Starting phenix.real_space_refine (version: dev) on Mon Feb 20 20:46:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/02_2023/7sil_25143_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/02_2023/7sil_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_25143/02_2023/7sil_25143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/02_2023/7sil_25143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/02_2023/7sil_25143_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/02_2023/7sil_25143_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 7.36, per 1000 atoms: 0.57 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: 5.14 Conformation dependent library (CDL) restraints added in 1.6 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: 1.73 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: 3.96 Time building geometry restraints manager: 5.54 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: 6962 17.77 - 35.53: 597 35.53 - 53.30: 97 53.30 - 71.06: 24 71.06 - 88.83: 12 Dihedral angle restraints: 7692 sinusoidal: 3146 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 7689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1946 0.097 - 0.194: 98 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 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. 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: 0.180 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: 2.150 Check model and map are aligned: 0.190 Process input model: 34.530 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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= 0.245 Angle : 0.679 8.346 18032 Z= 0.348 Chirality : 0.052 0.485 2066 Planarity : 0.004 0.082 2212 Dihedral : 13.573 86.088 4698 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 % 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 *********************** 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 : 1.359 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 228 average time/residue: 1.1052 time to fit residues: 277.7726 Evaluate side-chains 205 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.494 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0587 ------------------------------------------------------------------------------- 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: 6.9990 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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: 0.7251 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 13256 Z= 0.304 Angle : 0.588 11.088 18032 Z= 0.309 Chirality : 0.044 0.302 2066 Planarity : 0.004 0.053 2212 Dihedral : 6.755 59.831 1844 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 2.43 % 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: 1.32 (0.19), residues: 718 sheet: -0.85 (0.33), residues: 228 loop : -0.20 (0.24), residues: 600 *********************** 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 249 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 1.455 Fit side-chains outliers start: 33 outliers final: 15 residues processed: 225 average time/residue: 1.1173 time to fit residues: 277.3779 Evaluate side-chains 224 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 209 time to evaluate : 1.447 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 4 residues processed: 11 average time/residue: 0.3895 time to fit residues: 7.5432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13256 Z= 0.193 Angle : 0.526 9.618 18032 Z= 0.277 Chirality : 0.042 0.309 2066 Planarity : 0.004 0.045 2212 Dihedral : 6.470 58.606 1844 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 2.06 % 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: 0.58 (0.21), residues: 1546 helix: 1.42 (0.19), residues: 716 sheet: -0.89 (0.34), residues: 228 loop : -0.24 (0.24), residues: 602 *********************** 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 244 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 1.542 Fit side-chains outliers start: 28 outliers final: 13 residues processed: 224 average time/residue: 1.0756 time to fit residues: 266.2543 Evaluate side-chains 221 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 208 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 5 residues processed: 8 average time/residue: 0.6004 time to fit residues: 7.6304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 73 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 27 GLN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.074 13256 Z= 0.455 Angle : 0.659 10.195 18032 Z= 0.346 Chirality : 0.048 0.320 2066 Planarity : 0.005 0.052 2212 Dihedral : 6.930 59.971 1844 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 3.17 % 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 (0.20), residues: 1546 helix: 1.20 (0.19), residues: 702 sheet: -1.16 (0.32), residues: 228 loop : -0.39 (0.24), residues: 616 *********************** 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 248 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 205 time to evaluate : 1.433 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 21 residues processed: 224 average time/residue: 1.0300 time to fit residues: 256.2905 Evaluate side-chains 221 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 200 time to evaluate : 1.433 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 9 residues processed: 12 average time/residue: 0.5899 time to fit residues: 10.3363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 2 optimal weight: 0.0870 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 128 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 135 optimal weight: 0.3980 chunk 38 optimal weight: 8.