cc_final: 0.8168 (tp) REVERT: A 313 MET cc_start: 0.8046 (tpp) cc_final: 0.7748 (tpt) REVERT: A 372 PHE cc_start: 0.8757 (m-10) cc_final: 0.8506 (m-80) REVERT: A 561 ARG cc_start: 0.9111 (mmm-85) cc_final: 0.8741 (mmm-85) REVERT: A 574 ASP cc_start: 0.8661 (m-30) cc_final: 0.7900 (p0) REVERT: A 671 MET cc_start: 0.8612 (tpt) cc_final: 0.8274 (tpp) REVERT: A 692 MET cc_start: 0.7619 (tpp) cc_final: 0.7199 (mmm) REVERT: B 68 MET cc_start: 0.5319 (tmm) cc_final: 0.4950 (tmm) REVERT: B 241 LEU cc_start: 0.9699 (mt) cc_final: 0.9444 (tp) REVERT: B 441 ASP cc_start: 0.8177 (m-30) cc_final: 0.7789 (p0) REVERT: B 617 MET cc_start: 0.8309 (mmt) cc_final: 0.7971 (ttm) REVERT: B 633 MET cc_start: 0.8857 (mtm) cc_final: 0.8553 (mtm) REVERT: B 697 ARG cc_start: 0.7215 (tpt90) cc_final: 0.6910 (tpt90) REVERT: B 717 ASN cc_start: 0.9138 (m-40) cc_final: 0.8816 (m-40) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2912 time to fit residues: 55.7740 Evaluate side-chains 97 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13700 Z= 0.190 Angle : 0.585 8.477 18746 Z= 0.303 Chirality : 0.041 0.218 2122 Planarity : 0.004 0.047 2288 Dihedral : 18.048 89.843 2292 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.08 (0.20), residues: 1568 helix: 1.03 (0.20), residues: 702 sheet: -0.78 (0.32), residues: 212 loop : -0.92 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 137 HIS 0.003 0.001 HIS A 752 PHE 0.021 0.002 PHE B 155 TYR 0.015 0.001 TYR A 528 ARG 0.007 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8062 (tpp) cc_final: 0.7775 (tpt) REVERT: A 368 MET cc_start: 0.8844 (ptt) cc_final: 0.8606 (ptt) REVERT: A 372 PHE cc_start: 0.8784 (m-10) cc_final: 0.8541 (m-80) REVERT: A 413 ASP cc_start: 0.7940 (p0) cc_final: 0.7729 (p0) REVERT: A 561 ARG cc_start: 0.9115 (mmm-85) cc_final: 0.8749 (mmm-85) REVERT: A 574 ASP cc_start: 0.8663 (m-30) cc_final: 0.7895 (p0) REVERT: A 671 MET cc_start: 0.8574 (tpt) cc_final: 0.8253 (tpp) REVERT: A 692 MET cc_start: 0.7536 (tpp) cc_final: 0.7015 (mmm) REVERT: B 68 MET cc_start: 0.5558 (tmm) cc_final: 0.5210 (tmm) REVERT: B 241 LEU cc_start: 0.9700 (mt) cc_final: 0.9434 (tp) REVERT: B 441 ASP cc_start: 0.8181 (m-30) cc_final: 0.7817 (p0) REVERT: B 543 GLN cc_start: 0.8668 (mt0) cc_final: 0.8110 (mt0) REVERT: B 617 MET cc_start: 0.8347 (mmt) cc_final: 0.8013 (ttm) REVERT: B 633 MET cc_start: 0.8849 (mtm) cc_final: 0.8262 (mtm) REVERT: B 697 ARG cc_start: 0.7192 (tpt90) cc_final: 0.6902 (tpt90) REVERT: B 717 ASN cc_start: 0.9131 (m-40) cc_final: 0.8802 (m-40) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2744 time to fit residues: 53.1862 Evaluate side-chains 97 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 72 optimal weight: 0.0980 chunk 105 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13700 Z= 0.371 Angle : 0.745 9.720 18746 Z= 0.383 Chirality : 0.044 0.215 2122 Planarity : 0.006 0.076 2288 Dihedral : 18.201 89.494 2292 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 23.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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: -0.57 (0.20), residues: 1568 helix: 0.53 (0.19), residues: 702 sheet: -1.04 (0.32), residues: 212 loop : -1.05 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 137 HIS 0.005 0.002 HIS A 74 PHE 0.027 0.002 PHE B 155 TYR 0.021 0.002 TYR B 729 ARG 0.007 0.001 ARG B 367 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.9250 (tpt) cc_final: 0.9007 (tpt) REVERT: A 372 PHE cc_start: 0.8829 (m-10) cc_final: 0.8623 (m-80) REVERT: A 561 ARG cc_start: 0.9204 (mmm-85) cc_final: 0.8700 (mmm-85) REVERT: A 574 ASP cc_start: 0.8639 (m-30) cc_final: 0.7761 (p0) REVERT: A 671 MET cc_start: 0.8805 (tpt) cc_final: 0.8602 (tpp) REVERT: A 692 MET cc_start: 0.7801 (tpp) cc_final: 0.7478 (mmm) REVERT: B 68 MET cc_start: 0.5937 (tmm) cc_final: 0.5167 (tmm) REVERT: B 306 MET cc_start: 0.8619 (tpt) cc_final: 0.8197 (tpt) REVERT: B 368 MET cc_start: 0.7297 (mmp) cc_final: 0.7009 (mmp) REVERT: B 441 ASP cc_start: 0.8269 (m-30) cc_final: 0.7956 (m-30) REVERT: B 617 MET cc_start: 0.8335 (mmt) cc_final: 0.8106 (ttm) REVERT: B 633 MET cc_start: 0.9070 (mtm) cc_final: 0.8698 (mtm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2789 time to fit residues: 46.1356 Evaluate side-chains 85 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.072912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.052876 restraints weight = 85783.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.054263 restraints weight = 53652.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.055224 restraints weight = 38352.316| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13700 Z= 0.168 Angle : 0.588 8.277 18746 Z= 0.303 Chirality : 0.041 0.243 2122 Planarity : 0.004 0.047 2288 Dihedral : 18.075 89.422 2292 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.11 (0.21), residues: 1568 helix: 1.03 (0.19), residues: 700 sheet: -0.90 (0.32), residues: 213 loop : -0.93 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 137 HIS 0.004 0.001 HIS A 760 PHE 0.017 0.001 PHE B 155 TYR 0.018 0.001 TYR A 528 ARG 0.009 0.000 ARG B 305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2516.26 seconds wall clock time: 46 minutes 43.19 seconds (2803.19 seconds total)