Starting phenix.real_space_refine on Sat Jul 4 13:12:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tjf_25924/07_2026/7tjf_25924.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjf_25924/07_2026/7tjf_25924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tjf_25924/07_2026/7tjf_25924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjf_25924/07_2026/7tjf_25924.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tjf_25924/07_2026/7tjf_25924.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tjf_25924/07_2026/7tjf_25924.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tjf_25924/07_2026/7tjf_25924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjf_25924/07_2026/7tjf_25924.cif" } resolution = 2.6 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= 0.002 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: 6 Type Number sf(0) Gaussians P 90 5.49 5 Mg 3 5.21 5 S 80 5.16 5 C 13126 2.51 5 N 3485 2.21 5 O 4341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21125 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3897 Classifications: {'peptide': 486} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 476} Chain breaks: 4 Chain: "B" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2103 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Chain breaks: 1 Chain: "C" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4575 Classifications: {'peptide': 554} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 537} Chain breaks: 5 Chain: "D" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3536 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 3 Chain: "E" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3608 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1335 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 3, 'TRANS': 156} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 832 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 846 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Time building chain proxies: 4.06, per 1000 atoms: 0.19 Number of scatterers: 21125 At special positions: 0 Unit cell: (114.38, 127.28, 184.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 90 15.00 Mg 3 11.99 O 4341 8.00 N 3485 7.00 C 13126 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: 1.95 Conformation dependent library (CDL) restraints added in 732.9 milliseconds 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4520 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 11 sheets defined 62.0% alpha, 7.6% beta 41 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 381 through 385 removed outlier: 3.766A pdb=" N ILE A 385 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 4.176A pdb=" N GLY A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.839A pdb=" N LYS A 411 " --> pdb=" O ASN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.772A pdb=" N LYS A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 469 Processing helix chain 'A' and resid 484 through 502 removed outlier: 3.563A pdb=" N THR A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 534 removed outlier: 3.656A pdb=" N GLU A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.675A pdb=" N VAL A 553 " --> pdb=" O TYR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.569A pdb=" N LYS A 558 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 571 Processing helix chain 'A' and resid 576 through 586 removed outlier: 3.857A pdb=" N THR A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 628 through 640 Processing helix chain 'A' and resid 685 through 700 removed outlier: 3.688A pdb=" N ILE A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 726 removed outlier: 3.763A pdb=" N ALA A 706 " --> pdb=" O ASP A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 787 removed outlier: 3.569A pdb=" N VAL A 778 " --> pdb=" O HIS A 774 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 796 removed outlier: 3.580A pdb=" N ARG A 796 " --> pdb=" O THR A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 815 Processing helix chain 'A' and resid 822 through 836 removed outlier: 3.511A pdb=" N ASN A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 852 removed outlier: 4.943A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N THR A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 876 Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.125A pdb=" N ALA A 901 " --> pdb=" O SER A 897 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.856A pdb=" N ASN A 913 " --> pdb=" O THR A 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 250 Processing helix chain 'B' and resid 262 through 266 removed outlier: 3.781A pdb=" N MET B 265 " --> pdb=" O THR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.634A pdb=" N GLU B 283 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'B' and resid 371 through 384 Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 434 through 447 removed outlier: 3.961A pdb=" N ILE B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.578A pdb=" N TRP B 465 " --> pdb=" O PRO B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.877A pdb=" N PHE B 492 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 50 through 92 removed outlier: 3.882A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 157 removed outlier: 3.648A pdb=" N GLU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.922A pdb=" N LYS C 228 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 removed outlier: 3.692A pdb=" N ILE C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing helix chain 'C' and resid 274 through 289 removed outlier: 3.749A pdb=" N GLN C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 308 removed outlier: 3.639A pdb=" N ASN C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 332 Processing helix chain 'C' and resid 333 through 343 removed outlier: 4.001A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Proline residue: C 340 - end of helix removed outlier: 3.785A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 355 removed outlier: 3.549A pdb=" N LEU C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 Processing helix chain 'C' and resid 374 through 381 removed outlier: 3.518A pdb=" N SER