Starting phenix.real_space_refine on Fri Mar 15 23:33:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3f_23653/03_2024/7m3f_23653_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3f_23653/03_2024/7m3f_23653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3f_23653/03_2024/7m3f_23653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3f_23653/03_2024/7m3f_23653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3f_23653/03_2024/7m3f_23653_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3f_23653/03_2024/7m3f_23653_neut_updated.pdb" } resolution = 2.8 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= 0.006 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 2 5.49 5 S 71 5.16 5 C 8470 2.51 5 N 2113 2.21 5 O 2418 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 23": "OD1" <-> "OD2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ASP 570": "OD1" <-> "OD2" Residue "A ASP 587": "OD1" <-> "OD2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13084 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6395 Classifications: {'peptide': 818} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 31, 'TRANS': 786} Chain breaks: 3 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 6383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6383 Classifications: {'peptide': 811} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 31, 'TRANS': 779} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 105 Unusual residues: {' CA': 3, 'NAG': 4, 'PO4': 1, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A 906 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 117 Unusual residues: {' CA': 1, 'NAG': 5, 'PO4': 1, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B 907 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.63, per 1000 atoms: 0.51 Number of scatterers: 13084 At special positions: 0 Unit cell: (95.46, 92.13, 190.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 71 16.00 P 2 15.00 F 6 9.00 O 2418 8.00 N 2113 7.00 C 8470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.04 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.02 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.04 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.04 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.04 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.04 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.04 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.02 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.04 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.04 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.04 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.04 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A 901 " - " ASN A 261 " " NAG A 902 " - " ASN A 287 " " NAG A 903 " - " ASN A 468 " " NAG A 904 " - " ASN A 594 " " NAG B 901 " - " ASN B 261 " " NAG B 902 " - " ASN B 287 " " NAG B 903 " - " ASN B 488 " " NAG B 904 " - " ASN B 468 " " NAG B 905 " - " ASN B 594 " " NAG C 1 " - " ASN A 488 " " NAG D 1 " - " ASN A 541 " " NAG E 1 " - " ASN B 541 " Time building additional restraints: 4.80 Conformation dependent library (CDL) restraints added in 2.1 seconds 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3070 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 13 sheets defined 42.1% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 65 through 83 removed outlier: 3.690A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.651A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.514A pdb=" N ILE A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 157 removed outlier: 3.611A pdb=" N ALA A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 191 through 203 removed outlier: 3.720A pdb=" N ALA A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 273 through 286 Proline residue: A 278 - end of helix removed outlier: 3.771A pdb=" N ARG A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 removed outlier: 3.722A pdb=" N PHE A 311 " --> pdb=" O PRO A 308 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N HIS A 312 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 314 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.696A pdb=" N LYS A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.719A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 611 through 636 removed outlier: 4.024A pdb=" N PHE