Starting phenix.real_space_refine on Thu Feb 5 20:26:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vyh_65453/02_2026/9vyh_65453.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vyh_65453/02_2026/9vyh_65453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vyh_65453/02_2026/9vyh_65453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vyh_65453/02_2026/9vyh_65453.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vyh_65453/02_2026/9vyh_65453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vyh_65453/02_2026/9vyh_65453.map" } resolution = 3.5 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 12412 2.51 5 N 3550 2.21 5 O 3906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19910 Number of models: 1 Model: "" Number of chains: 6 Chain: "m" Number of atoms: 4598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4598 Classifications: {'peptide': 630} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 598} Chain: "n" Number of atoms: 4598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4598 Classifications: {'peptide': 630} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 598} Chain: "o" Number of atoms: 4588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4588 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 31, 'TRANS': 596} Chain: "q" Number of atoms: 2042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2042 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 12, 'TRANS': 256} Chain: "r" Number of atoms: 2042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2042 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 12, 'TRANS': 256} Chain: "p" Number of atoms: 2042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2042 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 12, 'TRANS': 256} Time building chain proxies: 4.74, per 1000 atoms: 0.24 Number of scatterers: 19910 At special positions: 0 Unit cell: (133.75, 185.11, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 3906 8.00 N 3550 7.00 C 12412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4900 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 34 sheets defined 25.2% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'm' and resid 116 through 139 removed outlier: 4.103A pdb=" N ALA m 120 " --> pdb=" O ALA m 116 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU m 138 " --> pdb=" O GLU m 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 141 through 149 Processing helix chain 'm' and resid 150 through 159 Processing helix chain 'm' and resid 159 through 169 removed outlier: 3.678A pdb=" N GLY m 169 " --> pdb=" O LEU m 165 " (cutoff:3.500A) Processing helix chain 'm' and resid 169 through 179 Processing helix chain 'm' and resid 179 through 186 removed outlier: 3.537A pdb=" N ILE m 183 " --> pdb=" O ASN m 179 " (cutoff:3.500A) Processing helix chain 'm' and resid 324 through 329 removed outlier: 3.742A pdb=" N ILE m 328 " --> pdb=" O GLN m 324 " (cutoff:3.500A) Processing helix chain 'm' and resid 378 through 380 No H-bonds generated for 'chain 'm' and resid 378 through 380' Processing helix chain 'm' and resid 406 through 424 removed outlier: 4.616A pdb=" N ARG m 410 " --> pdb=" O SER m 406 " (cutoff:3.500A) Processing helix chain 'm' and resid 441 through 445 removed outlier: 3.666A pdb=" N MET m 444 " --> pdb=" O ILE m 441 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN m 445 " --> pdb=" O ASP m 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 441 through 445' Processing helix chain 'm' and resid 458 through 478 Processing helix chain 'm' and resid 499 through 520 Processing helix chain 'm' and resid 540 through 552 Processing helix chain 'm' and resid 561 through 566 removed outlier: 3.614A pdb=" N GLY m 566 " --> pdb=" O GLN m 563 " (cutoff:3.500A) Processing helix chain 'm' and resid 587 through 607 Processing helix chain 'm' and resid 650 through 652 No H-bonds generated for 'chain 'm' and resid 650 through 652' Processing helix chain 'n' and resid 117 through 149 Processing helix chain 'n' and resid 150 through 159 Processing helix chain 'n' and resid 159 through 169 Processing helix chain 'n' and resid 169 through 179 Processing helix chain 'n' and resid 179 through 186 removed outlier: 3.985A pdb=" N LEU n 186 " --> pdb=" O SER n 182 " (cutoff:3.500A) Processing helix chain 'n' and resid 230 through 235 removed outlier: 3.536A pdb=" N THR n 235 " --> pdb=" O SER n 231 " (cutoff:3.500A) Processing helix chain 'n' and resid 324 through 329 Processing helix chain 'n' and resid 378 through 380 No H-bonds generated for 'chain 'n' and resid 378 through 380' Processing helix chain 'n' and resid 397 through 401 removed outlier: 3.782A pdb=" N VAL n 401 " --> pdb=" O TRP n 398 " (cutoff:3.500A) Processing helix chain 'n' and resid 406 through 423 removed outlier: 4.245A pdb=" N ARG n 410 " --> pdb=" O SER n 406 " (cutoff:3.500A) Processing helix chain 'n' and resid 440 through 445 removed outlier: 3.669A pdb=" N GLN n 445 " --> pdb=" O ASP n 442 " (cutoff:3.500A) Processing helix chain 'n' and resid 458 through 478 Processing helix chain 'n' and resid 499 through 520 Processing helix chain 'n' and resid 540 through 553 removed outlier: 3.869A pdb=" N LYS n 544 " --> pdb=" O ILE n 540 " (cutoff:3.500A) Processing helix chain 'n' and resid 562 through 568 removed outlier: 4.113A pdb=" N GLN n 568 " --> pdb=" O LEU n 565 " (cutoff:3.500A) Processing helix chain 'n' and resid 587 through 607 Processing helix chain 'n' and resid 649 through 654 removed outlier: 3.835A pdb=" N LEU n 652 " --> pdb=" O PRO n 649 " (cutoff:3.500A) Processing helix chain 'o' and resid 117 through 149 Processing helix chain 'o' and resid 150 through 159 removed outlier: 3.625A pdb=" N ALA o 159 " --> pdb=" O ALA o 155 " (cutoff:3.500A) Processing helix chain 'o' and resid 159 through 169 Processing helix chain 'o' and resid 169 through 178 Processing helix chain 'o' and resid 324 through 329 Processing helix chain 'o' and resid 406 through 423 removed outlier: 4.505A pdb=" N ARG o 410 " --> pdb=" O SER o 406 " (cutoff:3.500A) Processing helix chain 'o' and resid 458 through 478 Processing helix chain 'o' and resid 499 through 520 Processing helix chain 'o' and resid 540 through 552 Processing helix chain 'o' and resid 562 through 566 Processing helix chain 'o' and resid 587 through 607 Processing helix chain 'q' and resid 22 through 30 Processing helix chain 'q' and resid 39 through 43 Processing helix chain 'q' and resid 53 through 58 removed outlier: 3.856A pdb=" N GLN q 57 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing helix chain 'q' and resid 254 through 269 removed outlier: 3.502A pdb=" N ASN q 263 " --> pdb=" O THR q 259 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG q 264 " --> pdb=" O SER q 260 " (cutoff:3.500A) Processing helix chain 'r' and resid 22 through 30 Processing helix chain 'r' and resid 53 through 58 removed outlier: 3.887A pdb=" N GLN r 57 " --> pdb=" O ASN r 53 " (cutoff:3.500A) Processing helix chain 'r' and resid 254 through 269 removed outlier: 3.623A pdb=" N SER r 260 " --> pdb=" O ALA r 256 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR r 267 " --> pdb=" O ASN r 263 " (cutoff:3.500A) Processing helix chain 'p' and resid 22 through 30 Processing helix chain 'p' and resid 39 through 43 Processing helix chain 'p' and resid 53 through 58 removed outlier: 3.867A pdb=" N GLN p 57 " --> pdb=" O ASN p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 211 through 215 removed outlier: 3.928A pdb=" N THR p 215 " --> pdb=" O THR p 212 " (cutoff:3.500A) Processing helix chain 'p' and resid 254 through 270 Processing sheet with id=AA1, first strand: chain 'm' and resid 189 through 193 removed outlier: 3.513A pdb=" N THR m 189 " --> pdb=" O ASN r 7 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG m 214 " --> pdb=" O GLU m 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'm' and resid 241 through 244 removed outlier: 3.666A pdb=" N VAL m 258 " --> pdb=" O VAL m 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'm' and resid 275 through 280 removed outlier: 6.796A pdb=" N VAL m 285 " --> pdb=" O ALA m 277 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE m 279 " --> pdb=" O ARG m 283 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG m 283 " --> pdb=" O ILE m 279 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER m 284 " --> pdb=" O VAL m 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'm' and resid 382 through 387 removed outlier: 3.934A pdb=" N GLY m 384 " --> pdb=" O GLN m 354 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU m 353 " --> pdb=" O ILE m 431 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N ALA m 433 " --> pdb=" O LEU m 353 " (cutoff:3.500A) removed outlier: 12.198A pdb=" N ARG m 355 " --> pdb=" O ALA m 433 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N HIS m 428 " --> pdb=" O LEU m 315 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA m 321 " --> pdb=" O ILE m 432 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N VAL m 316 " --> pdb=" O VAL m 483 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N GLY m 485 " --> pdb=" O VAL m 316 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE m 318 " --> pdb=" O GLY m 485 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU m 487 " --> pdb=" O ILE m 318 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU m 320 " --> pdb=" O LEU m 487 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS m 489 " --> pdb=" O LEU m 320 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP m 322 " --> pdb=" O LYS m 489 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE m 526 " --> pdb=" O VAL m 484 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'm' and resid 654 through 658 removed outlier: 5.970A pdb=" N ARG m 691 " --> pdb=" O VAL m 742 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N SER m 618 " --> pdb=" O SER m 741 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR m 743 " --> pdb=" O SER m 618 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ALA m 620 " --> pdb=" O THR m 743 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA m 