C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 394 removed outlier: 3.653A pdb=" N VAL C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 389 through 394' Processing helix chain 'C' and resid 401 through 416 Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 473 through 480 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 511 through 517 Processing helix chain 'C' and resid 519 through 530 removed outlier: 3.516A pdb=" N LEU C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 548 removed outlier: 3.846A pdb=" N THR C 547 " --> pdb=" O ALA C 543 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 548 " --> pdb=" O PHE C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 557 removed outlier: 3.542A pdb=" N ILE C 553 " --> pdb=" O PRO C 549 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 571 removed outlier: 3.731A pdb=" N LEU C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU C 571 " --> pdb=" O LEU C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 595 removed outlier: 3.580A pdb=" N LYS C 578 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 72 through 91 removed outlier: 4.510A pdb=" N ASP D 77 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N CYS D 78 " --> pdb=" O TYR D 74 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D 91 " --> pdb=" O LYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.800A pdb=" N GLN D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 156 removed outlier: 3.740A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 Processing helix chain 'D' and resid 219 through 222 Processing helix chain 'D' and resid 228 through 241 removed outlier: 3.529A pdb=" N SER D 241 " --> pdb=" O MET D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 removed outlier: 3.724A pdb=" N TYR D 259 " --> pdb=" O ASN D 255 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 260' Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.784A pdb=" N MET D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 Processing helix chain 'D' and resid 318 through 331 Processing helix chain 'D' and resid 333 through 347 removed outlier: 3.565A pdb=" N SER D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 350 through 361 Processing helix chain 'D' and resid 361 through 372 removed outlier: 3.560A pdb=" N ASP D 365 " --> pdb=" O CYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 381 removed outlier: 3.540A pdb=" N LEU D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 401 Processing helix chain 'D' and resid 407 through 425 removed outlier: 3.652A pdb=" N ARG D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 466 removed outlier: 4.164A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.565A pdb=" N ARG D 502 " --> pdb=" O PHE D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'D' and resid 523 through 528 removed outlier: 3.841A pdb=" N GLN D 528 " --> pdb=" O SER D 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 22 Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.752A pdb=" N THR E 29 " --> pdb=" O PRO E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 54 Processing helix chain 'E' and resid 69 through 89 Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 104 through 117 Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 135 through 138 Processing helix chain 'E' and resid 144 through 151 removed outlier: 3.739A pdb=" N LYS E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 removed outlier: 3.528A pdb=" N LEU E 156 " --> pdb=" O ASN E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 178 Processing helix chain 'E' and resid 179 through 183 removed outlier: 3.580A pdb=" N HIS E 182 " --> pdb=" O TYR E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 211 removed outlier: 5.685A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 222 removed outlier: 3.539A pdb=" N ARG E 216 " --> pdb=" O ASP E 212 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 252 removed outlier: 6.031A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 271 Proline residue: E 267 - end of helix Processing helix chain 'E' and resid 274 through 279 removed outlier: 4.601A pdb=" N PHE E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 288 Processing helix chain 'E' and resid 289 through 293 removed outlier: 3.621A pdb=" N LEU E 293 " --> pdb=" O LYS E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 341 Processing helix chain 'E' and resid 345 through 349 Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 382 through 394 Processing helix chain 'E' and resid 417 through 430 Processing helix chain 'E' and resid 455 through 466 Processing helix chain 'E' and resid 471 through 476 removed outlier: 4.637A pdb=" N ASP E 476 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.631A pdb=" N ILE F 285 " --> pdb=" O THR F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 308 Processing helix chain 'F' and resid 309 through 313 removed outlier: 4.185A pdb=" N LEU F 313 " --> pdb=" O ALA F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 332 removed outlier: 3.855A pdb=" N LEU F 319 " --> pdb=" O CYS F 315 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 339 Processing helix chain 'F' and resid 342 through 351 removed outlier: 4.362A pdb=" N VAL F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER F 348 " --> pdb=" O HIS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 374 removed outlier: 3.659A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 386 Processing helix chain 'F' and resid 393 through 402 removed outlier: 4.228A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 430 removed outlier: 3.667A pdb=" N ALA F 430 " --> pdb=" O GLU F 426 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 508 through 514 removed outlier: 6.327A pdb=" N LEU A 509 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU A 564 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL A 511 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ASP A 566 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A 513 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 657 through 659 removed outlier: 3.637A pdb=" N SER A 646 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLN A 771 