A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 646 No H-bonds generated for 'chain 'A' and resid 644 through 646' Processing helix chain 'A' and resid 648 through 668 removed outlier: 3.548A pdb=" N TYR A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU A 666 " --> pdb=" O PHE A 662 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 679 removed outlier: 3.919A pdb=" N LEU A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 697 Processing helix chain 'A' and resid 725 through 745 removed outlier: 3.787A pdb=" N THR A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE A 738 " --> pdb=" O MET A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 794 removed outlier: 3.632A pdb=" N CYS A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 820 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 833 through 853 removed outlier: 4.158A pdb=" N PHE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 861 removed outlier: 4.084A pdb=" N ILE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 881 through 886 Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 104 through 114 removed outlier: 3.756A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 123 removed outlier: 3.737A pdb=" N ASP B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 157 removed outlier: 3.920A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 219 through 233 removed outlier: 3.828A pdb=" N GLU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 273 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.605A pdb=" N PHE B 311 " --> pdb=" O PRO B 308 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N HIS B 312 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.939A pdb=" N LYS B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 525 through 527 No H-bonds generated for 'chain 'B' and resid 525 through 527' Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 613 through 636 Processing helix chain 'B' and resid 641 through 645 Processing helix chain 'B' and resid 648 through 667 removed outlier: 4.317A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU B 666 " --> pdb=" O PHE B 662 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 677 No H-bonds generated for 'chain 'B' and resid 674 through 677' Processing helix chain 'B' and resid 680 through 697 removed outlier: 4.150A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 745 removed outlier: 4.270A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 794 removed outlier: 4.112A pdb=" N THR B 780 " --> pdb=" O LEU B 776 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER B 794 " --> pdb=" O PHE B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 820 Processing helix chain 'B' and resid 822 through 825 No H-bonds generated for 'chain 'B' and resid 822 through 825' Processing helix chain 'B' and resid 831 through 860 removed outlier: 3.578A pdb=" N ALA B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 874 No H-bonds generated for 'chain 'B' and resid 871 through 874' Processing sheet with id= A, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.479A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY A 35 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A 141 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU A 37 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 240 through 243 removed outlier: 9.411A pdb=" N GLU A 241 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A 211 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE A 243 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA A 213 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL A 266 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE A 212 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL A 268 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA A 214 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE A 270 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 292 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL A 269 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A 294 " --> pdb=" O VAL A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.257A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 550 through 554 Processing sheet with id= E, first strand: chain 'A' and resid 589 through 591 Processing sheet with id= F, first strand: chain 'A' and resid 602 through 604 removed outlier: 3.629A pdb=" N ILE A 763 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 