619 " --> pdb=" O THR m 630 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR m 676 " --> pdb=" O LEU m 672 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU m 672 " --> pdb=" O THR m 676 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR m 680 " --> pdb=" O GLY m 668 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY m 668 " --> pdb=" O THR m 680 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'm' and resid 638 through 640 Processing sheet with id=AA7, first strand: chain 'm' and resid 722 through 723 removed outlier: 4.028A pdb=" N GLY m 722 " --> pdb=" O ARG m 731 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'n' and resid 189 through 193 removed outlier: 3.504A pdb=" N THR n 189 " --> pdb=" O ASN p 7 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG n 203 " --> pdb=" O SER n 215 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER n 215 " --> pdb=" O ARG n 203 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU n 205 " --> pdb=" O LEU n 213 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'n' and resid 240 through 244 Processing sheet with id=AB1, first strand: chain 'n' and resid 275 through 280 removed outlier: 5.747A pdb=" N LEU n 276 " --> pdb=" O THR n 287 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR n 287 " --> pdb=" O LEU n 276 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER n 284 " --> pdb=" O VAL n 301 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'n' and resid 382 through 387 removed outlier: 3.944A pdb=" N GLY n 384 " --> pdb=" O GLN n 354 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU n 353 " --> pdb=" O ILE n 431 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU n 315 " --> pdb=" O HIS n 428 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU n 430 " --> pdb=" O LEU n 315 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N HIS n 317 " --> pdb=" O LEU n 430 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU n 320 " --> pdb=" O VAL n 484 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N VAL n 486 " --> pdb=" O LEU n 320 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS n 530 " --> pdb=" O ARG n 488 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL n 531 " --> pdb=" O ALA n 558 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'n' and resid 616 through 622 removed outlier: 5.730A pdb=" N ALA n 617 " --> pdb=" O THR n 632 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N THR n 632 " --> pdb=" O ALA n 617 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA n 619 " --> pdb=" O THR n 630 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'n' and resid 638 through 640 Processing sheet with id=AB5, first strand: chain 'n' and resid 655 through 657 Processing sheet with id=AB6, first strand: chain 'n' and resid 722 through 723 removed outlier: 3.709A pdb=" N GLY n 722 " --> pdb=" O ARG n 731 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'o' and resid 189 through 193 removed outlier: 6.300A pdb=" N ARG o 203 " --> pdb=" O SER o 215 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER o 215 " --> pdb=" O ARG o 203 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU o 205 " --> pdb=" O LEU o 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'o' and resid 240 through 244 removed outlier: 3.620A pdb=" N VAL o 258 " --> pdb=" O VAL o 250 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'o' and resid 275 through 280 removed outlier: 5.575A pdb=" N LEU o 276 " --> pdb=" O THR o 287 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR o 287 " --> pdb=" O LEU o 276 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N SER o 284 " --> pdb=" O VAL o 301 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'o' and resid 385 through 387 removed outlier: 3.660A pdb=" N ILE o 386 " --> pdb=" O MET o 352 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET o 352 " --> pdb=" O ILE o 386 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP o 351 " --> pdb=" O ILE o 431 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ALA o 433 " --> pdb=" O TRP o 351 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N LEU o 353 " --> pdb=" O ALA o 433 " (cutoff:3.500A) removed outlier: 13.616A pdb=" N GLY o 435 " --> pdb=" O LEU o 353 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N HIS o 428 " --> pdb=" O LEU o 315 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY o 323 " --> pdb=" O ILE o 434 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU o 320 " --> pdb=" O VAL o 484 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL o 486 " --> pdb=" O LEU o 320 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASP o 322 " --> pdb=" O VAL o 486 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG o 488 " --> pdb=" O ASP o 322 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS o 530 " --> pdb=" O ARG o 488 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU o 557 " --> pdb=" O TRP o 527 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU o 529 " --> pdb=" O LEU o 557 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLY o 559 " --> pdb=" O GLU o 529 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'o' and resid 616 through 623 removed outlier: 5.608A pdb=" N ALA o 617 " --> pdb=" O THR o 632 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR o 632 " --> pdb=" O ALA o 617 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA o 619 " --> pdb=" O THR o 630 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'o' and resid 638 through 640 Processing sheet with id=AC4, first strand: chain 'o' and resid 654 through 657 Processing sheet with id=AC5, first strand: chain 'q' and resid 34 through 38 removed outlier: 6.160A pdb=" N ASP q 241 " --> pdb=" O THR q 79 " (cutoff:3.500A) removed outlier: 11.381A pdb=" N THR q 79 " --> pdb=" O ASP q 241 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR q 71 " --> pdb=" O ASN q 82 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'q' and resid 34 through 38 removed outlier: 5.424A pdb=" N VAL q 107 " --> pdb=" O GLY q 240 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE q 242 " --> pdb=" O ALA q 105 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA q 105 " --> pdb=" O ILE q 242 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL q 244 " --> pdb=" O THR q 103 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR q 103 " --> pdb=" O VAL q 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'q' and resid 47 through 48 removed outlier: 5.953A pdb=" N ASN q 117 " --> pdb=" O ASN q 144 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN q 144 " --> pdb=" O ASN q 117 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TRP q 119 " --> pdb=" O MET q 142 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N MET q 142 " --> pdb=" O TRP q 119 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL q 121 " --> pdb=" O VAL q 140 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'q' and resid 47 through 48 removed outlier: 5.953A pdb=" N ASN q 117 " --> pdb=" O ASN q 144 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN q 144 " --> pdb=" O ASN q 117 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TRP q 119 " --> pdb=" O MET q 142 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N MET q 142 " --> pdb=" O TRP q 119 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL q 121 " --> pdb=" O VAL q 140 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'r' and resid 34 through 38 removed outlier: 6.543A pdb=" N VAL r 244 " --> pdb=" O THR r 35 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TRP r 37 " --> pdb=" O ILE r 242 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE r 242 " --> pdb=" O TRP r 37 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU r 239 " --> pdb=" O VAL r 81 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL r 81 " --> pdb=" O LEU r 239 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP r 241 " --> pdb=" O THR r 79 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N THR r 79 " --> pdb=" O ASP r 241 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'r' and resid 34 through 38 removed outlier: 6.543A pdb=" N VAL r 244 " --> pdb=" O THR r 35 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TRP r 37 " --> pdb=" O ILE r 242 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE r 242 " --> pdb=" O TRP r 37 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL r 107 " --> pdb=" O GLY r 240 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE r 242 " --> pdb=" O ALA r 105 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA r 105 " --> pdb=" O ILE r 242 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL r 244 " --> pdb=" O THR r 103 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR r 103 " --> pdb=" O VAL r 244 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 47 through 48 removed outlier: 6.524A pdb=" N VAL r 140 " --> pdb=" O PRO r 120 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N CYS r 122 " --> pdb=" O LEU r 138 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU r 138 " --> pdb=" O CYS r 122 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'r' and resid 47 through 48 removed outlier: 6.524A pdb=" N VAL r 140 " --> pdb=" O PRO r 120 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N CYS r 122 " --> pdb=" O LEU r 138 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU r 138 " --> pdb=" O CYS r 122 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'p' and resid 34 through 38 removed outlier: 6.228A pdb=" N ASP p 241 " --> pdb=" O THR p 79 " (cutoff:3.500A) removed outlier: 11.521A pdb=" N THR p 79 " --> pdb=" O ASP p 241 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR p 71 " --> pdb=" O ASN p 82 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'p' and resid 34 through 38 removed outlier: 4.826A pdb=" N ASP p 241 " --> pdb=" O VAL p 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'p' and resid 47 through 48 removed outlier: 7.081A pdb=" N VAL p 140 " --> pdb=" O PRO p 120 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N CYS p 122 " --> pdb=" O LEU p 138 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU p 138 " --> pdb=" O CYS p 122 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'p' and resid 47 through 48 removed outlier: 7.081A pdb=" N VAL p 140 " --> pdb=" O PRO p 120 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N CYS p 122 " --> pdb=" O LEU p 138 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU p 138 " --> pdb=" O CYS p 122 " (cutoff:3.500A) 863 hydrogen bonds defined for protein. 