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG A 681 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N VAL A 773 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG A 683 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 820 through 821 Processing sheet with id=AA4, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.232A pdb=" N SER B 313 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS B 478 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 315 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU B 314 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU B 361 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N HIS B 425 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU B 363 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 124 through 131 removed outlier: 6.350A pdb=" N TYR C 125 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL C 202 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 127 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ASN C 204 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE C 129 " --> pdb=" O ASN C 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 293 through 294 removed outlier: 6.994A pdb=" N ASN C 293 " --> pdb=" O LEU C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 534 through 536 Processing sheet with id=AA8, first strand: chain 'D' and resid 127 through 133 removed outlier: 6.419A pdb=" N ILE D 128 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE D 215 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE D 130 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASP D 217 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU D 132 " --> pdb=" O ASP D 217 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG D 271 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 469 through 471 Processing sheet with id=AB1, first strand: chain 'E' and resid 59 through 62 removed outlier: 6.448A pdb=" N THR E 126 " --> pdb=" O ASN E 163 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LYS E 165 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU E 128 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE E 167 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU E 130 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR E 169 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU E 132 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU E 33 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N MET E 170 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU E 35 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N VAL E 187 " --> pdb=" O ASN E 32 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE E 34 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N PHE E 189 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN E 36 " --> pdb=" O PHE E 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 433 through 435 937 hydrogen bonds defined for protein. 2676 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 3.89 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3241 1.31 - 1.44: 6093 1.44 - 1.57: 11768 1.57 - 1.70: 177 1.70 - 1.83: 132 Bond restraints: 21411 Sorted by residual: bond pdb=" C PRO C 27 " pdb=" O PRO C 27 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.21e-02 6.83e+03 1.88e+01 bond pdb=" C LEU A 568 " pdb=" O LEU A 568 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.28e-02 6.10e+03 1.64e+01 bond pdb=" C ASP A 569 " pdb=" O ASP A 569 " ideal model delta sigma weight residual 1.236 1.186 0.051 1.26e-02 6.30e+03 1.62e+01 bond pdb=" C ARG D 227 " pdb=" O ARG D 227 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.26e-02 6.30e+03 1.38e+01 bond pdb=" C ARG D 227 " pdb=" N GLN D 228 " ideal model delta sigma weight residual 1.334 1.289 0.045 1.25e-02 6.40e+03 1.28e+01 ... (remaining 21406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 29001 3.39 - 6.78: 254 6.78 - 10.17: 38 10.17 - 13.56: 3 13.56 - 16.95: 2 Bond angle restraints: 29298 Sorted by residual: angle pdb=" CB MET A 779 " pdb=" CG MET A 779 " pdb=" SD MET A 779 " ideal model delta sigma weight residual 112.70 129.59 -16.89 3.00e+00 1.11e-01 3.17e+01 angle pdb=" C PRO C 27 " pdb=" CA PRO C 27 " pdb=" CB PRO C 27 " ideal model delta sigma weight residual 111.12 118.02 -6.90 1.29e+00 6.01e-01 2.86e+01 angle pdb=" O4' DG H 44 " pdb=" C1' DG H 44 " pdb=" N9 DG H 44 " ideal model delta sigma weight residual 108.00 111.47 -3.47 7.00e-01 2.04e+00 2.45e+01 angle pdb=" C TYR C 26 " pdb=" CA TYR C 26 " pdb=" CB TYR C 26 " ideal model delta sigma weight residual 110.17 119.92 -9.75 1.97e+00 2.58e-01 2.45e+01 angle pdb=" CA GLU C 59 " pdb=" CB GLU C 59 " pdb=" CG GLU C 59 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 ... (remaining 29293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 10591 18.16 - 36.32: 1423 36.32 - 54.48: 580 54.48 - 72.64: 109 72.64 - 90.80: 35 Dihedral angle restraints: 12738 sinusoidal: 5816 harmonic: 6922 Sorted by residual: dihedral pdb=" CA VAL E 8 " pdb=" C VAL E 8 " pdb=" N ALA E 9 " pdb=" CA ALA E 9 " ideal model delta harmonic sigma weight residual -180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LYS E 431 " pdb=" C LYS E 431 " pdb=" N LEU E 432 " pdb=" CA LEU E 432 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE B 475 " pdb=" C PHE B 475 " pdb=" N VAL B 476 " pdb=" CA VAL B 476 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 12735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2624 0.060 - 0.121: 606 0.121 - 0.181: 77 0.181 - 0.242: 12 0.242 - 0.302: 3 Chirality restraints: 3322 Sorted by residual: chirality pdb=" CB THR A 474 " pdb=" CA THR A 474 " pdb=" OG1 THR A 474 " pdb=" CG2 THR A 474 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB ILE E 326 " pdb=" CA ILE E 326 " pdb=" CG1 ILE E 326 " pdb=" CG2 ILE E 326 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB THR E 87 " pdb=" CA THR E 87 " pdb=" OG1 THR E 87 " pdb=" CG2 THR E 87 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 3319 not shown) Planarity restraints: 3392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 25 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C VAL C 25 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL C 25 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR C 26 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 332 " 0.022 2.00e-02 2.50e+03 2.44e-02 1.04e+01 pdb=" CG PHE F 332 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE F 332 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE F 332 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE F 332 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 332 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 484 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO B 485 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.041 5.00e-02 4.00e+02 ... (remaining 3389 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 115 2.42 - 3.04: 10927 3.04 - 3.66: 34166 3.66 - 4.28: 52883 4.28 - 4.90: 82310 Nonbonded interactions: 180401 Sorted by model distance: nonbonded pdb=" OD1 ASP E 136 " pdb=" O HOH E1101 " model vdw 1.795 3.040 nonbonded pdb=" O PRO B 415 " pdb=" O HOH B 701 " model vdw 1.811 3.040 nonbonded pdb=" OD1 ASP A 867 " pdb=" O HOH A1101 " model vdw 1.879 3.040 nonbonded pdb=" O ILE E 184 " pdb=" O HOH E1102 " model vdw 1.948 3.040 nonbonded pdb=" OD2 ASP B 479 " pdb=" O HOH B 702 " model vdw 1.996 3.040 ... (remaining 180396 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.290 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 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 : 0.005 0.073 21411 Z= 0.325 Angle : 0.894 16.948 29298 Z= 0.551 Chirality : 0.052 0.302 3322 Planarity : 0.006 0.084 3392 Dihedral : 19.569 90.804 8218 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.87 % Allowed : 17.86 % Favored : 80.27 % 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: -1.60 (0.15), residues: 2283 helix: -1.12 (0.12), residues: 1279 sheet: 0.14 (0.32), residues: 222 loop : -1.00 (0.19), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 393 TYR 0.025 0.002 TYR F 300 PHE 0.057 0.002 PHE F 332 TRP 0.041 0.002 TRP F 317 HIS 0.026 0.002 HIS E 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.32 (21411) covalent geometry : angle 0.89429 / 0.55 (29298) hydrogen bonds : bond 0.15329 / 10.29 ( 1029) hydrogen bonds : angle 5.98073 / 4.22 ( 2860) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 352 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7559 (tp30) REVERT: C 395 PHE cc_start: 0.7118 (m-80) cc_final: 0.6621 (m-10) REVERT: C 454 HIS cc_start: 0.7624 (t70) cc_final: 0.7136 (t70) REVERT: E 212 ASP cc_start: 0.8344 (t70) cc_final: 0.8124 (t0) REVERT: E 284 LEU cc_start: 0.8997 (tp) cc_final: 0.8793 (tp) REVERT: F 277 TYR cc_start: 0.8325 (m-80) cc_final: 0.7815 (m-80) REVERT: F 287 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7962 (ttp-110) REVERT: F 344 HIS cc_start: 0.7439 (t-90) cc_final: 0.7055 (m-70) REVERT: F 363 ILE cc_start: 0.7964 (pt) cc_final: 0.7758 (pp) REVERT: F 364 GLU cc_start: 0.8158 (tt0) cc_final: 0.7851 (tm-30) REVERT: F 368 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8551 (mt) REVERT: F 400 ARG cc_start: 0.8221 (mtp180) cc_final: 0.8014 (mtm180) REVERT: F 414 THR cc_start: 0.8797 (p) cc_final: 0.8152 (p) outliers start: 40 outliers final: 13 residues processed: 384 average time/residue: 0.7050 time to fit residues: 300.9149 Evaluate side-chains 239 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 30.0000 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 405 GLN B 493 GLN C 67 HIS C 271 ASN C 312 HIS C 370 GLN ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 493 GLN E 2 ASN E 241 HIS F 307 ASN F 318 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.097905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.070405 restraints weight = 35724.586| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.10 r_work: 0.2789 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21411 Z= 0.162 Angle : 0.615 9.995 29298 Z= 0.335 Chirality : 0.044 0.232 3322 Planarity : 0.004 0.057 3392 Dihedral : 18.252 72.385 3481 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.38 % Allowed : 19.36 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.30 (0.16), residues: 2283 helix: 0.14 (0.14), residues: 1293 sheet: 0.32 (0.33), residues: 212 loop : -0.70 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 271 TYR 0.020 0.001 TYR C 528 PHE 0.016 0.001 PHE F 292 TRP 0.014 0.001 TRP C 494 HIS 0.010 0.001 HIS E 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (21411) covalent geometry : angle 0.61461 / 0.33 (29298) hydrogen bonds : bond 0.04851 / 3.27 ( 1029) hydrogen bonds : angle 4.41263 / 3.14 ( 2860) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7809 (mm-30) REVERT: B 390 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8309 (ttt90) REVERT: C 130 GLU cc_start: 0.8609 (mp0) cc_final: 0.8403 (mt-10) REVERT: C 454 HIS cc_start: 0.8032 (t70) cc_final: 0.7472 (t70) REVERT: C 568 GLU cc_start: 0.9057 (tt0) cc_final: 0.8823 (pp20) REVERT: C 592 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8418 (tm-30) REVERT: E 212 ASP cc_start: 0.8663 (t70) cc_final: 0.8369 (t0) REVERT: E 277 ASN cc_start: 0.8200 (m-40) cc_final: 0.7912 (m-40) REVERT: E 414 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8302 (ttt) REVERT: E 437 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7640 (ppp) REVERT: E 441 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7824 (tp) REVERT: F 277 TYR cc_start: 0.8436 (m-80) cc_final: 0.7985 (m-80) REVERT: F 284 GLU cc_start: 0.8339 (tp30) cc_final: 0.7816 (tp30) REVERT: F 344 HIS cc_start: 0.7817 (t-90) cc_final: 0.7460 (m-70) REVERT: F 364 GLU cc_start: 0.8442 (tt0) cc_final: 0.8075 (tm-30) REVERT: F 400 ARG cc_start: 0.9013 (mtp180) cc_final: 0.8795 (mtm180) outliers start: 51 outliers final: 18 residues processed: 266 average time/residue: 0.7163 time to fit residues: 211.8467 Evaluate side-chains 220 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 206 CYS Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 437 MET Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 278 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 199 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 186 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 470 ASN D 155 GLN F 