762 " --> pdb=" O ASN A 753 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.356A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLY B 35 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL B 141 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU B 37 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 240 through 243 removed outlier: 9.388A pdb=" N GLU B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR B 211 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE B 243 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA B 213 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 266 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE B 212 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL B 268 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ALA B 214 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE B 270 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL B 269 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 294 " --> pdb=" O VAL B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.407A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE B 505 " --> pdb=" O HIS B 495 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 468 through 470 Processing sheet with id= K, first strand: chain 'B' and resid 550 through 554 Processing sheet with id= L, first strand: chain 'B' and resid 589 through 591 Processing sheet with id= M, first strand: chain 'B' and resid 602 through 604 478 hydrogen bonds defined for protein. 1392 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: 4.04 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3637 1.34 - 1.46: 3268 1.46 - 1.58: 6410 1.58 - 1.70: 0 1.70 - 1.83: 84 Bond restraints: 13399 Sorted by residual: bond pdb=" N YP4 A 905 " pdb=" C3 YP4 A 905 " ideal model delta sigma weight residual 1.452 1.538 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" N YP4 B 906 " pdb=" C3 YP4 B 906 " ideal model delta sigma weight residual 1.452 1.538 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" N YP4 A 905 " pdb=" CA YP4 A 905 " ideal model delta sigma weight residual 1.457 1.539 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" N YP4 B 906 " pdb=" CA YP4 B 906 " ideal model delta sigma weight residual 1.457 1.537 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" O3 PO4 B 909 " pdb=" P PO4 B 909 " ideal model delta sigma weight residual 1.569 1.495 0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 13394 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.86: 236 105.86 - 112.97: 6927 112.97 - 120.08: 5213 120.08 - 127.20: 5669 127.20 - 134.31: 154 Bond angle restraints: 18199 Sorted by residual: angle pdb=" N LYS A 882 " pdb=" CA LYS A 882 " pdb=" C LYS A 882 " ideal model delta sigma weight residual 113.23 106.69 6.54 1.22e+00 6.72e-01 2.87e+01 angle pdb=" C PRO B 89 " pdb=" N ASN B 90 " pdb=" CA ASN B 90 " ideal model delta sigma weight residual 121.54 131.60 -10.06 1.91e+00 2.74e-01 2.77e+01 angle pdb=" CA PHE A 881 " pdb=" CB PHE A 881 " pdb=" CG PHE A 881 " ideal model delta sigma weight residual 113.80 118.60 -4.80 1.00e+00 1.00e+00 2.30e+01 angle pdb=" CB LYS B 119 " pdb=" CG LYS B 119 " pdb=" CD LYS B 119 " ideal model delta sigma weight residual 111.30 100.67 10.63 2.30e+00 1.89e-01 2.13e+01 angle pdb=" N PHE B 862 " pdb=" CA PHE B 862 " pdb=" CB PHE B 862 " ideal model delta sigma weight residual 110.45 117.06 -6.61 1.44e+00 4.82e-01 2.10e+01 ... (remaining 18194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7511 17.87 - 35.75: 467 35.75 - 53.62: 72 53.62 - 71.49: 20 71.49 - 89.37: 9 Dihedral angle restraints: 8079 sinusoidal: 3334 harmonic: 4745 Sorted by residual: dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual 93.00 173.61 -80.61 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 765 " pdb=" CB CYS A 765 " ideal model delta sinusoidal sigma weight residual 93.00 154.65 -61.65 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CA VAL A 142 " pdb=" C VAL A 142 " pdb=" N GLY A 143 " pdb=" CA GLY A 143 " ideal model delta harmonic sigma weight residual -180.00 -151.97 -28.03 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 8076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1722 0.080 - 0.160: 317 0.160 - 0.240: 33 0.240 - 0.320: 6 0.320 - 0.400: 1 Chirality restraints: 2079 Sorted by residual: chirality pdb=" CB VAL B 702 " pdb=" CA VAL B 702 " pdb=" CG1 