Starting phenix.real_space_refine on Mon Apr 8 07:58:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/04_2024/7sil_25143_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/04_2024/7sil_25143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/04_2024/7sil_25143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/04_2024/7sil_25143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/04_2024/7sil_25143_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/04_2024/7sil_25143_updated.pdb" } resolution = 2.7 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 ------------------------------------------------------------------------------- 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= 0.060 sd= 0.251 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 8 9.91 5 P 2 5.49 5 S 70 5.16 5 Cl 2 4.86 5 C 8454 2.51 5 N 2036 2.21 5 O 2352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 190": "OD1" <-> "OD2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 216": "OD1" <-> "OD2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A ASP 588": "OD1" <-> "OD2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 757": "OE1" <-> "OE2" Residue "A PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "B GLU 507": "OE1" <-> "OE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 604": "OE1" <-> "OE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B GLU 649": "OE1" <-> "OE2" Residue "B PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12924 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6206 Classifications: {'peptide': 781} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 749} Chain breaks: 3 Chain: "B" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6206 Classifications: {'peptide': 781} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 749} Chain breaks: 3 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: "F" 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: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 200 Unusual residues: {' CA': 4, '9IG': 1, 'CLR': 4, 'NAG': 3, 'PO4': 1, 'TCR': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 200 Unusual residues: {' CA': 4, '9IG': 1, 'CLR': 4, 'NAG': 3, 'PO4': 1, 'TCR': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.63, per 1000 atoms: 0.59 Number of scatterers: 12924 At special positions: 0 Unit cell: (98.77, 97.11, 172.64, 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 8 19.99 Cl 2 17.00 S 70 16.00 P 2 15.00 O 2352 8.00 N 2036 7.00 C 8454 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=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 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=2.03 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 F 1 " - " NAG F 2 " NAG-ASN " NAG A 901 " - " ASN A 261 " " NAG A 902 " - " ASN A 287 " " NAG A 903 " - " ASN A 468 " " NAG B 901 " - " ASN B 261 " " NAG B 902 " - " ASN B 287 " " NAG B 903 " - " ASN B 468 " " NAG C 1 " - " ASN A 488 " " NAG D 1 " - " ASN A 541 " " NAG E 1 " - " ASN B 488 " " NAG F 1 " - " ASN B 541 " Time building additional restraints: 5.90 Conformation dependent library (CDL) restraints added in 2.2 seconds 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 12 sheets defined 44.8% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.737A 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 Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 273 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 308 through 314 removed outlier: 5.094A pdb=" N HIS A 312 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 314 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 346 through 356 removed outlier: 3.883A pdb=" N LYS A 349 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 350 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE A 356 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' 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 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 611 through 636 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 648 through 668 removed outlier: 3.845A pdb=" N PHE A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 678 Processing helix chain 'A' and resid 681 through 702 Processing helix chain 'A' and resid 723 through 745 Processing helix chain 'A' and resid 770 through 793 Processing helix chain 'A' and resid 803 through 820 Processing helix chain 'A' and resid 822 through 825 No H-bonds generated for 'chain 'A' and resid 822 through 825' Processing helix chain 'A' and resid 832 through 860 removed outlier: 4.887A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.732A 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 232 Processing helix chain 'B' and resid 249 through 261 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: 5.105A pdb=" N HIS B 312 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 314 " --> pdb=" O PHE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 346 through 355 removed outlier: 3.897A pdb=" N LYS B 349 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 350 " --> pdb=" O PHE B 347 " (cutoff:3.500A) 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 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' 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 611 through 636 Processing helix chain 'B' and resid 641 through 645 Processing helix chain 