307 ASN F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.099431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.073002 restraints weight = 36799.586| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.05 r_work: 0.2873 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9139 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21411 Z= 0.128 Angle : 0.547 8.440 29298 Z= 0.300 Chirality : 0.042 0.209 3322 Planarity : 0.003 0.053 3392 Dihedral : 18.187 74.202 3467 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.19 % Allowed : 19.17 % Favored : 78.64 % 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: 0.25 (0.17), residues: 2283 helix: 0.70 (0.14), residues: 1299 sheet: 0.21 (0.34), residues: 206 loop : -0.60 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 287 TYR 0.018 0.001 TYR F 306 PHE 0.024 0.001 PHE C 412 TRP 0.013 0.001 TRP C 494 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (21411) covalent geometry : angle 0.54725 / 0.30 (29298) hydrogen bonds : bond 0.04031 / 2.71 ( 1029) hydrogen bonds : angle 4.08059 / 2.91 ( 2860) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 429 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8541 (mm-40) REVERT: B 390 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8686 (ttt90) REVERT: C 454 HIS cc_start: 0.7984 (t70) cc_final: 0.7445 (t70) REVERT: C 470 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8514 (p0) REVERT: D 186 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9301 (mp) REVERT: D 425 ARG cc_start: 0.6467 (ppt90) cc_final: 0.6214 (ppt170) REVERT: E 141 LEU cc_start: 0.8126 (tp) cc_final: 0.7906 (mt) REVERT: E 212 ASP cc_start: 0.8730 (t70) cc_final: 0.8402 (t0) REVERT: E 245 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8403 (mp10) REVERT: E 277 ASN cc_start: 0.8191 (m-40) cc_final: 0.7894 (m-40) REVERT: E 437 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7420 (ppp) REVERT: E 438 ASN cc_start: 0.7442 (m-40) cc_final: 0.7140 (t0) REVERT: E 441 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7871 (tp) REVERT: F 277 TYR cc_start: 0.8504 (m-80) cc_final: 0.8098 (m-80) REVERT: F 284 GLU cc_start: 0.8017 (tp30) cc_final: 0.6822 (tp30) REVERT: F 287 ARG cc_start: 0.8745 (ttp80) cc_final: 0.8468 (ttp-110) REVERT: F 344 HIS cc_start: 0.8003 (t-90) cc_final: 0.7496 (m-70) REVERT: F 364 GLU cc_start: 0.8434 (tt0) cc_final: 0.8083 (tm-30) REVERT: F 400 ARG cc_start: 0.9043 (mtp180) cc_final: 0.8811 (mtp180) outliers start: 47 outliers final: 15 residues processed: 255 average time/residue: 0.7743 time to fit residues: 220.5828 Evaluate side-chains 221 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 206 CYS Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 437 MET Chi-restraints excluded: chain E residue 441 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 230 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 198 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 470 ASN C 532 ASN D 96 HIS D 155 GLN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 ASN F 318 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.095430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.068979 restraints weight = 37406.681| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.05 r_work: 0.2821 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9206 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 21411 Z= 0.286 Angle : 0.638 8.636 29298 Z= 0.341 Chirality : 0.047 0.224 3322 Planarity : 0.004 0.055 3392 Dihedral : 18.383 74.971 3466 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.80 % Allowed : 18.56 % Favored : 78.64 % 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: 0.44 (0.17), residues: 2283 helix: 0.84 (0.14), residues: 1299 sheet: 0.33 (0.34), residues: 205 loop : -0.49 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 271 TYR 0.025 0.002 TYR C 483 PHE 0.025 0.002 PHE C 412 TRP 0.012 0.002 TRP D 526 HIS 0.005 0.001 HIS C 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.29 (21411) covalent geometry : angle 0.63812 / 0.34 (29298) hydrogen bonds : bond 0.04862 / 3.26 ( 1029) hydrogen bonds : angle 4.13184 / 2.94 ( 2860) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 205 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 ILE cc_start: 0.9311 (mp) cc_final: 0.8704 (mp) REVERT: A 420 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7701 (mp0) REVERT: A 429 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8589 (mm-40) REVERT: A 504 GLU cc_start: 0.8310 (mp0) cc_final: 0.8110 (mp0) REVERT: A 518 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8419 (mtt) REVERT: A 576 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7517 (pp30) REVERT: B 496 MET cc_start: 0.8547 (mmm) cc_final: 0.7157 (tmt) REVERT: C 417 LEU cc_start: 0.9186 (mt) cc_final: 0.8973 (mt) REVERT: C 454 HIS cc_start: 0.7948 (t70) cc_final: 0.7445 (t70) REVERT: C 552 GLU cc_start: 0.8281 (mp0) cc_final: 0.8064 (mp0) REVERT: C 592 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8462 (tm-30) REVERT: D 186 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9342 (mp) REVERT: D 425 ARG cc_start: 0.6488 (ppt90) cc_final: 0.6244 (ppt170) REVERT: E 212 ASP cc_start: 0.8720 (t70) cc_final: 0.8362 (t0) REVERT: E 245 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8495 (mp10) REVERT: E 277 ASN cc_start: 0.8258 (m-40) cc_final: 0.7924 (m-40) REVERT: E 441 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7896 (tp) REVERT: F 277 TYR cc_start: 0.8620 (m-80) cc_final: 0.8245 (m-80) REVERT: F 344 HIS cc_start: 0.8134 (t-90) cc_final: 0.7641 (m-70) REVERT: F 364 GLU cc_start: 0.8458 (tt0) cc_final: 0.7914 (tm-30) REVERT: F 368 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8385 (mp) outliers start: 60 outliers final: 30 residues processed: 248 average time/residue: 0.7565 time to fit residues: 209.5291 Evaluate side-chains 224 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 206 CYS Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 113 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 470 ASN D 155 GLN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 ASN