2358 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5288 1.33 - 1.45: 3652 1.45 - 1.57: 11278 1.57 - 1.69: 1 1.69 - 1.82: 78 Bond restraints: 20297 Sorted by residual: bond pdb=" C ILE n 452 " pdb=" N PRO n 453 " ideal model delta sigma weight residual 1.332 1.368 -0.036 1.33e-02 5.65e+03 7.31e+00 bond pdb=" N ARG n 688 " pdb=" CA ARG n 688 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.25e-02 6.40e+03 6.81e+00 bond pdb=" N ASP o 648 " pdb=" CA ASP o 648 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.39e-02 5.18e+03 6.02e+00 bond pdb=" N SER n 643 " pdb=" CA SER n 643 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.10e-02 8.26e+03 5.96e+00 bond pdb=" N THR o 676 " pdb=" CA THR o 676 " ideal model delta sigma weight residual 1.454 1.483 -0.028 1.17e-02 7.31e+03 5.86e+00 ... (remaining 20292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 27478 2.31 - 4.62: 265 4.62 - 6.93: 32 6.93 - 9.23: 4 9.23 - 11.54: 2 Bond angle restraints: 27781 Sorted by residual: angle pdb=" O ASN o 673 " pdb=" C ASN o 673 " pdb=" N PRO o 674 " ideal model delta sigma weight residual 121.32 117.40 3.92 8.50e-01 1.38e+00 2.13e+01 angle pdb=" CA ASN o 673 " pdb=" C ASN o 673 " pdb=" N PRO o 674 " ideal model delta sigma weight residual 117.59 121.83 -4.24 9.90e-01 1.02e+00 1.83e+01 angle pdb=" CA PRO m 581 " pdb=" N PRO m 581 " pdb=" CD PRO m 581 " ideal model delta sigma weight residual 112.00 106.15 5.85 1.40e+00 5.10e-01 1.74e+01 angle pdb=" N ASN o 651 " pdb=" CA ASN o 651 " pdb=" C ASN o 651 " ideal model delta sigma weight residual 109.39 102.84 6.55 1.59e+00 3.96e-01 1.69e+01 angle pdb=" CB MET n 444 " pdb=" CG MET n 444 " pdb=" SD MET n 444 " ideal model delta sigma weight residual 112.70 124.24 -11.54 3.00e+00 1.11e-01 1.48e+01 ... (remaining 27776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 10284 17.31 - 34.61: 1294 34.61 - 51.92: 322 51.92 - 69.22: 57 69.22 - 86.53: 14 Dihedral angle restraints: 11971 sinusoidal: 4340 harmonic: 7631 Sorted by residual: dihedral pdb=" CA GLY q 91 " pdb=" C GLY q 91 " pdb=" N PHE q 92 " pdb=" CA PHE q 92 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER m 643 " pdb=" C SER m 643 " pdb=" N PRO m 644 " pdb=" CA PRO m 644 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PHE r 223 " pdb=" C PHE r 223 " pdb=" N GLY r 224 " pdb=" CA GLY r 224 " ideal model delta harmonic sigma weight residual 180.00 162.48 17.52 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 11968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2573 0.045 - 0.089: 501 0.089 - 0.134: 227 0.134 - 0.178: 8 0.178 - 0.223: 2 Chirality restraints: 3311 Sorted by residual: chirality pdb=" CB VAL m 396 " pdb=" CA VAL m 396 " pdb=" CG1 VAL m 396 " pdb=" CG2 VAL m 396 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB THR n 343 " pdb=" CA THR n 343 " pdb=" OG1 THR n 343 " pdb=" CG2 THR n 343 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CB THR n 139 " pdb=" CA THR n 139 " pdb=" OG1 THR n 139 " pdb=" CG2 THR n 139 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 3308 not shown) Planarity restraints: 3648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY m 559 " 0.046 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO m 560 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO m 560 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO m 560 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN m 580 " 0.040 5.00e-02 4.00e+02 5.89e-02 5.56e+00 pdb=" N PRO m 581 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO m 581 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO m 581 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP o 281 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" CG ASP o 281 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP o 281 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP o 281 " 0.014 2.00e-02 2.50e+03 ... (remaining 3645 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3739 2.77 - 3.30: 18533 3.30 - 3.84: 34116 3.84 - 4.37: 38529 4.37 - 4.90: 69971 Nonbonded interactions: 164888 Sorted by model distance: nonbonded pdb=" O SER p 209 " pdb=" OG SER p 209 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR r 211 " pdb=" OE1 GLN r 214 " model vdw 2.244 3.040 nonbonded pdb=" O SER r 209 " pdb=" OG SER r 209 " model vdw 2.246 3.040 nonbonded pdb=" NE2 GLN q 115 " pdb=" O SER q 232 " model vdw 2.246 3.120 nonbonded pdb=" O THR o 577 " pdb=" OG1 THR o 577 " model vdw 2.249 3.040 ... (remaining 164883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'm' and resid 116 through 743) selection = (chain 'n' and resid 116 through 743) selection = chain 'o' } ncs_group { reference = chain 'p' selection = chain 'q' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.220 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.003 0.100 20297 Z= 0.131 Angle : 0.557 11.543 27781 Z= 0.302 Chirality : 0.042 0.223 3311 Planarity : 0.004 0.071 3648 Dihedral : 16.181 86.531 7071 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.42 % Rotamer: Outliers : 0.57 % Allowed : 29.16 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2683 helix: 2.29 (0.22), residues: 591 sheet: 0.11 (0.24), residues: 506 loop : -1.18 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG n 712 TYR 0.010 0.001 TYR o 562 PHE 0.019 0.001 PHE p 173 TRP 0.009 0.001 TRP o 351 HIS 0.003 0.001 HIS o 490 Details of bonding type rmsd covalent geometry : bond 0.00263 (20297) covalent geometry : angle 0.55688 (27781) hydrogen bonds : bond 0.13636 ( 807) hydrogen bonds : angle 6.37987 ( 2358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 269 time to evaluate : 0.679 Fit side-chains REVERT: m 599 ILE cc_start: 0.8662 (tp) cc_final: 0.8462 (tp) REVERT: m 656 TYR cc_start: 0.6869 (t80) cc_final: 0.6426 (t80) REVERT: o 648 ASP cc_start: 0.7049 (t70) cc_final: 0.6810 (t0) outliers start: 12 outliers final: 7 residues processed: 274 average time/residue: 0.1165 time to fit residues: 53.2995 Evaluate side-chains 271 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 264 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain m residue 244 THR Chi-restraints excluded: chain m residue 615 THR Chi-restraints excluded: chain m residue 629 VAL Chi-restraints excluded: chain n residue 643 SER Chi-restraints excluded: chain o residue 326 LEU Chi-restraints excluded: chain q residue 233 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.0370 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0020 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.5868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 117 ASN r 217 ASN ** r 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.136722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.109140 restraints weight = 27140.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.112059 restraints weight = 15138.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.113912 restraints weight = 10356.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.115105 restraints weight = 8088.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.115746 restraints weight = 6915.623| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20297 Z= 0.097 Angle : 0.501 8.639 27781 Z= 0.257 Chirality : 0.042 0.150 3311 Planarity : 0.004 0.049 3648 Dihedral : 3.913 51.710 2883 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.08 % Allowed : 25.70 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.16), residues: 2683 helix: 2.41 (0.21), residues: 601 sheet: -0.00 (0.23), residues: 509 loop : -1.21 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG n 712 TYR 0.011 0.001 TYR o 656 PHE 0.012 0.001 PHE r 227 TRP 0.009 0.001 TRP p 37 HIS 0.003 0.001 HIS o 530 Details of bonding type rmsd covalent geometry : bond 0.00224 (20297) covalent geometry : angle 0.50085 (27781) hydrogen bonds : bond 0.03154 ( 807) hydrogen bonds : angle 4.69523 ( 2358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 284 time to evaluate : 0.739 Fit side-chains REVERT: m 442 ASP cc_start: 0.7929 (p0) cc_final: 0.7558 (p0) REVERT: m 571 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7275 (tp40) REVERT: m 599 ILE cc_start: 0.8376 (tp) cc_final: 0.8113 (tp) REVERT: m 656 TYR cc_start: 0.7144 (t80) cc_final: 0.6760 (t80) REVERT: m 714 MET cc_start: 0.8210 (mmm) cc_final: 0.7971 (mmm) REVERT: n 272 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7835 (mt) REVERT: n 331 ASN cc_start: 0.7249 (t0) cc_final: 0.7022 (t0) REVERT: o 648 ASP cc_start: 0.7349 (t70) cc_final: 0.7070 (t0) REVERT: r 43 TYR cc_start: 0.8773 (t80) cc_final: 0.7665 (t80) outliers start: 65 outliers final: 35 residues processed: 329 average time/residue: 0.1151 time to fit residues: 62.6933 Evaluate side-chains 301 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 264 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 186 LEU Chi-restraints excluded: chain m residue 345 VAL Chi-restraints excluded: chain m residue 571 GLN Chi-restraints excluded: chain m residue 629 VAL Chi-restraints excluded: chain m residue 719 THR Chi-restraints excluded: chain n residue 199 ASP Chi-restraints excluded: chain n residue 272 LEU Chi-restraints excluded: chain n residue 304 ASP Chi-restraints excluded: chain n residue 358 VAL Chi-restraints excluded: chain n residue 367 SER Chi-restraints excluded: chain n residue 439 ILE Chi-restraints excluded: chain n residue 457 THR Chi-restraints excluded: chain n residue 510 ASP Chi-restraints excluded: chain o residue 163 ILE Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 224 ASN Chi-restraints excluded: chain o residue 396 VAL Chi-restraints excluded: chain o residue 547 LEU Chi-restraints excluded: chain o residue 573 THR Chi-restraints excluded: chain o residue 597 GLU Chi-restraints excluded: chain o residue 598 MET Chi-restraints excluded: chain o residue 629 VAL Chi-restraints excluded: chain o residue 700 THR Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 90 VAL Chi-restraints excluded: chain q residue 104 LEU Chi-restraints excluded: chain q residue 201 VAL Chi-restraints excluded: chain q residue 262 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain p residue 11 ASP Chi-restraints excluded: chain p residue 62 SER Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 128 VAL Chi-restraints excluded: chain p residue 183 ILE Chi-restraints excluded: chain p residue 226 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 209 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 462 GLN n 324 GLN n 341 HIS n 651 ASN o 179 ASN r 127 GLN ** r 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.125895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.099808 restraints weight = 28082.