VAL B 702 " pdb=" CG2 VAL B 702 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CA CYS B 598 " pdb=" N CYS B 598 " pdb=" C CYS B 598 " pdb=" CB CYS B 598 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB THR B 445 " pdb=" CA THR B 445 " pdb=" OG1 THR B 445 " pdb=" CG2 THR B 445 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 2076 not shown) Planarity restraints: 2297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 287 " 0.039 2.00e-02 2.50e+03 4.00e-02 2.00e+01 pdb=" CG ASN A 287 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 287 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 287 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG A 902 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 640 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO A 641 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 641 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 641 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA YP4 A 905 " 0.047 2.00e-02 2.50e+03 2.24e-02 1.38e+01 pdb=" CB YP4 A 905 " -0.011 2.00e-02 2.50e+03 pdb=" CG YP4 A 905 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 YP4 A 905 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 YP4 A 905 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 YP4 A 905 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 YP4 A 905 " -0.024 2.00e-02 2.50e+03 pdb=" CZ YP4 A 905 " -0.001 2.00e-02 2.50e+03 pdb=" C14 YP4 A 905 " -0.027 2.00e-02 2.50e+03 pdb=" C15 YP4 A 905 " -0.016 2.00e-02 2.50e+03 pdb=" C16 YP4 A 905 " 0.013 2.00e-02 2.50e+03 ... (remaining 2294 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2678 2.78 - 3.31: 11275 3.31 - 3.84: 20426 3.84 - 4.37: 24260 4.37 - 4.90: 42070 Nonbonded interactions: 100709 Sorted by model distance: nonbonded pdb=" O LYS A 805 " pdb=" OG1 THR A 808 " model vdw 2.245 2.440 nonbonded pdb=" O ALA A 548 " pdb=" OG SER A 574 " model vdw 2.262 2.440 nonbonded pdb=" O PHE A 846 " pdb=" O GLY A 847 " model vdw 2.311 3.040 nonbonded pdb=" O ALA B 824 " pdb=" OG1 THR B 828 " model vdw 2.317 2.440 nonbonded pdb=" OD2 ASP A 238 " pdb=" OG SER A 262 " model vdw 2.321 2.440 ... (remaining 100704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 131 or (resid 132 through 135 and (name N or na \ me CA or name C or name O or name CB )) or resid 136 through 362 or resid 392 th \ rough 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) \ or resid 514 through 516 or (resid 517 and (name N or name CA or name C or name \ O or name CB )) or resid 518 through 635 or (resid 636 through 637 and (name N \ or name CA or name C or name O or name CB )) or resid 638 through 700 or (resid \ 701 and (name N or name CA or name C or name O or name CB )) or resid 702 throug \ h 831 or (resid 832 and (name N or name CA or name C or name O or name CB )) or \ resid 833 through 861 or (resid 862 through 863 and (name N or name CA or name C \ or name O or name CB )) or resid 864 through 865 or (resid 866 through 867 and \ (name N or name CA or name C or name O or name CB )) or resid 868 through 876 or \ resid 901 through 907)) selection = (chain 'B' and (resid 20 through 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and (na \ me N or name CA or name C or name O or name CB )) or resid 53 through 124 or (re \ sid 125 and (name N or name CA or name C or name O or name CB )) or (resid 131 t \ hrough 135 and (name N or name CA or name C or name O or name CB )) or resid 136 \ through 361 or (resid 362 and (name N or name CA or name C or name O or name CB \ )) or resid 392 through 480 or (resid 481 and (name N or name CA or name C or n \ ame O or name CB )) or resid 482 through 498 or (resid 499 through 500 and (name \ N or name CA or name C or name O or name CB )) or resid 501 through 591 or (res \ id 592 through 593 and (name N or name CA or name C or name O or name CB )) or r \ esid 594 through 650 or (resid 651 and (name N or name CA or name C or name O or \ name CB )) or resid 652 through 663 or (resid 664 through 665 and (name N or na \ me CA or name C or name O or name CB )) or resid 666 through 670 or (resid 671 a \ nd (name N or name CA or name C or name O or name CB )) or resid 672 through 698 \ or (resid 699 and (name N or name CA or name C or name O or name CB )) or resid \ 700 through 703 or (resid 704 and (name N or name CA or name C or name O or nam \ e CB )) or resid 722 through 728 or (resid 729 and (name N or name CA or name C \ or name O or name CB )) or resid 730 through 733 or (resid 734 and (name N or na \ me CA or name C or name O or name CB )) or resid 735 through 758 or (resid 759 a \ nd (name N or name CA or name C or name O or name CB )) or resid 760 through 853 \ or (resid 854 and (name N or name CA or name C or name O or name CB )) or resid \ 855 through 870 or (resid 871 and (name N or name CA or name C or name O or nam \ e CB )) or resid 872 through 876 or resid 902 through 908)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 9.930 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 34.670 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.008 0.086 13399 Z= 0.532 Angle : 1.012 11.514 18199 Z= 0.570 Chirality : 0.063 0.400 2079 Planarity : 0.008 0.109 2285 Dihedral : 12.467 89.365 4955 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.18), residues: 1613 helix: -1.41 (0.17), residues: 675 sheet: -1.53 (0.33), residues: 212 loop : -1.92 (0.20), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 818 HIS 0.025 0.002 HIS A 463 PHE 0.036 0.003 PHE B 846 TYR 0.037 0.003 TYR B 425 ARG 0.008 0.001 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.425 Fit side-chains revert: symmetry clash REVERT: A 751 TYR cc_start: 0.8128 (t80) cc_final: 0.7895 (t80) REVERT: A 792 PHE cc_start: 0.8874 (t80) cc_final: 0.8628 (t80) REVERT: A 796 LYS cc_start: 0.8749 (mttm) cc_final: 0.8050 (pmtt) outliers start: 0 outliers final: 3 residues processed: 193 average time/residue: 0.8192 time to fit residues: 179.7328 Evaluate side-chains 161 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain B residue 695 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 94 optimal weight: 0.2980 chunk 147 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 ASN B 463 HIS B 673 GLN B 753 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13399 Z= 0.235 Angle : 0.581 9.999 18199 Z= 0.307 Chirality : 0.045 0.234 2079 Planarity : 0.005 0.077 2285 Dihedral : 7.211 59.818 2084 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.84 % Favored : 96.09 % Rotamer: Outliers : 2.04 % Allowed : 7.51 % Favored : 90.44 % 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: -1.34 (0.19), residues: 1613 helix: 0.21 (0.19), residues: 685 sheet: -1.47 (0.33), residues: 208 loop : -1.77 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 675 HIS 0.005 0.001 HIS A 463 PHE 0.015 0.001 PHE B 688 TYR 0.022 0.002 TYR A 744 ARG 0.002 0.000 ARG B 795 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 1.515 Fit side-chains REVERT: A 340 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7204 (mtp180) REVERT: A 751 TYR cc_start: 0.8141 (t80) cc_final: 0.7845 (t80) REVERT: A 792 PHE cc_start: 0.8910 (t80) cc_final: 0.8613 (t80) REVERT: A 796 LYS cc_start: 0.8765 (mttm) cc_final: 0.8102 (pmtt) REVERT: B 587 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7682 (p0) REVERT: B 771 MET cc_start: 0.3292 (OUTLIER) cc_final: 0.2606 (ttp) outliers start: 28 outliers final: 12 residues processed: 181 average time/residue: 0.6928 time to fit residues: 145.2763 Evaluate side-chains 171 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 131 optimal weight: 0.1980 chunk 146 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 855 ASN B 673 GLN B 753 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13399 Z= 0.222 Angle : 0.555 8.911 18199 Z= 0.289 Chirality : 0.044 0.224 2079 Planarity : 0.004 0.069 2285 Dihedral : 6.643 59.236 2082 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 2.12 % Allowed : 9.70 % Favored : 88.18 % 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: -0.86 (0.20), residues: 1613 helix: 0.84 (0.20), residues: 682 sheet: -1.44 (0.33), residues: 204 loop : -1.69 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 675 HIS 0.004 0.001 HIS A 463 PHE 0.022 0.001 PHE A 788 TYR 0.019 0.002 TYR A 744 ARG 0.003 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.428 Fit side-chains REVERT: A 340 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7170 (mtp180) REVERT: A 701 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6585 (mmp-170) REVERT: A 751 TYR cc_start: 0.8100 (t80) cc_final: 0.7768 (t80) REVERT: A 792 PHE cc_start: 0.8879 (t80) cc_final: 0.8601 (t80) REVERT: A 796 LYS cc_start: 0.8753 (mttm) cc_final: 0.8096 (pmtt) REVERT: A 855 ASN cc_start: 0.8966 (t0) cc_final: 0.8431 (t0) REVERT: B 688 PHE cc_start: 0.8639 (t80) cc_final: 0.8375 (t80) outliers start: 29 outliers final: 11 residues processed: 178 average time/residue: 0.7603 time to fit residues: 155.8427 Evaluate side-chains 174 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 819 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 70 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 ASN B 463 HIS B 673 GLN B 753 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13399 Z= 0.206 Angle : 0.526 7.593 18199 Z= 0.275 Chirality : 0.043 0.217 2079 Planarity : 0.004 0.063 2285 Dihedral : 6.268 58.257 2080 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 2.55 % Allowed : 10.58 % Favored : 86.87 % 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: -0.63 (0.20), residues: 1613 helix: 1.10 (0.20), residues: 682 sheet: -1.41 (0.33), residues: 211 loop : -1.61 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 675 HIS 0.003 0.001 HIS B 429 PHE 0.012 0.001 PHE A 444 TYR 0.027 0.001 TYR A 744 ARG 0.002 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 1.459 Fit side-chains REVERT: A 340 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7168 (mtp180) REVERT: A 751 TYR cc_start: 0.8133 (t80) cc_final: 0.7720 (t80) REVERT: A 792 PHE cc_start: 0.8901 (t80) cc_final: 0.8586 (t80) REVERT: A 796 LYS cc_start: 0.8751 (mttm) cc_final: 0.8094 (pmtt) REVERT: A 799 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7226 (pt0) REVERT: A 855 ASN cc_start: 0.8923 (t0) cc_final: 0.8454 (t0) REVERT: A 881 PHE cc_start: 0.5631 (OUTLIER) cc_final: 0.2841 (t80) REVERT: B 760 ILE cc_start: 0.8574 (pt) cc_final: 0.8314 (pp) REVERT: B 771 MET cc_start: 0.2968 (OUTLIER) cc_final: 0.2261 (ttp) REVERT: B 811 MET cc_start: 0.8807 (mpt) cc_final: 0.8444 (mmm) outliers start: 35 outliers final: 19 residues processed: 178 average time/residue: 0.7293 time to fit residues: 150.1564 Evaluate side-chains 178 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 819 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 ASN B 118 ASN B 673 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13399 Z= 0.281 Angle : 0.566 9.230 18199 Z= 0.294 Chirality : 0.045 0.220 2079 Planarity : 0.004 0.062 2285 Dihedral : 6.219 57.975 2080 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 2.77 % Allowed : 11.16 % Favored : 86.07 % 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: -0.61 (0.20), residues: 1613 helix: 1.12 (0.20), residues: 680 sheet: -1.37 (0.33), residues: 215 loop : -1.62 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 530 HIS 0.005 0.001 HIS B 429 PHE 0.024 0.002 PHE B 789 TYR 0.026 0.002 TYR A 744 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 160 time to evaluate : 1.444 Fit side-chains REVERT: A 340 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7179 (mtp180) REVERT: A 701 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6628 (mmp-170) REVERT: A 751 TYR cc_start: 0.8118 (t80) cc_final: 0.7731 (t80) REVERT: A 796 LYS cc_start: 0.8793 (mttm) cc_final: 0.8142 (pmtt) REVERT: A 799 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7299 (pt0) REVERT: A 855 ASN cc_start: 0.8927 (t0) cc_final: 0.8493 (t0) REVERT: A 881 PHE cc_start: 0.5596 (OUTLIER) cc_final: 0.2823 (t80) REVERT: B 760 ILE cc_start: 0.8598 (pt) cc_final: 0.8347 (pp) REVERT: B 811 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8008 (mpt) outliers start: 38 outliers final: 23 residues processed: 175 average time/residue: 0.7558 time to fit residues: 152.0560 Evaluate side-chains 182 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 811 MET Chi-restraints excluded: chain B residue 819 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 30 optimal weight: 0.0770 chunk 91 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 ASN B 463 HIS ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN B 753 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13399 Z= 0.161 Angle : 0.504 8.937 18199 Z= 0.262 Chirality : 0.043 0.232 2079 Planarity : 0.004 0.058 2285 Dihedral : 5.906 56.615 2080 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 2.84 % Allowed : 11.45 % Favored : 85.70 % 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: -0.45 (0.21), residues: 1613 helix: 1.26 (0.20), residues: 682 sheet: -1.36 (0.33), residues: 213 loop : -1.51 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 530 HIS 0.003 0.001 HIS A 429 PHE 0.021 0.001 