F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.096778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.070294 restraints weight = 36918.400| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.05 r_work: 0.2843 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9178 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21411 Z= 0.146 Angle : 0.557 7.343 29298 Z= 0.303 Chirality : 0.042 0.211 3322 Planarity : 0.003 0.052 3392 Dihedral : 18.354 76.694 3465 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.96 % Allowed : 19.59 % Favored : 78.45 % 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: 0.70 (0.17), residues: 2283 helix: 1.09 (0.15), residues: 1299 sheet: 0.20 (0.34), residues: 206 loop : -0.40 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 287 TYR 0.017 0.001 TYR B 372 PHE 0.024 0.001 PHE C 392 TRP 0.012 0.001 TRP C 494 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (21411) covalent geometry : angle 0.55707 / 0.30 (29298) hydrogen bonds : bond 0.04064 / 2.73 ( 1029) hydrogen bonds : angle 3.97780 / 2.83 ( 2860) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 ILE cc_start: 0.9239 (mp) cc_final: 0.8709 (mp) REVERT: A 420 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7573 (mp0) REVERT: A 429 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8590 (mm-40) REVERT: A 504 GLU cc_start: 0.8357 (mp0) cc_final: 0.8138 (mp0) REVERT: A 518 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8393 (mtt) REVERT: A 576 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.7530 (pp30) REVERT: C 454 HIS cc_start: 0.7953 (t70) cc_final: 0.7569 (t70) REVERT: C 488 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8574 (mt-10) REVERT: C 592 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8374 (tm-30) REVERT: D 186 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9323 (mp) REVERT: E 172 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8683 (mm-30) REVERT: E 212 ASP cc_start: 0.8732 (t70) cc_final: 0.8354 (t0) REVERT: E 245 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8477 (mp10) REVERT: E 277 ASN cc_start: 0.8119 (m-40) cc_final: 0.7740 (m-40) REVERT: E 441 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7948 (tp) REVERT: F 277 TYR cc_start: 0.8583 (m-80) cc_final: 0.8248 (m-80) REVERT: F 280 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7239 (ptm) REVERT: F 364 GLU cc_start: 0.8408 (tt0) cc_final: 0.7938 (tm-30) REVERT: F 368 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8445 (mt) outliers start: 42 outliers final: 20 residues processed: 226 average time/residue: 0.7180 time to fit residues: 182.4008 Evaluate side-chains 214 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 465 SER Chi-restraints excluded: chain F residue 280 MET Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 9 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 81 optimal weight: 0.0370 chunk 75 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 470 ASN D 155 GLN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 ASN F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.069701 restraints weight = 37304.931| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.06 r_work: 0.2800 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9188 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21411 Z= 0.188 Angle : 0.574 7.803 29298 Z= 0.311 Chirality : 0.043 0.212 3322 Planarity : 0.003 0.052 3392 Dihedral : 18.344 77.104 3465 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.61 % Allowed : 19.12 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.82 (0.17), residues: 2283 helix: 1.18 (0.15), residues: 1301 sheet: 0.24 (0.34), residues: 204 loop : -0.34 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 287 TYR 0.018 0.001 TYR C 483 PHE 0.037 0.002 PHE C 412 TRP 0.012 0.001 TRP C 494 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (21411) covalent geometry : angle 0.57420 / 0.31 (29298) hydrogen bonds : bond 0.04184 / 2.81 ( 1029) hydrogen bonds : angle 3.96277 / 2.82 ( 2860) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7826 (mm-30) REVERT: A 504 GLU cc_start: 0.8394 (mp0) cc_final: 0.8166 (mp0) REVERT: A 518 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8388 (mtp) REVERT: A 576 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7563 (pp30) REVERT: C 454 HIS cc_start: 0.8061 (t70) cc_final: 0.7383 (t70) REVERT: C 488 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8623 (mt-10) REVERT: C 552 GLU cc_start: 0.8304 (mp0) cc_final: 0.8075 (mp0) REVERT: C 592 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8441 (tm-30) REVERT: D 186 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9333 (mp) REVERT: E 172 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8706 (mm-30) REVERT: E 212 ASP cc_start: 0.8753 (t70) cc_final: 0.8313 (t0) REVERT: E 217 LYS cc_start: 0.7184 (mmpt) cc_final: 0.6668 (mttm) REVERT: E 245 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8503 (mp10) REVERT: E 277 ASN cc_start: 0.8082 (m-40) cc_final: 0.7667 (m-40) REVERT: E 441 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7977 (tp) REVERT: F 277 TYR cc_start: 0.8563 (m-80) cc_final: 0.8190 (m-80) REVERT: F 312 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7759 (ptt180) REVERT: F 364 GLU cc_start: 0.8430 (tt0) cc_final: 0.7974 (tm-30) REVERT: F 368 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8436 (mt) outliers start: 56 outliers final: 25 residues processed: 231 average time/residue: 0.7127 time to fit residues: 184.6846 Evaluate side-chains 215 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 465 SER Chi-restraints excluded: chain F residue 312 ARG Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 228 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 203 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN C 470 ASN D 155 GLN F 307 ASN F 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.094600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.067407 restraints weight = 35997.684| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.09 r_work: 0.2736 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21411 Z= 0.173 Angle : 0.569 8.255 29298 Z= 0.309 Chirality : 0.043 0.208 3322 Planarity : 0.003 0.051 3392 