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.101864 restraints weight = 16718.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.102838 restraints weight = 11449.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.103729 restraints weight = 9118.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.103833 restraints weight = 8243.010| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20297 Z= 0.269 Angle : 0.634 8.349 27781 Z= 0.326 Chirality : 0.046 0.195 3311 Planarity : 0.005 0.051 3648 Dihedral : 4.509 25.445 2875 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.79 % Allowed : 25.32 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2683 helix: 1.95 (0.21), residues: 612 sheet: -0.22 (0.22), residues: 522 loop : -1.35 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG q 220 TYR 0.014 0.002 TYR r 269 PHE 0.032 0.002 PHE r 227 TRP 0.011 0.001 TRP o 266 HIS 0.011 0.002 HIS o 530 Details of bonding type rmsd covalent geometry : bond 0.00642 (20297) covalent geometry : angle 0.63430 (27781) hydrogen bonds : bond 0.03965 ( 807) hydrogen bonds : angle 4.76735 ( 2358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 265 time to evaluate : 0.573 Fit side-chains REVERT: m 442 ASP cc_start: 0.8152 (p0) cc_final: 0.7848 (p0) REVERT: m 489 LYS cc_start: 0.8737 (mtpp) cc_final: 0.8526 (mtpp) REVERT: m 571 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7183 (tp40) REVERT: m 599 ILE cc_start: 0.8642 (tp) cc_final: 0.8427 (tp) REVERT: m 656 TYR cc_start: 0.7182 (t80) cc_final: 0.6650 (t80) REVERT: n 134 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7152 (pp20) REVERT: n 272 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7962 (mt) REVERT: n 442 ASP cc_start: 0.7491 (t70) cc_final: 0.7216 (t0) REVERT: o 428 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.6897 (m-70) REVERT: o 540 ILE cc_start: 0.8937 (mm) cc_final: 0.8690 (mm) REVERT: o 597 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7127 (mm-30) REVERT: o 648 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6969 (t0) REVERT: r 93 GLU cc_start: 0.7805 (mp0) cc_final: 0.7058 (mp0) outliers start: 101 outliers final: 70 residues processed: 344 average time/residue: 0.1100 time to fit residues: 62.5292 Evaluate side-chains 322 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 247 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 176 VAL Chi-restraints excluded: chain m residue 186 LEU Chi-restraints excluded: chain m residue 189 THR Chi-restraints excluded: chain m residue 199 ASP Chi-restraints excluded: chain m residue 204 ILE Chi-restraints excluded: chain m residue 315 LEU Chi-restraints excluded: chain m residue 343 THR Chi-restraints excluded: chain m residue 345 VAL Chi-restraints excluded: chain m residue 565 LEU Chi-restraints excluded: chain m residue 571 GLN Chi-restraints excluded: chain m residue 629 VAL Chi-restraints excluded: chain m residue 632 THR Chi-restraints excluded: chain m residue 643 SER Chi-restraints excluded: chain m residue 719 THR Chi-restraints excluded: chain n residue 134 GLU Chi-restraints excluded: chain n residue 199 ASP Chi-restraints excluded: chain n residue 223 VAL Chi-restraints excluded: chain n residue 225 THR Chi-restraints excluded: chain n residue 247 ASP Chi-restraints excluded: chain n residue 251 ILE Chi-restraints excluded: chain n residue 272 LEU Chi-restraints excluded: chain n residue 304 ASP Chi-restraints excluded: chain n residue 326 LEU Chi-restraints excluded: chain n residue 358 VAL Chi-restraints excluded: chain n residue 367 SER Chi-restraints excluded: chain n residue 402 ILE Chi-restraints excluded: chain n residue 439 ILE Chi-restraints excluded: chain n residue 457 THR Chi-restraints excluded: chain n residue 510 ASP Chi-restraints excluded: chain n residue 528 ILE Chi-restraints excluded: chain n residue 534 SER Chi-restraints excluded: chain n residue 615 THR Chi-restraints excluded: chain o residue 163 ILE Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 224 ASN Chi-restraints excluded: chain o residue 236 SER Chi-restraints excluded: chain o residue 396 VAL Chi-restraints excluded: chain o residue 428 HIS Chi-restraints excluded: chain o residue 441 ILE Chi-restraints excluded: chain o residue 502 THR Chi-restraints excluded: chain o residue 530 HIS Chi-restraints excluded: chain o residue 542 SER Chi-restraints excluded: chain o residue 547 LEU Chi-restraints excluded: chain o residue 563 GLN Chi-restraints excluded: chain o residue 629 VAL Chi-restraints excluded: chain o residue 648 ASP Chi-restraints excluded: chain o residue 700 THR Chi-restraints excluded: chain o residue 715 ILE Chi-restraints excluded: chain o residue 723 THR Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 100 SER Chi-restraints excluded: chain q residue 104 LEU Chi-restraints excluded: chain q residue 172 THR Chi-restraints excluded: chain q residue 201 VAL Chi-restraints excluded: chain q residue 212 THR Chi-restraints excluded: chain q residue 216 ILE Chi-restraints excluded: chain q residue 222 GLN Chi-restraints excluded: chain q residue 262 ILE Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 75 ILE Chi-restraints excluded: chain r residue 117 ASN Chi-restraints excluded: chain r residue 127 GLN Chi-restraints excluded: chain r residue 259 THR Chi-restraints excluded: chain p residue 11 ASP Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 62 SER Chi-restraints excluded: chain p residue 68 THR Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 128 VAL Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 226 LEU Chi-restraints excluded: chain p residue 228 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 209 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 chunk 54 optimal weight: 30.0000 chunk 65 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 52 optimal weight: 0.1980 chunk 183 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 651 ASN o 294 GLN o 698 ASN ** r 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 127 GLN ** r 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.127134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.100616 restraints weight = 27850.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.103122 restraints weight = 16560.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.103748 restraints weight = 11744.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.104630 restraints weight = 9315.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.104829 restraints weight = 8460.502| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20297 Z= 0.180 Angle : 0.564 9.913 27781 Z= 0.290 Chirality : 0.044 0.171 3311 Planarity : 0.004 0.053 3648 Dihedral : 4.463 24.832 2875 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 5.31 % Allowed : 25.51 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.16), residues: 2683 helix: 1.94 (0.21), residues: 612 sheet: -0.21 (0.23), residues: 484 loop : -1.43 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG q 220 TYR 0.010 0.001 TYR n 695 PHE 0.027 0.001 PHE r 227 TRP 0.010 0.001 TRP o 266 HIS 0.008 0.001 HIS o 530 Details of bonding type rmsd covalent geometry : bond 0.00432 (20297) covalent geometry : angle 0.56433 (27781) hydrogen bonds : bond 0.03421 ( 807) hydrogen bonds : angle 4.64594 ( 2358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 255 time to evaluate : 0.691 Fit side-chains REVERT: m 434 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7367 (pp) REVERT: m 442 ASP cc_start: 0.8186 (p0) cc_final: 0.7882 (p0) REVERT: m 571 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7182 (tp40) REVERT: m 599 ILE cc_start: 0.8555 (tp) cc_final: 0.8339 (tp) REVERT: m 714 MET cc_start: 0.8194 (mmm) cc_final: 0.7875 (mmm) REVERT: n 134 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7160 (pp20) REVERT: n 272 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7903 (mt) REVERT: n 326 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7671 (tt) REVERT: n 383 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8526 (mt) REVERT: n 442 ASP cc_start: 0.7550 (t70) cc_final: 0.7234 (t0) REVERT: o 199 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7587 (p0) REVERT: o 428 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.7058 (t70) REVERT: r 93 GLU cc_start: 0.7774 (mp0) cc_final: 0.7014 (mp0) REVERT: r 257 ILE cc_start: 0.8892 (mm) cc_final: 0.8670 (mm) outliers start: 112 outliers final: 81 residues processed: 349 average time/residue: 0.1129 time to fit residues: 65.1704 Evaluate side-chains 328 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 239 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 186 LEU Chi-restraints excluded: chain m residue 189 THR Chi-restraints excluded: chain m residue 199 ASP Chi-restraints excluded: chain m residue 204 ILE Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain m residue 319 LEU Chi-restraints excluded: chain m residue 343 THR Chi-restraints excluded: chain m residue 345 VAL Chi-restraints excluded: chain m residue 383 LEU Chi-restraints excluded: chain m residue 434 ILE Chi-restraints excluded: chain m residue 514 ASP