'B' and resid 648 through 668 removed outlier: 3.754A pdb=" N PHE B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 681 through 702 Processing helix chain 'B' and resid 723 through 745 Processing helix chain 'B' and resid 770 through 793 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 832 through 860 removed outlier: 4.908A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.160A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA A 140 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU A 37 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 142 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 240 through 243 removed outlier: 9.172A pdb=" N GLU A 241 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR A 211 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE A 243 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA A 213 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 266 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE A 212 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL A 268 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA A 214 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE A 270 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE A 292 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 269 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.413A 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 322 removed outlier: 6.195A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 468 through 470 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 Processing sheet with id= G, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.148A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLY B 35 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL B 141 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 6.963A 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: 9.191A pdb=" N GLU B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR B 211 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE B 243 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA B 213 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 266 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE B 212 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL B 268 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA B 214 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE B 270 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.350A 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 322 removed outlier: 6.221A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.204A 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 589 through 591 Processing sheet with id= L, first strand: chain 'B' and resid 602 through 604 521 hydrogen bonds defined for protein. 1503 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3957 1.34 - 1.46: 3211 1.46 - 1.58: 6002 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 13256 Sorted by residual: bond pdb=" CG TCR A 904 " pdb=" CD1 TCR A 904 " ideal model delta sigma weight residual 1.364 1.477 -0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" CG TCR B 904 " pdb=" CD1 TCR B 904 " ideal model delta sigma weight residual 1.364 1.476 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CD2 TCR A 904 " pdb=" CE2 TCR A 904 " ideal model delta sigma weight residual 1.416 1.479 -0.063 2.00e-02 2.50e+03 9.86e+00 bond pdb=" CD2 TCR B 904 " pdb=" CE2 TCR B 904 " ideal model delta sigma weight residual 1.416 1.478 -0.062 2.00e-02 2.50e+03 9.47e+00 bond pdb=" O3 PO4 A 905 " pdb=" P PO4 A 905 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.25e+00 ... (remaining 13251 not shown) Histogram of bond angle deviations from ideal: 95.73 - 103.40: 127 103.40 - 111.06: 5247 111.06 - 118.72: 5456 118.72 - 126.38: 6993 126.38 - 134.05: 209 Bond angle restraints: 18032 Sorted by residual: angle pdb=" C PHE B 762 " pdb=" N ILE B 763 " pdb=" CA ILE B 763 " ideal model delta sigma weight residual 122.43 118.02 4.41 1.26e+00 6.30e-01 1.22e+01 angle pdb=" C ASN B 468 " pdb=" N PHE B 469 " pdb=" CA PHE B 469 " ideal model delta sigma weight residual 122.21 116.69 5.52 1.62e+00 3.81e-01 1.16e+01 angle pdb=" C ASN A 468 " pdb=" N PHE A 469 " pdb=" CA PHE A 469 " ideal model delta sigma weight residual 121.75 115.99 5.76 1.73e+00 3.34e-01 1.11e+01 angle pdb=" C GLU B 604 " pdb=" N PHE B 605 " pdb=" CA PHE B 605 " ideal model delta sigma weight residual 122.32 127.79 -5.47 1.76e+00 3.23e-01 9.67e+00 angle pdb=" N VAL A 508 " pdb=" CA VAL A 508 " pdb=" C VAL A 508 " ideal model delta sigma weight residual 113.47 110.41 3.06 1.01e+00 9.80e-01 9.16e+00 ... (remaining 18027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7559 17.77 - 35.53: 643 35.53 - 53.30: 112 53.30 - 71.06: 36 71.06 - 88.83: 12 Dihedral angle restraints: 8362 sinusoidal: 3816 harmonic: 4546 Sorted by residual: dihedral pdb=" CB CYS A 546 " pdb=" SG CYS A 546 " pdb=" SG CYS A 565 " pdb=" CB CYS A 565 " ideal model delta sinusoidal sigma weight residual -86.00 -174.83 88.83 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS B 546 " pdb=" SG CYS B 546 " pdb=" SG CYS B 565 " pdb=" CB CYS B 565 " ideal model delta sinusoidal sigma weight residual 93.00 -179.25 -87.75 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 101 " pdb=" CB CYS B 101 " ideal model delta sinusoidal sigma weight