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- 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 B 27 GLN B 179 GLN B 338 HIS B 466 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 13256 Z= 0.154 Angle : 0.514 9.136 18032 Z= 0.269 Chirality : 0.042 0.276 2066 Planarity : 0.004 0.042 2212 Dihedral : 6.477 59.034 1844 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 2.29 % 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: 0.47 (0.21), residues: 1546 helix: 1.34 (0.19), residues: 714 sheet: -1.12 (0.33), residues: 228 loop : -0.22 (0.25), residues: 604 *********************** 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 247 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 216 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 13 residues processed: 230 average time/residue: 1.0817 time to fit residues: 275.3443 Evaluate side-chains 222 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 209 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.5269 time to fit residues: 5.1360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 594 ASN B 338 HIS B 466 HIS B 766 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 13256 Z= 0.290 Angle : 0.560 9.511 18032 Z= 0.293 Chirality : 0.044 0.324 2066 Planarity : 0.004 0.042 2212 Dihedral : 6.578 59.992 1844 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 2.58 % 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: 0.51 (0.21), residues: 1546 helix: 1.44 (0.19), residues: 702 sheet: -1.17 (0.32), residues: 228 loop : -0.22 (0.24), residues: 616 *********************** 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 251 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 216 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 14 residues processed: 233 average time/residue: 1.1040 time to fit residues: 284.0757 Evaluate side-chains 226 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 212 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.5433 time to fit residues: 5.1978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 B 338 HIS B 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 13256 Z= 0.285 Angle : 0.562 8.523 18032 Z= 0.297 Chirality : 0.043 0.314 2066 Planarity : 0.004 0.042 2212 Dihedral : 6.605 59.067 1844 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 2.95 % 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: 0.47 (0.21), residues: 1546 helix: 1.42 (0.19), residues: 700 sheet: -1.29 (0.32), residues: 228 loop : -0.23 (0.24), residues: 618 *********************** 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 251 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 211 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 19 residues processed: 232 average time/residue: 1.1104 time to fit residues: 285.2512 Evaluate side-chains 223 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.1288 time to fit residues: 2.9105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 344 HIS B 466 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 13256 Z= 0.238 Angle : 0.556 11.457 18032 Z= 0.291 Chirality : 0.044 0.558 2066 Planarity : 0.004 0.042 2212 Dihedral : 6.532 58.790 1844 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 2.65 % 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: 0.47 (0.21), residues: 1546 helix: 1.39 (0.19), residues: 700 sheet: -1.30 (0.32), residues: 228 loop : -0.17 (0.24), residues: 618 *********************** 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 246 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 22 residues processed: 232 average time/residue: 1.0643 time to fit residues: 274.1819 Evaluate side-chains 228 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 206 time to evaluate : 1.510 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 6 average time/residue: 0.8185 time to fit residues: 7.5494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.3980 chunk 140 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 84 optimal weight: 0.0970 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 802 ASN B 338 HIS B 466 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 13256 Z= 0.156 Angle : 0.508 8.299 18032 Z= 0.269 Chirality : 0.042 0.503 2066 Planarity : 0.004 0.041 2212 Dihedral : 6.294 59.386 1844 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 1.84 % 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: 0.49 (0.21), residues: 1546 helix: 1.42 (0.19), residues: 712 sheet: -1.33 (0.32), residues: 242 loop : -0.16 (0.25), residues: 592 *********************** 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 237 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 212 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 18 residues processed: 226 average time/residue: 1.0734 time to fit residues: 268.7880 Evaluate side-chains 225 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 207 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.5536 time to fit residues: 4.5530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 338 HIS A 466 HIS A 594 ASN B 253 GLN B 338 HIS B 466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1713 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= 0.187 Angle : 0.531 11.278 18032 Z= 0.278 Chirality : 0.042 0.345 2066 Planarity : 0.004 0.042 2212 Dihedral : 6.226 59.744 1844 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 1.33 % 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: 0.61 (0.21), residues: 1546 helix: 1.45 (0.19), residues: 714 sheet: -1.18 (0.33), residues: 228 loop : -0.07 (0.25), residues: 604 ********************** 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 228 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 210 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 225 average time/residue: 1.0938 time to fit residues: 272.2049 Evaluate side-chains 221 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 206 time to evaluate : 1.456 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 2.0288 time to fit residues: 4.1603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4107 r_free = 0.4107 target = 0.174372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153499 restraints weight = 17300.766| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.31 r_work: 0.3586 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 13256 Z= 0.268 Angle : 0.574 9.091 18032 Z= 0.305 Chirality : 0.043 0.215 2066 Planarity : 0.004 0.043 2212 Dihedral : 6.304 59.809 1844 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 1.77 % 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: 0.52 (0.21), residues: 1546 helix: 1.39 (0.19), residues: 712 sheet: -1.24 (0.33), residues: 228 loop : -0.14 (0.25), residues: 606 =============================================================================== Job complete usr+sys time: 4722.44 seconds wall clock time: 84 minutes 23.90 seconds (5063.90 seconds total)