Chi-restraints excluded: chain m residue 565 LEU Chi-restraints excluded: chain m residue 571 GLN Chi-restraints excluded: chain m residue 629 VAL Chi-restraints excluded: chain m residue 719 THR Chi-restraints excluded: chain n residue 134 GLU Chi-restraints excluded: chain n residue 174 GLU Chi-restraints excluded: chain n residue 199 ASP Chi-restraints excluded: chain n residue 223 VAL Chi-restraints excluded: chain n residue 225 THR Chi-restraints excluded: chain n residue 235 THR Chi-restraints excluded: chain n residue 251 ILE Chi-restraints excluded: chain n residue 271 THR Chi-restraints excluded: chain n residue 272 LEU Chi-restraints excluded: chain n residue 301 VAL Chi-restraints excluded: chain n residue 304 ASP Chi-restraints excluded: chain n residue 326 LEU Chi-restraints excluded: chain n residue 345 VAL Chi-restraints excluded: chain n residue 356 SER Chi-restraints excluded: chain n residue 358 VAL Chi-restraints excluded: chain n residue 367 SER Chi-restraints excluded: chain n residue 370 ASN Chi-restraints excluded: chain n residue 377 VAL Chi-restraints excluded: chain n residue 383 LEU Chi-restraints excluded: chain n residue 439 ILE Chi-restraints excluded: chain n residue 457 THR Chi-restraints excluded: chain n residue 510 ASP Chi-restraints excluded: chain n residue 528 ILE Chi-restraints excluded: chain n residue 534 SER Chi-restraints excluded: chain n residue 615 THR Chi-restraints excluded: chain n residue 680 THR Chi-restraints excluded: chain o residue 163 ILE Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain o residue 189 THR Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 224 ASN Chi-restraints excluded: chain o residue 236 SER Chi-restraints excluded: chain o residue 393 LEU Chi-restraints excluded: chain o residue 396 VAL Chi-restraints excluded: chain o residue 404 SER Chi-restraints excluded: chain o residue 428 HIS Chi-restraints excluded: chain o residue 441 ILE Chi-restraints excluded: chain o residue 458 THR Chi-restraints excluded: chain o residue 502 THR Chi-restraints excluded: chain o residue 530 HIS Chi-restraints excluded: chain o residue 542 SER Chi-restraints excluded: chain o residue 547 LEU Chi-restraints excluded: chain o residue 572 VAL Chi-restraints excluded: chain o residue 618 SER Chi-restraints excluded: chain o residue 629 VAL Chi-restraints excluded: chain o residue 648 ASP Chi-restraints excluded: chain o residue 700 THR Chi-restraints excluded: chain o residue 715 ILE Chi-restraints excluded: chain o residue 740 VAL Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 90 VAL Chi-restraints excluded: chain q residue 100 SER Chi-restraints excluded: chain q residue 104 LEU Chi-restraints excluded: chain q residue 151 CYS Chi-restraints excluded: chain q residue 201 VAL Chi-restraints excluded: chain q residue 222 GLN Chi-restraints excluded: chain q residue 262 ILE Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 117 ASN Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 11 ASP Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 62 SER Chi-restraints excluded: chain p residue 68 THR Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 128 VAL Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 226 LEU Chi-restraints excluded: chain p residue 228 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 27 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 230 optimal weight: 0.0270 chunk 103 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 211 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 651 ASN ** r 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.131290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.104960 restraints weight = 27296.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.107152 restraints weight = 16546.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.108168 restraints weight = 11367.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.109017 restraints weight = 8923.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.109208 restraints weight = 7995.984| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20297 Z= 0.100 Angle : 0.511 10.755 27781 Z= 0.262 Chirality : 0.042 0.158 3311 Planarity : 0.004 0.051 3648 Dihedral : 4.171 26.791 2875 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.94 % Allowed : 26.84 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 2683 helix: 2.23 (0.21), residues: 607 sheet: -0.15 (0.23), residues: 487 loop : -1.33 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG p 197 TYR 0.013 0.001 TYR o 656 PHE 0.018 0.001 PHE r 227 TRP 0.010 0.001 TRP o 266 HIS 0.003 0.001 HIS r 47 Details of bonding type rmsd covalent geometry : bond 0.00231 (20297) covalent geometry : angle 0.51128 (27781) hydrogen bonds : bond 0.02788 ( 807) hydrogen bonds : angle 4.40231 ( 2358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 264 time to evaluate : 0.696 Fit side-chains REVERT: m 442 ASP cc_start: 0.8110 (p0) cc_final: 0.7788 (p0) REVERT: m 571 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7136 (tp40) REVERT: m 599 ILE cc_start: 0.8541 (tp) cc_final: 0.8339 (tp) REVERT: m 714 MET cc_start: 0.8284 (mmm) cc_final: 0.8022 (mmm) REVERT: n 134 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7326 (pp20) REVERT: n 326 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7729 (tt) REVERT: n 442 ASP cc_start: 0.7501 (t70) cc_final: 0.7164 (t0) REVERT: o 199 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7539 (p0) REVERT: o 540 ILE cc_start: 0.8871 (mm) cc_final: 0.8552 (mm) REVERT: o 648 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.7076 (t0) outliers start: 83 outliers final: 55 residues processed: 331 average time/residue: 0.1130 time to fit residues: 61.9762 Evaluate side-chains 307 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 247 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 186 LEU Chi-restraints excluded: chain m residue 189 THR Chi-restraints excluded: chain m residue 199 ASP Chi-restraints excluded: chain m residue 202 GLU Chi-restraints excluded: chain m residue 204 ILE Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain m residue 345 VAL Chi-restraints excluded: chain m residue 565 LEU Chi-restraints excluded: chain m residue 571 GLN Chi-restraints excluded: chain m residue 629 VAL Chi-restraints excluded: chain m residue 643 SER Chi-restraints excluded: chain m residue 719 THR Chi-restraints excluded: chain n residue 134 GLU Chi-restraints excluded: chain n residue 199 ASP Chi-restraints excluded: chain n residue 271 THR Chi-restraints excluded: chain n residue 326 LEU Chi-restraints excluded: chain n residue 345 VAL Chi-restraints excluded: chain n residue 358 VAL Chi-restraints excluded: chain n residue 367 SER Chi-restraints excluded: chain n residue 377 VAL Chi-restraints excluded: chain n residue 439 ILE Chi-restraints excluded: chain n residue 510 ASP Chi-restraints excluded: chain n residue 615 THR Chi-restraints excluded: chain n residue 680 THR Chi-restraints excluded: chain o residue 163 ILE Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 396 VAL Chi-restraints excluded: chain o residue 404 SER Chi-restraints excluded: chain o residue 542 SER Chi-restraints excluded: chain o residue 547 LEU Chi-restraints excluded: chain o residue 572 VAL Chi-restraints excluded: chain o residue 627 ILE Chi-restraints excluded: chain o residue 629 VAL Chi-restraints excluded: chain o residue 648 ASP Chi-restraints excluded: chain o residue 700 THR Chi-restraints excluded: chain o residue 702 VAL Chi-restraints excluded: chain o residue 715 ILE Chi-restraints excluded: chain o residue 740 VAL Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 100 SER Chi-restraints excluded: chain q residue 151 CYS Chi-restraints excluded: chain q residue 201 VAL Chi-restraints excluded: chain q residue 222 GLN Chi-restraints excluded: chain q residue 239 LEU Chi-restraints excluded: chain q residue 262 ILE Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 117 ASN Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 11 ASP Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 128 VAL Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 226 LEU Chi-restraints excluded: chain p residue 227 PHE Chi-restraints excluded: chain p residue 228 GLN Chi-restraints excluded: chain p residue 239 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 219 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 205 optimal weight: 0.0770 chunk 162 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 159 optimal weight: 0.5980 chunk 158 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 651 ASN ** r 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.130561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.104139 restraints weight = 27318.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.106473 restraints weight = 16189.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.107201 restraints weight = 11519.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.108076 restraints weight = 9077.