residual -86.00 -23.86 -62.14 1 1.00e+01 1.00e-02 5.11e+01 ... (remaining 8359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1944 0.097 - 0.194: 100 0.194 - 0.291: 13 0.291 - 0.388: 8 0.388 - 0.485: 1 Chirality restraints: 2066 Sorted by residual: chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 261 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C14 CLR B 913 " pdb=" C13 CLR B 913 " pdb=" C15 CLR B 913 " pdb=" C8 CLR B 913 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C14 CLR A 912 " pdb=" C13 CLR A 912 " pdb=" C15 CLR A 912 " pdb=" C8 CLR A 912 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 2063 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 746 " -0.054 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO B 747 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 747 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 747 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 438 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO A 439 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 439 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 439 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 438 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO B 439 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 439 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 439 " -0.033 5.00e-02 4.00e+02 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 292 2.71 - 3.26: 13125 3.26 - 3.80: 21865 3.80 - 4.35: 28313 4.35 - 4.90: 45642 Nonbonded interactions: 109237 Sorted by model distance: nonbonded pdb=" OG SER B 657 " pdb=" O SER B 687 " model vdw 2.160 2.440 nonbonded pdb=" OG SER A 657 " pdb=" O SER A 687 " model vdw 2.173 2.440 nonbonded pdb=" OE2 GLU B 232 " pdb=" NH1 ARG B 233 " model vdw 2.232 2.520 nonbonded pdb=" OD2 ASP B 238 " pdb=" OG SER B 262 " model vdw 2.239 2.440 nonbonded pdb=" OG SER B 175 " pdb=" NH2 ARG B 185 " model vdw 2.249 2.520 ... (remaining 109232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 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: 0.160 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: 1.770 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.990 Find NCS groups from input model: 0.640 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:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 13256 Z= 0.262 Angle : 0.698 8.346 18032 Z= 0.352 Chirality : 0.053 0.485 2066 Planarity : 0.004 0.082 2212 Dihedral : 13.548 86.088 5368 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.15 % Allowed : 0.07 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.60 (0.21), residues: 1546 helix: 1.27 (0.19), residues: 716 sheet: -0.67 (0.36), residues: 198 loop : -0.12 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 742 HIS 0.003 0.001 HIS A 463 PHE 0.019 0.001 PHE A 619 TYR 0.025 0.001 TYR A 425 ARG 0.003 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 226 time to evaluate : 1.448 Fit side-chains REVERT: A 285 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7409 (ttp80) REVERT: B 285 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7376 (ttp80) REVERT: B 536 GLU cc_start: 0.6952 (pm20) cc_final: 0.6697 (pm20) outliers start: 2 outliers final: 0 residues processed: 228 average time/residue: 1.1734 time to fit residues: 293.6619 Evaluate side-chains 205 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 253 GLN A 338 HIS A 466 HIS ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 253 GLN B 338 HIS B 466 HIS ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13256 Z= 0.264 Angle : 0.575 11.196 18032 Z= 0.298 Chirality : 0.043 0.296 2066 Planarity : 0.004 0.053 2212 Dihedral : 8.573 59.125 2514 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.29 % Allowed : 8.19 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.59 (0.21), residues: 1546 helix: 1.37 (0.19), residues: 716 sheet: -0.78 (0.34), residues: 228 loop : -0.19 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 742 HIS 0.003 0.001 HIS A 429 PHE 0.022 0.002 PHE A 789 TYR 0.022 0.002 TYR A 425 ARG 0.002 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 1.474 Fit side-chains REVERT: A 285 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7481 (ttp80) REVERT: B 285 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7501 (ttp80) REVERT: B 536 GLU cc_start: 0.6981 (pm20) cc_final: 0.6737 (pm20) outliers start: 31 outliers final: 11 residues processed: 222 average time/residue: 1.2714 time to fit residues: 310.8265 Evaluate side-chains 219 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 208 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 696 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.0000 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 179 GLN A 253 GLN A 338 HIS A 466 HIS ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 338 HIS B 466 HIS ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13256 Z= 0.193 Angle : 0.524 9.138 18032 Z= 0.273 Chirality : 0.042 0.266 2066 Planarity : 0.004 0.045 2212 Dihedral : 8.144 59.673 2514 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.77 % Allowed : 11.14 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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 (0.21), residues: 1546 helix: 1.43 (0.19), residues: 716 sheet: -0.84 (0.34), residues: 228 loop : -0.18 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 742 HIS 0.006 0.001 HIS A 312 PHE 0.016 0.001 PHE B 226 TYR 0.015 0.001 TYR A 425 ARG 0.002 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 214 time to evaluate : 1.377 Fit side-chains REVERT: A 285 ARG cc_start: 0.7702 (ttp80) cc_final: 0.7490 (ttp80) REVERT: B 536 GLU cc_start: 0.6986 (pm20) cc_final: 0.6743 (pm20) REVERT: B 605 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6632 (p90) outliers start: 24 outliers final: 8 residues processed: 221 average time/residue: 1.1504 time to fit residues: 280.3291 Evaluate side-chains 215 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 206 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 338 HIS A 466 HIS A 493 ASN A 594 ASN B 338 HIS B 466 HIS B 493 ASN ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 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 : 0.009 0.093 13256 Z= 0.573 Angle : 0.747 11.158 18032 Z= 0.390 Chirality : 0.052 0.311 2066 Planarity : 0.006 0.067 2212 Dihedral : 8.619 59.582 2514 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.76 % Allowed : 12.17 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.07 (0.20), residues: 1546 helix: 1.01 (0.19), residues: 700 sheet: -1.22 (0.32), residues: 228 loop : -0.43 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 742 HIS 0.008 0.002 HIS A 338 PHE 0.023 0.003 PHE B 469 TYR 0.023 0.003 TYR B 425 ARG 0.006 0.001 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 208 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7941 (mm-30) REVERT: A 261 ASN cc_start: 0.7554 (OUTLIER) cc_final: 0.7340 (m-40) REVERT: A 270 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: B 270 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7573 (m-80) outliers start: 51 outliers final: 19 residues processed: 229 average time/residue: 1.1285 time to fit residues: 284.6968 Evaluate side-chains 224 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 696 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 338 HIS A 466 HIS A 592 ASN A 594 ASN B 338 HIS B 466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13256 Z= 0.275 Angle : 0.580 10.376 18032 Z= 0.304 Chirality : 0.044 0.313 2066 Planarity : 0.004 0.043 2212 Dihedral : 8.195 59.891 2514 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.69 % Allowed : 14.01 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.25 (0.21), residues: 1546 helix: 1.21 (0.19), residues: 700 sheet: -1.25 (0.32), residues: 228 loop : -0.36 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 742 HIS 0.004 0.001 HIS A 463 PHE 0.026 0.002 PHE B 789 TYR 0.013 0.002 TYR A 425 ARG 0.003 0.000 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 210 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: A 285 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7368 (ttp80) REVERT: A 409 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7900 (tp) REVERT: B 270 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: B 409 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7888 (tp) outliers start: 50 outliers final: 24 residues processed: 233 average time/residue: 1.1832 time to fit residues: 306.8623 Evaluate side-chains 232 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 204 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 799 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 37 optimal weight: 0.0980 chunk 150 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 338 HIS A 466 HIS B 338 HIS B 466 HIS B 766 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13256 Z= 0.170 Angle : 0.522 9.334 18032 Z= 0.273 Chirality : 0.043 0.489 2066 Planarity : 0.004 0.042 2212 Dihedral : 7.789 61.119 2514 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.02 % Allowed : 15.19 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.43 (0.21), residues: 1546 helix: 1.35 (0.19), residues: 712 sheet: -1.24 (0.32), residues: 228 loop : -0.26 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 742 HIS 0.008 0.001 HIS B 766 PHE 0.025 0.001 PHE A 789 TYR 0.012 0.001 TYR A 573 ARG 0.002 0.000 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: A 285 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7273 (ttp80) REVERT: B 270 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: B 605 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6825 (p90) REVERT: B 738 ILE cc_start: 0.6931 (pp) cc_final: 0.6729 (pt) outliers start: 41 outliers final: 17 residues processed: 234 average time/residue: 1.1244 time to fit residues: 290.4808 Evaluate side-chains 234 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 214 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.0980 chunk 17 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 338 HIS A 466 HIS A 594 ASN A 802 ASN B 338 HIS B 344 HIS B 466 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13256 Z= 0.239 Angle : 0.549 9.578 18032 Z= 0.286 Chirality : 0.043 0.361 2066 Planarity : 0.004 0.043 2212 Dihedral : 7.699 61.232 2514 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.80 % Allowed : 16.08 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.48 (0.21), residues: 1546 helix: 1.43 (0.19), residues: 700 sheet: -1.26 (0.32), residues: 228 loop : -0.21 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 742 HIS 0.004 0.001 HIS B 463 PHE 