PHE B 789 TYR 0.027 0.001 TYR A 744 ARG 0.002 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 159 time to evaluate : 1.563 Fit side-chains REVERT: A 340 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7235 (mtp180) REVERT: A 701 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6563 (mmp-170) REVERT: A 751 TYR cc_start: 0.8089 (t80) cc_final: 0.7719 (t80) REVERT: A 796 LYS cc_start: 0.8783 (mttm) cc_final: 0.8116 (pmtt) REVERT: A 799 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7307 (pt0) REVERT: A 881 PHE cc_start: 0.5514 (OUTLIER) cc_final: 0.2856 (t80) REVERT: B 760 ILE cc_start: 0.8567 (pt) cc_final: 0.8308 (pp) outliers start: 39 outliers final: 18 residues processed: 177 average time/residue: 0.8395 time to fit residues: 170.4194 Evaluate side-chains 173 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 819 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 131 optimal weight: 0.3980 chunk 87 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 855 ASN B 673 GLN B 724 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13399 Z= 0.199 Angle : 0.526 9.644 18199 Z= 0.271 Chirality : 0.043 0.220 2079 Planarity : 0.004 0.057 2285 Dihedral : 5.901 56.305 2080 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 2.33 % Allowed : 12.55 % Favored : 85.12 % 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: -0.39 (0.21), residues: 1613 helix: 1.32 (0.20), residues: 681 sheet: -1.32 (0.33), residues: 213 loop : -1.49 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 530 HIS 0.004 0.001 HIS B 429 PHE 0.022 0.001 PHE A 814 TYR 0.026 0.001 TYR A 744 ARG 0.002 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.454 Fit side-chains REVERT: A 340 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7221 (mtp180) REVERT: A 701 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6559 (mmp-170) REVERT: A 751 TYR cc_start: 0.8095 (t80) cc_final: 0.7690 (t80) REVERT: A 793 LYS cc_start: 0.8495 (ttmt) cc_final: 0.8185 (tptt) REVERT: A 796 LYS cc_start: 0.8848 (mttm) cc_final: 0.8148 (pmtt) REVERT: A 881 PHE cc_start: 0.5389 (OUTLIER) cc_final: 0.2780 (t80) REVERT: B 760 ILE cc_start: 0.8590 (pt) cc_final: 0.8340 (pp) REVERT: B 817 VAL cc_start: 0.8869 (t) cc_final: 0.8550 (t) outliers start: 32 outliers final: 18 residues processed: 169 average time/residue: 0.7735 time to fit residues: 149.7852 Evaluate side-chains 172 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 819 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 ASN B 463 HIS B 673 GLN B 724 GLN B 753 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13399 Z= 0.221 Angle : 0.538 12.164 18199 Z= 0.278 Chirality : 0.044 0.209 2079 Planarity : 0.004 0.057 2285 Dihedral : 5.840 56.642 2080 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.97 % Favored : 95.97 % Rotamer: Outliers : 2.63 % Allowed : 12.62 % Favored : 84.76 % 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: -0.36 (0.21), residues: 1613 helix: 1.32 (0.20), residues: 679 sheet: -1.34 (0.33), residues: 213 loop : -1.43 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 818 HIS 0.004 0.001 HIS B 429 PHE 0.026 0.001 PHE A 814 TYR 0.025 0.002 TYR A 744 ARG 0.003 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 1.376 Fit side-chains REVERT: A 340 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7216 (mtp180) REVERT: A 701 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6608 (mmp-170) REVERT: A 751 TYR cc_start: 0.8088 (t80) cc_final: 0.7717 (t80) REVERT: A 793 LYS cc_start: 0.8467 (ttmt) cc_final: 0.8119 (tptt) REVERT: A 796 LYS cc_start: 0.8854 (mttm) cc_final: 0.8151 (pmtt) REVERT: B 724 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: B 760 ILE cc_start: 0.8605 (pt) cc_final: 0.8359 (pp) REVERT: B 811 MET cc_start: 0.8862 (mpt) cc_final: 0.8485 (mmm) REVERT: B 817 VAL cc_start: 0.8884 (t) cc_final: 0.8581 (t) outliers start: 36 outliers final: 24 residues processed: 172 average time/residue: 0.7630 time to fit residues: 150.4659 Evaluate side-chains 180 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 724 GLN Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 852 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.0170 chunk 136 optimal weight: 4.9990 chunk 145 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 673 GLN B 753 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13399 Z= 0.195 Angle : 0.535 13.778 