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.108181 restraints weight = 8225.186| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20297 Z= 0.121 Angle : 0.523 11.129 27781 Z= 0.268 Chirality : 0.043 0.213 3311 Planarity : 0.004 0.051 3648 Dihedral : 4.157 27.100 2875 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.89 % Allowed : 26.51 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 2683 helix: 2.26 (0.21), residues: 607 sheet: -0.15 (0.23), residues: 487 loop : -1.33 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG q 220 TYR 0.009 0.001 TYR n 415 PHE 0.020 0.001 PHE r 227 TRP 0.010 0.001 TRP o 266 HIS 0.005 0.001 HIS o 530 Details of bonding type rmsd covalent geometry : bond 0.00291 (20297) covalent geometry : angle 0.52332 (27781) hydrogen bonds : bond 0.02879 ( 807) hydrogen bonds : angle 4.37820 ( 2358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 251 time to evaluate : 0.740 Fit side-chains REVERT: m 442 ASP cc_start: 0.8119 (p0) cc_final: 0.7805 (p0) REVERT: m 571 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7080 (tp40) REVERT: m 599 ILE cc_start: 0.8530 (tp) cc_final: 0.8318 (tp) REVERT: n 134 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7153 (pp20) REVERT: n 272 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7909 (mt) REVERT: n 326 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7740 (tt) REVERT: n 442 ASP cc_start: 0.7593 (t70) cc_final: 0.7246 (t0) REVERT: n 541 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6937 (mm-30) REVERT: o 199 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7495 (p0) REVERT: o 540 ILE cc_start: 0.8871 (mm) cc_final: 0.8535 (mm) REVERT: o 597 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6788 (mm-30) REVERT: o 648 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.7003 (t0) REVERT: r 93 GLU cc_start: 0.7707 (mp0) cc_final: 0.6956 (mp0) outliers start: 82 outliers final: 63 residues processed: 318 average time/residue: 0.1062 time to fit residues: 55.9952 Evaluate side-chains 309 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 240 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 186 LEU Chi-restraints excluded: chain m residue 189 THR Chi-restraints excluded: chain m residue 199 ASP Chi-restraints excluded: chain m residue 202 GLU Chi-restraints excluded: chain m residue 204 ILE Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain m residue 345 VAL Chi-restraints excluded: chain m residue 565 LEU Chi-restraints excluded: chain m residue 571 GLN Chi-restraints excluded: chain m residue 629 VAL Chi-restraints excluded: chain m residue 643 SER Chi-restraints excluded: chain m residue 719 THR Chi-restraints excluded: chain n residue 134 GLU Chi-restraints excluded: chain n residue 199 ASP Chi-restraints excluded: chain n residue 247 ASP Chi-restraints excluded: chain n residue 272 LEU Chi-restraints excluded: chain n residue 301 VAL Chi-restraints excluded: chain n residue 304 ASP Chi-restraints excluded: chain n residue 326 LEU Chi-restraints excluded: chain n residue 345 VAL Chi-restraints excluded: chain n residue 358 VAL Chi-restraints excluded: chain n residue 367 SER Chi-restraints excluded: chain n residue 370 ASN Chi-restraints excluded: chain n residue 377 VAL Chi-restraints excluded: chain n residue 439 ILE Chi-restraints excluded: chain n residue 510 ASP Chi-restraints excluded: chain n residue 528 ILE Chi-restraints excluded: chain n residue 615 THR Chi-restraints excluded: chain n residue 680 THR Chi-restraints excluded: chain o residue 163 ILE Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 396 VAL Chi-restraints excluded: chain o residue 404 SER Chi-restraints excluded: chain o residue 530 HIS Chi-restraints excluded: chain o residue 542 SER Chi-restraints excluded: chain o residue 547 LEU Chi-restraints excluded: chain o residue 572 VAL Chi-restraints excluded: chain o residue 618 SER Chi-restraints excluded: chain o residue 627 ILE Chi-restraints excluded: chain o residue 629 VAL Chi-restraints excluded: chain o residue 648 ASP Chi-restraints excluded: chain o residue 700 THR Chi-restraints excluded: chain o residue 715 ILE Chi-restraints excluded: chain o residue 740 VAL Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 100 SER Chi-restraints excluded: chain q residue 151 CYS Chi-restraints excluded: chain q residue 201 VAL Chi-restraints excluded: chain q residue 216 ILE Chi-restraints excluded: chain q residue 222 GLN Chi-restraints excluded: chain q residue 239 LEU Chi-restraints excluded: chain q residue 262 ILE Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 117 ASN Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 11 ASP Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 62 SER Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 128 VAL Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 226 LEU Chi-restraints excluded: chain p residue 227 PHE Chi-restraints excluded: chain p residue 228 GLN Chi-restraints excluded: chain p residue 239 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 230 optimal weight: 0.0040 chunk 175 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 651 ASN ** r 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.130862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.104471 restraints weight = 27378.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.106758 restraints weight = 16058.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.107501 restraints weight = 11443.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.108405 restraints weight = 9052.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.108516 restraints weight = 8171.880| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20297 Z= 0.117 Angle : 0.519 9.831 27781 Z= 0.265 Chirality : 0.043 0.192 3311 Planarity : 0.004 0.051 3648 Dihedral : 4.138 27.418 2875 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.27 % Allowed : 26.13 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.16), residues: 2683 helix: 2.27 (0.21), residues: 607 sheet: -0.13 (0.23), residues: 487 loop : -1.32 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG q 220 TYR 0.012 0.001 TYR o 656 PHE 0.019 0.001 PHE r 227 TRP 0.010 0.001 TRP o 266 HIS 0.005 0.001 HIS o 530 Details of bonding type rmsd covalent geometry : bond 0.00283 (20297) covalent geometry : angle 0.51863 (27781) hydrogen bonds : bond 0.02829 ( 807) hydrogen bonds : angle 4.34656 ( 2358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 252 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: m 434 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.7116 (pp) REVERT: m 442 ASP cc_start: 0.8114 (p0) cc_final: 0.7800 (p0) REVERT: m 571 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7074 (tp40) REVERT: m 599 ILE cc_start: 0.8518 (tp) cc_final: 0.8295 (tp) REVERT: m 612 ARG cc_start: 0.8157 (mtm110) cc_final: 0.7905 (mtm110) REVERT: m 714 MET cc_start: 0.8264 (mmm) cc_final: 0.7958 (mmm) REVERT: n 134 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7147 (pp20) REVERT: n 272 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7892 (mt) REVERT: n 326 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7794 (tt) REVERT: n 442 ASP cc_start: 0.7628 (t70) cc_final: 0.7259 (t0) REVERT: o 199 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7567 (p0) REVERT: o 304 ASP cc_start: 0.8311 (p0) cc_final: 0.8074 (p0) REVERT: o 540 ILE cc_start: 0.8868 (mm) cc_final: 0.8530 (mm) REVERT: o 597 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6768 (mm-30) REVERT: o 648 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6994 (t0) REVERT: q 10 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7147 (mm) REVERT: r 93 GLU cc_start: 0.7716 (mp0) cc_final: 0.6970 (mp0) outliers start: 90 outliers final: 68 residues processed: 324 average time/residue: 0.1086 time to fit residues: 58.1950 Evaluate side-chains 318 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 242 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 189 THR Chi-restraints excluded: chain m residue 199 ASP Chi-restraints excluded: chain m residue 202 GLU Chi-restraints excluded: chain m residue 204 ILE Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain m residue 251 ILE Chi-restraints excluded: chain m residue 345 VAL Chi-restraints excluded: chain m residue 434 ILE Chi-restraints excluded: chain m residue 565 LEU Chi-restraints excluded: chain m residue 571 GLN Chi-restraints excluded: chain m residue 572 VAL Chi-restraints excluded: chain m residue 629 VAL Chi-restraints excluded: chain m residue 643 SER Chi-restraints excluded: chain m residue 719 THR Chi-restraints excluded: chain n residue 134 GLU Chi-restraints excluded: chain n residue 174 GLU Chi-restraints excluded: chain n residue 199 ASP Chi-restraints excluded: chain n residue 247 ASP Chi-restraints excluded: chain n residue 251 ILE Chi-restraints excluded: chain n residue 272 LEU Chi-restraints excluded: chain n residue 292 PHE Chi-restraints excluded: chain n residue 301 VAL Chi-restraints excluded: chain n residue 326 LEU Chi-restraints excluded: chain n residue 358 VAL Chi-restraints excluded: chain n residue 367 SER Chi-restraints excluded: chain n residue 370 ASN Chi-restraints excluded: chain n residue 377 VAL Chi-restraints excluded: chain n residue 439 ILE Chi-restraints excluded: chain n residue 510 ASP Chi-restraints excluded: chain n residue 615 THR Chi-restraints excluded: chain n residue 651 ASN Chi-restraints excluded: chain n residue 680 THR Chi-restraints excluded: chain o residue 163 ILE Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 236 SER Chi-restraints excluded: chain o residue 396 VAL Chi-restraints excluded: chain o residue 404 SER Chi-restraints excluded: chain o residue 530 HIS Chi-restraints excluded: chain o residue 542 SER Chi-restraints excluded: chain o residue 547 LEU Chi-restraints excluded: chain o residue 572 VAL Chi-restraints excluded: chain o residue 618 SER Chi-restraints excluded: chain o residue 627 ILE Chi-restraints excluded: chain o residue 629 VAL Chi-restraints excluded: chain o residue 648 ASP Chi-restraints excluded: chain o residue 700 THR Chi-restraints excluded: chain o residue 715 ILE Chi-restraints excluded: chain o residue 740 VAL Chi-restraints excluded: chain q residue 10 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 100 SER Chi-restraints excluded: chain q residue 151 CYS Chi-restraints excluded: chain q residue 201 VAL Chi-restraints excluded: chain q residue 216 ILE Chi-restraints excluded: chain q residue 222 GLN Chi-restraints excluded: chain q residue 239 LEU Chi-restraints excluded: chain q residue 262 ILE Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 117 ASN Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 11 ASP Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 62 SER Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 128 VAL Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 226 LEU Chi-restraints excluded: chain p residue 227 PHE Chi-restraints excluded: chain p residue 228 GLN Chi-restraints excluded: chain p residue 239 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 184 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 258 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 651 ASN ** r 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.128464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.102062 restraints weight = 27647.