0.017 0.001 PHE A 469 TYR 0.012 0.002 TYR A 421 ARG 0.003 0.000 ARG B 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 214 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: A 285 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7295 (ttp80) REVERT: B 270 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: B 738 ILE cc_start: 0.6967 (pp) cc_final: 0.6761 (pt) REVERT: B 743 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6428 (mp) outliers start: 38 outliers final: 21 residues processed: 230 average time/residue: 1.1466 time to fit residues: 291.6445 Evaluate side-chains 233 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 209 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Chi-restraints excluded: chain B residue 743 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 338 HIS A 466 HIS B 338 HIS B 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 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 : 0.004 0.041 13256 Z= 0.248 Angle : 0.551 8.843 18032 Z= 0.290 Chirality : 0.043 0.371 2066 Planarity : 0.004 0.044 2212 Dihedral : 7.601 61.306 2514 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.17 % Allowed : 16.22 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.44 (0.21), residues: 1546 helix: 1.39 (0.19), residues: 704 sheet: -1.32 (0.32), residues: 228 loop : -0.22 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 742 HIS 0.004 0.001 HIS B 463 PHE 0.027 0.001 PHE A 789 TYR 0.012 0.002 TYR A 421 ARG 0.004 0.000 ARG B 286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 216 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: A 285 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7321 (ttp80) REVERT: A 409 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7977 (tp) REVERT: B 270 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7675 (m-80) REVERT: B 409 ILE cc_start: 0.8204 (mm) cc_final: 0.7986 (tp) outliers start: 43 outliers final: 25 residues processed: 238 average time/residue: 1.1064 time to fit residues: 291.0751 Evaluate side-chains 231 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 338 HIS A 466 HIS B 338 HIS B 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13256 Z= 0.181 Angle : 0.531 10.772 18032 Z= 0.276 Chirality : 0.041 0.258 2066 Planarity : 0.004 0.043 2212 Dihedral : 7.402 61.984 2514 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.65 % Allowed : 17.18 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.53 (0.21), residues: 1546 helix: 1.40 (0.19), residues: 718 sheet: -1.26 (0.32), residues: 228 loop : -0.13 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 742 HIS 0.004 0.001 HIS A 463 PHE 0.014 0.001 PHE A 469 TYR 0.033 0.001 TYR A 573 ARG 0.003 0.000 ARG B 286 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: A 285 ARG cc_start: 0.7709 (ttp80) cc_final: 0.7284 (ttp80) REVERT: B 270 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: B 605 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6843 (p90) outliers start: 36 outliers final: 21 residues processed: 228 average time/residue: 1.1943 time to fit residues: 301.3277 Evaluate side-chains 228 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 204 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 155 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 338 HIS A 466 HIS B 338 HIS B 466 HIS ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13256 Z= 0.300 Angle : 0.588 9.020 18032 Z= 0.306 Chirality : 0.044 0.274 2066 Planarity : 0.004 0.043 2212 Dihedral : 7.650 61.077 2514 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.21 % Allowed : 18.14 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.46 (0.21), residues: 1546 helix: 1.37 (0.19), residues: 702 sheet: -1.32 (0.32), residues: 228 loop : -0.15 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 742 HIS 0.004 0.001 HIS A 595 PHE 0.028 0.002 PHE A 789 TYR 0.032 0.002 TYR A 573 ARG 0.005 0.000 ARG B 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 206 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: B 270 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7703 (m-80) outliers start: 30 outliers final: 21 residues processed: 224 average time/residue: 1.1340 time to fit residues: 280.0376 Evaluate side-chains 225 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 338 HIS A 466 HIS B 338 HIS B 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.174879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.154202 restraints weight = 17405.615| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.35 r_work: 0.3597 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13256 Z= 0.200 Angle : 0.544 9.638 18032 Z= 0.282 Chirality : 0.042 0.395 2066 Planarity : 0.004 0.042 2212 Dihedral : 7.475 61.667 2514 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.99 % Allowed : 18.36 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.56 (0.21), residues: 1546 helix: 1.42 (0.19), residues: 714 sheet: -1.27 (0.32), residues: 228 loop : -0.09 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 742 HIS 0.004 0.001 HIS A 463 PHE 0.033 0.001 PHE B 789 TYR 0.027 0.002 TYR A 573 ARG 0.003 0.000 ARG A 286 =============================================================================== Job complete usr+sys time: 4962.39 seconds wall clock time: 90 minutes 22.31 seconds (5422.31 seconds total)