Dihedral : 18.347 77.679 3465 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.38 % Allowed : 19.68 % Favored : 77.94 % 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: 0.90 (0.17), residues: 2283 helix: 1.26 (0.15), residues: 1300 sheet: 0.23 (0.34), residues: 204 loop : -0.31 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 287 TYR 0.020 0.001 TYR F 306 PHE 0.027 0.001 PHE C 392 TRP 0.012 0.001 TRP C 494 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (21411) covalent geometry : angle 0.56853 / 0.31 (29298) hydrogen bonds : bond 0.04077 / 2.74 ( 1029) hydrogen bonds : angle 3.93431 / 2.80 ( 2860) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7553 (mp0) REVERT: A 504 GLU cc_start: 0.8340 (mp0) cc_final: 0.8139 (mp0) REVERT: A 518 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8368 (mtp) REVERT: A 576 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7576 (pp30) REVERT: C 454 HIS cc_start: 0.8077 (t70) cc_final: 0.7371 (t70) REVERT: C 488 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8659 (mt-10) REVERT: C 552 GLU cc_start: 0.8358 (mp0) cc_final: 0.7926 (mp0) REVERT: C 592 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8469 (tm-30) REVERT: D 186 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9325 (mp) REVERT: E 172 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8686 (mm-30) REVERT: E 217 LYS cc_start: 0.7159 (mmpt) cc_final: 0.6627 (mttm) REVERT: E 245 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8513 (mp10) REVERT: E 277 ASN cc_start: 0.8013 (m-40) cc_final: 0.7559 (m-40) REVERT: E 441 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7952 (tp) REVERT: F 277 TYR cc_start: 0.8548 (m-80) cc_final: 0.8280 (m-80) REVERT: F 312 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7720 (ptt180) REVERT: F 341 ARG cc_start: 0.8515 (mmp80) cc_final: 0.8303 (mmp80) REVERT: F 364 GLU cc_start: 0.8418 (tt0) cc_final: 0.7944 (tm-30) REVERT: F 368 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8366 (mt) outliers start: 51 outliers final: 29 residues processed: 226 average time/residue: 0.7288 time to fit residues: 185.0316 Evaluate side-chains 221 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 465 SER Chi-restraints excluded: chain F residue 312 ARG Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 45 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN F 307 ASN F 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.095388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.068296 restraints weight = 35920.446| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.09 r_work: 0.2753 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9162 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21411 Z= 0.134 Angle : 0.554 8.692 29298 Z= 0.300 Chirality : 0.042 0.198 3322 Planarity : 0.003 0.051 3392 Dihedral : 18.306 78.410 3465 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.05 % Allowed : 20.34 % Favored : 77.61 % 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: 1.00 (0.17), residues: 2283 helix: 1.38 (0.15), residues: 1300 sheet: 0.14 (0.34), residues: 206 loop : -0.30 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 400 TYR 0.020 0.001 TYR F 306 PHE 0.037 0.001 PHE C 412 TRP 0.012 0.001 TRP C 494 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (21411) covalent geometry : angle 0.55437 / 0.30 (29298) hydrogen bonds : bond 0.03812 / 2.56 ( 1029) hydrogen bonds : angle 3.87519 / 2.75 ( 2860) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 518 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8358 (mtp) REVERT: A 576 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7538 (pp30) REVERT: A 653 LYS cc_start: 0.8811 (ptpt) cc_final: 0.8512 (mptt) REVERT: B 496 MET cc_start: 0.8324 (mmm) cc_final: 0.7110 (tmt) REVERT: C 454 HIS cc_start: 0.8084 (t70) cc_final: 0.7383 (t70) REVERT: C 552 GLU cc_start: 0.8295 (mp0) cc_final: 0.8048 (mp0) REVERT: C 592 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8440 (tm-30) REVERT: D 186 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9334 (mp) REVERT: E 217 LYS cc_start: 0.7168 (mmpt) cc_final: 0.6636 (mttm) REVERT: E 245 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8523 (mp10) REVERT: E 277 ASN cc_start: 0.7913 (m-40) cc_final: 0.7475 (m-40) REVERT: E 441 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7936 (tp) REVERT: F 277 TYR cc_start: 0.8543 (m-80) cc_final: 0.8136 (m-80) REVERT: F 312 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7700 (ptt180) REVERT: F 364 GLU cc_start: 0.8407 (tt0) cc_final: 0.7934 (tm-30) REVERT: F 368 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8388 (mt) outliers start: 44 outliers final: 21 residues processed: 227 average time/residue: 0.7026 time to fit residues: 179.2305 Evaluate side-chains 215 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 465 SER Chi-restraints excluded: chain F residue 312 ARG Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 56 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 71 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 370 GLN C 470 ASN D 155 GLN F 307 ASN F 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.095946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.068872 restraints weight = 35872.972| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.10 r_work: 0.2764 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21411 Z= 0.122 Angle : 0.548 9.007 29298 Z= 0.298 Chirality : 0.041 0.188 3322 Planarity : 0.003 0.050 3392 Dihedral : 18.260 78.902 3465 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.73 % Allowed : 21.04 % Favored : 77.24 % 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: 1.08 (0.18), residues: 2283 helix: 1.45 (0.15), residues: 1300 sheet: 0.15 (0.34), residues: 206 loop : -0.27 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 503 TYR 0.019 0.001 TYR F 306 PHE 0.028 0.001 PHE C 392 TRP 0.012 0.001 TRP C 494 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (21411) covalent geometry : angle 0.54774 / 0.30 (29298) hydrogen bonds : bond 0.03644 / 2.44 ( 1029) hydrogen bonds : angle 3.83494 / 2.72 ( 2860) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7763 (mm-30) REVERT: A 504 GLU cc_start: 0.8231 (mp0) cc_final: 0.8011 (mp0) REVERT: A 518 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8428 (mtt) REVERT: A 576 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7511 (pp30) REVERT: A 653 LYS cc_start: 0.8826 (ptpt) cc_final: 0.8511 (mptt) REVERT: B 496 MET cc_start: 0.8331 (mmm) cc_final: 0.7134 (tmt) REVERT: C 454 HIS cc_start: 0.8089 (t70) cc_final: 0.7393 (t70) REVERT: C 552 GLU cc_start: 0.8305 (mp0) cc_final: 0.8064 (mp0) REVERT: C 592 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8453 (tm-30) REVERT: D 186 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9300 (mp) REVERT: D 242 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7299 (mtm-85) REVERT: D 425 ARG cc_start: 0.6889 (pmt-80) cc_final: 0.6687 (pmt-80) REVERT: E 141 LEU cc_start: 0.8390 (tp) cc_final: 0.8107 (mt) REVERT: E 217 LYS cc_start: 0.7091 (mmpt) cc_final: 0.6545 (mttm) REVERT: E 245 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8488 (mp10) REVERT: E 277 ASN cc_start: 0.7825 (m-40) cc_final: 0.7379 (m-40) REVERT: E 441 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7913 (tp) REVERT: F 277 TYR cc_start: 0.8532 (m-80) cc_final: 0.8232 (m-80) REVERT: F 312 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7702 (ptt180) REVERT: F 364 GLU cc_start: 0.8406 (tt0) cc_final: 0.7959 (tm-30) REVERT: F 368 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8354 (mt) outliers start: 37 outliers final: 19 residues processed: 217 average time/residue: 0.7178 time to fit residues: 174.8426 Evaluate side-chains 210 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 465 SER Chi-restraints excluded: chain F residue 312 ARG Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 138 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 236 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 470 ASN D 155 GLN E 2 ASN F 307 ASN F 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.094989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.067864 restraints weight = 36211.945| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.10 r_work: 0.2746 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9167 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21411 Z= 0.173 Angle : 0.579 10.471 29298 Z= 0.309 Chirality : 0.043 0.245 3322 Planarity : 0.004 0.093 3392 Dihedral : 18.275 78.750 3464 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.82 % Allowed : 20.99 % Favored : 77.19 % 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: 1.08 (0.17), residues: 2283 helix: 1.44 (0.15), residues: 1300 sheet: 0.20 (0.34), residues: 206 loop : -0.26 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 271 TYR 0.019 0.001 TYR F 306 PHE 0.037 0.001 PHE C 412 TRP 0.012 0.001 TRP C 494 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (21411) covalent geometry : angle 0.57875 / 0.31 (29298) hydrogen bonds : bond 0.03887 / 2.61 ( 1029) hydrogen bonds : angle 3.86056 / 2.74 ( 2860) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7784 (mm-30) REVERT: A 504 GLU cc_start: 0.8203 (mp0) cc_final: 0.7975 (mp0) REVERT: A 518 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8413 (mtt) REVERT: A 576 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.7568 (pp30) REVERT: A 653 LYS cc_start: 0.8777 (ptpt) cc_final: 0.8456 (mptt) REVERT: B 496 MET cc_start: 0.8468 (mmm) cc_final: 0.7105 (tmt) REVERT: C 417 LEU cc_start: 0.9328 (mt) cc_final: 0.9048 (mp) REVERT: C 454 HIS cc_start: 0.8060 (t70) cc_final: 0.7376 (t70) REVERT: C 552 GLU cc_start: 0.8317 (mp0) cc_final: 0.8074 (mp0) REVERT: C 592 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8437 (tm-30) REVERT: D 186 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9335 (mp) REVERT: D 242 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7319 (mtm-85) REVERT: E 217 LYS cc_start: 0.7169 (mmpt) cc_final: 0.6595 (mttm) REVERT: E 238 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8714 (t0) REVERT: E 245 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8491 (mp10) REVERT: E 277 ASN cc_start: 0.7840 (m-40) cc_final: 0.7409 (m-40) REVERT: E 441 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7896 (tp) REVERT: F 277 TYR cc_start: 0.8549 (m-80) cc_final: 0.8253 (m-80) REVERT: F 281 THR cc_start: 0.9291 (p) cc_final: 0.8919 (p) REVERT: F 312 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7723 (ptt180) REVERT: F 364 GLU cc_start: 0.8443 (tt0) cc_final: 0.8003 (tm-30) REVERT: F 368 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8406 (mt) outliers start: 39 outliers final: 18 residues processed: 214 average time/residue: 0.7212 time to fit residues: 173.9194 Evaluate side-chains 212 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 465 SER Chi-restraints excluded: chain F residue 312 ARG Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 217 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 230 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 53 ASN C 470 ASN D 155 GLN E 2 ASN F 307 ASN F 318 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.066578 restraints weight = 36123.917| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.09 r_work: 0.2719 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9185 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21411 Z= 0.217 Angle : 0.609 9.274 29298 Z= 0.326 Chirality : 0.045 0.206 3322 Planarity : 0.004 0.051 3392 Dihedral : 18.371 78.552 3464 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.77 % Allowed : 21.13 % Favored : 77.10 % 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: 1.06 (0.17), residues: 2283 helix: 1.41 (0.15), residues: 1300 sheet: 0.25 (0.34), residues: 205 loop : -0.26 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 503 TYR 0.019 0.002 TYR C 483 PHE 0.028 0.002 PHE C 392 TRP 0.010 0.001 TRP C 494 HIS 0.005 0.001 HIS C 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (21411) covalent geometry : angle 0.60915 / 0.33 (29298) hydrogen bonds : bond 0.04281 / 2.87 ( 1029) hydrogen bonds : angle 3.94494 / 2.79 ( 2860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8267.57 seconds wall clock time: 141 minutes 27.80 seconds (8487.80 seconds total)