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.104207 restraints weight = 16388.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.104990 restraints weight = 11782.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.105906 restraints weight = 9304.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.106083 restraints weight = 8436.990| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20297 Z= 0.163 Angle : 0.558 11.991 27781 Z= 0.284 Chirality : 0.044 0.195 3311 Planarity : 0.004 0.051 3648 Dihedral : 4.293 26.491 2875 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.31 % Allowed : 25.98 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2683 helix: 2.21 (0.21), residues: 607 sheet: -0.20 (0.23), residues: 493 loop : -1.38 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG q 220 TYR 0.010 0.001 TYR n 562 PHE 0.024 0.001 PHE r 227 TRP 0.010 0.001 TRP m 369 HIS 0.008 0.001 HIS o 530 Details of bonding type rmsd covalent geometry : bond 0.00393 (20297) covalent geometry : angle 0.55773 (27781) hydrogen bonds : bond 0.03156 ( 807) hydrogen bonds : angle 4.45107 ( 2358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 252 time to evaluate : 0.700 Fit side-chains REVERT: m 434 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7195 (pp) REVERT: m 442 ASP cc_start: 0.8171 (p0) cc_final: 0.7881 (p0) REVERT: m 571 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7132 (tp40) REVERT: m 599 ILE cc_start: 0.8523 (tp) cc_final: 0.8322 (tp) REVERT: m 714 MET cc_start: 0.8266 (mmm) cc_final: 0.7927 (mmm) REVERT: n 134 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7167 (pp20) REVERT: n 272 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7938 (mt) REVERT: n 326 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7799 (tt) REVERT: n 442 ASP cc_start: 0.7636 (t70) cc_final: 0.7275 (t0) REVERT: o 199 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7550 (p0) REVERT: o 304 ASP cc_start: 0.8364 (p0) cc_final: 0.8149 (p0) REVERT: o 540 ILE cc_start: 0.8900 (mm) cc_final: 0.8565 (mm) REVERT: o 597 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6816 (mm-30) REVERT: o 648 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.7028 (t0) REVERT: q 24 ARG cc_start: 0.7973 (ttt180) cc_final: 0.7648 (ttt90) REVERT: r 93 GLU cc_start: 0.7718 (mp0) cc_final: 0.6953 (mp0) REVERT: r 236 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: p 197 ARG cc_start: 0.7640 (mtp180) cc_final: 0.7366 (mtm180) REVERT: p 222 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8466 (pt0) outliers start: 91 outliers final: 73 residues processed: 328 average time/residue: 0.1132 time to fit residues: 60.8607 Evaluate side-chains 327 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 245 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 189 THR Chi-restraints excluded: chain m residue 199 ASP Chi-restraints excluded: chain m residue 202 GLU Chi-restraints excluded: chain m residue 204 ILE Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain m residue 251 ILE Chi-restraints excluded: chain m residue 315 LEU Chi-restraints excluded: chain m residue 343 THR Chi-restraints excluded: chain m residue 345 VAL Chi-restraints excluded: chain m residue 434 ILE Chi-restraints excluded: chain m residue 540 ILE Chi-restraints excluded: chain m residue 565 LEU Chi-restraints excluded: chain m residue 571 GLN Chi-restraints excluded: chain m residue 572 VAL Chi-restraints excluded: chain m residue 629 VAL Chi-restraints excluded: chain m residue 643 SER Chi-restraints excluded: chain m residue 719 THR Chi-restraints excluded: chain n residue 134 GLU Chi-restraints excluded: chain n residue 174 GLU Chi-restraints excluded: chain n residue 199 ASP Chi-restraints excluded: chain n residue 247 ASP Chi-restraints excluded: chain n residue 251 ILE Chi-restraints excluded: chain n residue 272 LEU Chi-restraints excluded: chain n residue 301 VAL Chi-restraints excluded: chain n residue 304 ASP Chi-restraints excluded: chain n residue 326 LEU Chi-restraints excluded: chain n residue 356 SER Chi-restraints excluded: chain n residue 358 VAL Chi-restraints excluded: chain n residue 367 SER Chi-restraints excluded: chain n residue 370 ASN Chi-restraints excluded: chain n residue 377 VAL Chi-restraints excluded: chain n residue 439 ILE Chi-restraints excluded: chain n residue 510 ASP Chi-restraints excluded: chain n residue 528 ILE Chi-restraints excluded: chain n residue 615 THR Chi-restraints excluded: chain n residue 680 THR Chi-restraints excluded: chain o residue 163 ILE Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 236 SER Chi-restraints excluded: chain o residue 244 THR Chi-restraints excluded: chain o residue 396 VAL Chi-restraints excluded: chain o residue 404 SER Chi-restraints excluded: chain o residue 530 HIS Chi-restraints excluded: chain o residue 542 SER Chi-restraints excluded: chain o residue 547 LEU Chi-restraints excluded: chain o residue 572 VAL Chi-restraints excluded: chain o residue 618 SER Chi-restraints excluded: chain o residue 627 ILE Chi-restraints excluded: chain o residue 629 VAL Chi-restraints excluded: chain o residue 648 ASP Chi-restraints excluded: chain o residue 700 THR Chi-restraints excluded: chain o residue 715 ILE Chi-restraints excluded: chain o residue 740 VAL Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 100 SER Chi-restraints excluded: chain q residue 151 CYS Chi-restraints excluded: chain q residue 201 VAL Chi-restraints excluded: chain q residue 216 ILE Chi-restraints excluded: chain q residue 222 GLN Chi-restraints excluded: chain q residue 239 LEU Chi-restraints excluded: chain q residue 255 SER Chi-restraints excluded: chain q residue 262 ILE Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 117 ASN Chi-restraints excluded: chain r residue 236 GLN Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 11 ASP Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 62 SER Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 128 VAL Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 222 GLN Chi-restraints excluded: chain p residue 226 LEU Chi-restraints excluded: chain p residue 228 GLN Chi-restraints excluded: chain p residue 239 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 67 optimal weight: 2.9990 chunk 223 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 651 ASN ** r 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.131241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.104865 restraints weight = 27255.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.106830 restraints weight = 16230.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.108280 restraints weight = 11480.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.109060 restraints weight = 8619.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.109315 restraints weight = 7753.437| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20297 Z= 0.109 Angle : 0.525 12.485 27781 Z= 0.268 Chirality : 0.043 0.185 3311 Planarity : 0.004 0.051 3648 Dihedral : 4.164 27.338 2875 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.84 % Allowed : 26.88 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 2683 helix: 2.25 (0.21), residues: 607 sheet: -0.14 (0.23), residues: 486 loop : -1.34 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG m 612 TYR 0.014 0.001 TYR o 656 PHE 0.019 0.001 PHE r 227 TRP 0.012 0.001 TRP n 527 HIS 0.003 0.001 HIS o 530 Details of bonding type rmsd covalent geometry : bond 0.00262 (20297) covalent geometry : angle 0.52466 (27781) hydrogen bonds : bond 0.02771 ( 807) hydrogen bonds : angle 4.34094 ( 2358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 256 time to evaluate : 0.648 Fit side-chains REVERT: m 434 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7148 (pp) REVERT: m 442 ASP cc_start: 0.8106 (p0) cc_final: 0.7804 (p0) REVERT: m 571 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7169 (tp40) REVERT: m 599 ILE cc_start: 0.8534 (tp) cc_final: 0.8311 (tp) REVERT: m 714 MET cc_start: 0.8256 (mmm) cc_final: 0.7940 (mmm) REVERT: n 134 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7167 (pp20) REVERT: n 272 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7853 (mt) REVERT: n 326 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7799 (tt) REVERT: n 442 ASP cc_start: 0.7617 (t70) cc_final: 0.7269 (t0) REVERT: o 199 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7496 (p0) REVERT: o 304 ASP cc_start: 0.8340 (p0) cc_final: 0.8119 (p0) REVERT: o 540 ILE cc_start: 0.8875 (mm) cc_final: 0.8553 (mm) REVERT: o 597 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6748 (mm-30) REVERT: o 648 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.7003 (t0) REVERT: r 93 GLU cc_start: 0.7695 (mp0) cc_final: 0.6962 (mp0) REVERT: p 197 ARG cc_start: 0.7545 (mtp180) cc_final: 0.7302 (mtm180) outliers start: 81 outliers final: 69 residues processed: 324 average time/residue: 0.1119 time to fit residues: 60.0642 Evaluate side-chains 320 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 244 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 189 THR Chi-restraints excluded: chain m residue 199 ASP Chi-restraints excluded: chain m residue 202 GLU Chi-restraints excluded: chain m residue 204 ILE Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain m residue 251 ILE Chi-restraints excluded: chain m residue 343 THR Chi-restraints excluded: chain m residue 345 VAL Chi-restraints excluded: chain m residue 434 ILE Chi-restraints excluded: chain m residue 565 LEU Chi-restraints excluded: chain m residue 571 GLN Chi-restraints excluded: chain m residue 572 VAL Chi-restraints excluded: chain m residue 629 VAL Chi-restraints excluded: chain m residue 643 SER Chi-restraints excluded: chain m residue 719 THR Chi-restraints excluded: chain n residue 134 GLU Chi-restraints excluded: chain n residue 174 GLU Chi-restraints excluded: chain