18199 Z= 0.275 Chirality : 0.043 0.203 2079 Planarity : 0.004 0.056 2285 Dihedral : 5.771 56.070 2080 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 1.75 % Allowed : 13.86 % Favored : 84.39 % 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: -0.33 (0.21), residues: 1613 helix: 1.34 (0.20), residues: 680 sheet: -1.32 (0.34), residues: 213 loop : -1.40 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 818 HIS 0.003 0.001 HIS B 429 PHE 0.023 0.001 PHE B 662 TYR 0.024 0.001 TYR A 744 ARG 0.002 0.000 ARG A 795 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 1.431 Fit side-chains REVERT: A 340 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7218 (mtp180) REVERT: A 751 TYR cc_start: 0.8105 (t80) cc_final: 0.7792 (t80) REVERT: A 793 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8113 (tptt) REVERT: A 796 LYS cc_start: 0.8839 (mttm) cc_final: 0.8160 (pmtt) REVERT: B 760 ILE cc_start: 0.8592 (pt) cc_final: 0.8351 (pp) REVERT: B 811 MET cc_start: 0.8869 (mpt) cc_final: 0.8483 (mmm) REVERT: B 817 VAL cc_start: 0.8916 (t) cc_final: 0.8617 (t) outliers start: 24 outliers final: 22 residues processed: 165 average time/residue: 0.8488 time to fit residues: 161.5276 Evaluate side-chains 173 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 819 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 13 optimal weight: 0.0770 chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 ASN B 673 GLN B 724 GLN B 753 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13399 Z= 0.227 Angle : 0.544 13.526 18199 Z= 0.281 Chirality : 0.044 0.230 2079 Planarity : 0.004 0.056 2285 Dihedral : 5.827 56.580 2080 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.84 % Favored : 96.09 % Rotamer: Outliers : 1.75 % Allowed : 13.71 % Favored : 84.54 % 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: -0.35 (0.21), residues: 1613 helix: 1.32 (0.20), residues: 678 sheet: -1.33 (0.33), residues: 219 loop : -1.39 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 818 HIS 0.004 0.001 HIS B 429 PHE 0.023 0.001 PHE A 814 TYR 0.022 0.001 TYR A 744 ARG 0.002 0.000 ARG A 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 1.446 Fit side-chains REVERT: A 340 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7216 (mtp180) REVERT: A 701 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6613 (mmp-170) REVERT: A 751 TYR cc_start: 0.8102 (t80) cc_final: 0.7803 (t80) REVERT: A 793 LYS cc_start: 0.8465 (ttmt) cc_final: 0.8116 (tptt) REVERT: A 796 LYS cc_start: 0.8861 (mttm) cc_final: 0.8174 (pmtt) REVERT: A 799 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7262 (pt0) REVERT: B 724 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: B 760 ILE cc_start: 0.8609 (pt) cc_final: 0.8365 (pp) REVERT: B 811 MET cc_start: 0.8900 (mpt) cc_final: 0.8502 (mmm) REVERT: B 817 VAL cc_start: 0.8892 (t) cc_final: 0.8594 (t) REVERT: B 846 PHE cc_start: 0.8051 (m-80) cc_final: 0.7778 (t80) outliers start: 24 outliers final: 19 residues processed: 163 average time/residue: 0.7995 time to fit residues: 149.2890 Evaluate side-chains 169 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 625 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 724 GLN Chi-restraints excluded: chain B residue 819 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 128 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.0470 chunk 113 optimal weight: 0.0270 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 673 GLN B 753 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.083960 restraints weight = 20908.389| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.71 r_work: 0.2862 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13399 Z= 0.165 Angle : 0.523 13.426 18199 Z= 0.268 Chirality : 0.043 0.269 2079 Planarity : 0.004 0.055 2285 Dihedral : 5.638 55.359 2080 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.28 % Rotamer: Outliers : 1.53 % Allowed : 14.15 % Favored : 84.32 % 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: -0.26 (0.21), residues: 1613 helix: 1.39 (0.20), residues: 679 sheet: -1.30 (0.34), residues: 213 loop : -1.36 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 818 HIS 0.003 0.001 HIS A 429 PHE 0.022 0.001 PHE A 814 TYR 0.024 0.001 TYR A 744 ARG 0.002 0.000 ARG A 795 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3817.24 seconds wall clock time: 68 minutes 24.57 seconds (4104.57 seconds total)