n residue 199 ASP Chi-restraints excluded: chain n residue 247 ASP Chi-restraints excluded: chain n residue 272 LEU Chi-restraints excluded: chain n residue 292 PHE Chi-restraints excluded: chain n residue 301 VAL Chi-restraints excluded: chain n residue 326 LEU Chi-restraints excluded: chain n residue 358 VAL Chi-restraints excluded: chain n residue 367 SER Chi-restraints excluded: chain n residue 370 ASN Chi-restraints excluded: chain n residue 377 VAL Chi-restraints excluded: chain n residue 439 ILE Chi-restraints excluded: chain n residue 510 ASP Chi-restraints excluded: chain n residue 528 ILE Chi-restraints excluded: chain n residue 615 THR Chi-restraints excluded: chain n residue 680 THR Chi-restraints excluded: chain o residue 163 ILE Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 236 SER Chi-restraints excluded: chain o residue 244 THR Chi-restraints excluded: chain o residue 396 VAL Chi-restraints excluded: chain o residue 404 SER Chi-restraints excluded: chain o residue 530 HIS Chi-restraints excluded: chain o residue 542 SER Chi-restraints excluded: chain o residue 547 LEU Chi-restraints excluded: chain o residue 572 VAL Chi-restraints excluded: chain o residue 618 SER Chi-restraints excluded: chain o residue 627 ILE Chi-restraints excluded: chain o residue 629 VAL Chi-restraints excluded: chain o residue 648 ASP Chi-restraints excluded: chain o residue 700 THR Chi-restraints excluded: chain o residue 715 ILE Chi-restraints excluded: chain o residue 723 THR Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 100 SER Chi-restraints excluded: chain q residue 151 CYS Chi-restraints excluded: chain q residue 201 VAL Chi-restraints excluded: chain q residue 216 ILE Chi-restraints excluded: chain q residue 222 GLN Chi-restraints excluded: chain q residue 239 LEU Chi-restraints excluded: chain q residue 262 ILE Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 117 ASN Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 11 ASP Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 62 SER Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 128 VAL Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 226 LEU Chi-restraints excluded: chain p residue 227 PHE Chi-restraints excluded: chain p residue 228 GLN Chi-restraints excluded: chain p residue 239 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 147 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 247 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 317 HIS ** r 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.125778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.100674 restraints weight = 27927.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.101987 restraints weight = 17178.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.102428 restraints weight = 13098.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.102638 restraints weight = 10858.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.103309 restraints weight = 10099.804| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 20297 Z= 0.235 Angle : 0.621 12.215 27781 Z= 0.318 Chirality : 0.045 0.186 3311 Planarity : 0.005 0.053 3648 Dihedral : 4.589 24.968 2875 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.03 % Allowed : 26.70 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 2683 helix: 2.03 (0.21), residues: 606 sheet: -0.36 (0.22), residues: 525 loop : -1.50 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG q 220 TYR 0.013 0.002 TYR n 562 PHE 0.031 0.002 PHE r 227 TRP 0.013 0.001 TRP m 369 HIS 0.011 0.001 HIS o 530 Details of bonding type rmsd covalent geometry : bond 0.00564 (20297) covalent geometry : angle 0.62093 (27781) hydrogen bonds : bond 0.03596 ( 807) hydrogen bonds : angle 4.62734 ( 2358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5366 Ramachandran restraints generated. 2683 Oldfield, 0 Emsley, 2683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 255 time to evaluate : 0.717 Fit side-chains REVERT: m 434 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7221 (pp) REVERT: m 489 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8488 (ttmm) REVERT: m 571 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7104 (tp40) REVERT: m 599 ILE cc_start: 0.8659 (tp) cc_final: 0.8443 (tp) REVERT: m 714 MET cc_start: 0.8253 (mmm) cc_final: 0.7873 (mmm) REVERT: n 134 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7074 (pp20) REVERT: n 272 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7950 (mt) REVERT: n 326 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7844 (tt) REVERT: n 442 ASP cc_start: 0.7600 (t70) cc_final: 0.7277 (t0) REVERT: o 199 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7559 (p0) REVERT: q 24 ARG cc_start: 0.8001 (ttt180) cc_final: 0.7694 (ttt90) REVERT: r 93 GLU cc_start: 0.7738 (mp0) cc_final: 0.6973 (mp0) REVERT: r 236 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7103 (mp10) REVERT: r 244 VAL cc_start: 0.9006 (t) cc_final: 0.8792 (t) REVERT: p 197 ARG cc_start: 0.7649 (mtp180) cc_final: 0.7376 (mtm180) REVERT: p 222 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8440 (pt0) outliers start: 85 outliers final: 70 residues processed: 328 average time/residue: 0.1141 time to fit residues: 61.1524 Evaluate side-chains 325 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 247 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 189 THR Chi-restraints excluded: chain m residue 199 ASP Chi-restraints excluded: chain m residue 202 GLU Chi-restraints excluded: chain m residue 204 ILE Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain m residue 251 ILE Chi-restraints excluded: chain m residue 315 LEU Chi-restraints excluded: chain m residue 343 THR Chi-restraints excluded: chain m residue 345 VAL Chi-restraints excluded: chain m residue 434 ILE Chi-restraints excluded: chain m residue 565 LEU Chi-restraints excluded: chain m residue 571 GLN Chi-restraints excluded: chain m residue 572 VAL Chi-restraints excluded: chain m residue 629 VAL Chi-restraints excluded: chain m residue 643 SER Chi-restraints excluded: chain m residue 719 THR Chi-restraints excluded: chain n residue 134 GLU Chi-restraints excluded: chain n residue 174 GLU Chi-restraints excluded: chain n residue 199 ASP Chi-restraints excluded: chain n residue 247 ASP Chi-restraints excluded: chain n residue 251 ILE Chi-restraints excluded: chain n residue 272 LEU Chi-restraints excluded: chain n residue 301 VAL Chi-restraints excluded: chain n residue 326 LEU Chi-restraints excluded: chain n residue 358 VAL Chi-restraints excluded: chain n residue 367 SER Chi-restraints excluded: chain n residue 370 ASN Chi-restraints excluded: chain n residue 377 VAL Chi-restraints excluded: chain n residue 439 ILE Chi-restraints excluded: chain n residue 510 ASP Chi-restraints excluded: chain n residue 534 SER Chi-restraints excluded: chain n residue 615 THR Chi-restraints excluded: chain n residue 680 THR Chi-restraints excluded: chain o residue 163 ILE Chi-restraints excluded: chain o residue 199 ASP Chi-restraints excluded: chain o residue 236 SER Chi-restraints excluded: chain o residue 244 THR Chi-restraints excluded: chain o residue 396 VAL Chi-restraints excluded: chain o residue 404 SER Chi-restraints excluded: chain o residue 530 HIS Chi-restraints excluded: chain o residue 542 SER Chi-restraints excluded: chain o residue 547 LEU Chi-restraints excluded: chain o residue 572 VAL Chi-restraints excluded: chain o residue 618 SER Chi-restraints excluded: chain o residue 627 ILE Chi-restraints excluded: chain o residue 629 VAL Chi-restraints excluded: chain o residue 648 ASP Chi-restraints excluded: chain o residue 700 THR Chi-restraints excluded: chain o residue 715 ILE Chi-restraints excluded: chain o residue 723 THR Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 100 SER Chi-restraints excluded: chain q residue 151 CYS Chi-restraints excluded: chain q residue 201 VAL Chi-restraints excluded: chain q residue 216 ILE Chi-restraints excluded: chain q residue 222 GLN Chi-restraints excluded: chain q residue 255 SER Chi-restraints excluded: chain q residue 262 ILE Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 117 ASN Chi-restraints excluded: chain r residue 201 VAL Chi-restraints excluded: chain r residue 236 GLN Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 11 ASP Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 62 SER Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 128 VAL Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 222 GLN Chi-restraints excluded: chain p residue 226 LEU Chi-restraints excluded: chain p residue 228 GLN Chi-restraints excluded: chain p residue 239 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 98 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.130610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.104410 restraints weight = 27561.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.106508 restraints weight = 15883.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.107419 restraints weight = 11323.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.108171 restraints weight = 8939.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.108371 restraints weight = 8206.201| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20297 Z= 0.105 Angle : 0.538 11.073 27781 Z= 0.274 Chirality : 0.043 0.180 3311 Planarity : 0.004 0.051 3648 Dihedral : 4.261 26.628 2875 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.65 % Allowed : 27.31 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.16), residues: 2683 helix: 2.18 (0.21), residues: 607 sheet: -0.17 (0.23), residues: 476 loop : -1.35 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG q 220 TYR 0.012 0.001 TYR n 695 PHE 0.018 0.001 PHE r 227 TRP 0.011 0.001 TRP o 266 HIS 0.003 0.001 HIS o 317 Details of bonding type rmsd covalent geometry : bond 0.00251 (20297) covalent geometry : angle 0.53763 (27781) hydrogen bonds : bond 0.02798 ( 807) hydrogen bonds : angle 4.40032 ( 2358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3216.88 seconds wall clock time: 56 minutes 21.59 seconds (3381.59 seconds total)