Starting phenix.real_space_refine on Sun Sep 13 05:13:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tjf_25924/09_2026/7tjf_25924.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjf_25924/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7tjf_25924/09_2026/7tjf_25924.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tjf_25924/09_2026/7tjf_25924.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tjf_25924/09_2026/7tjf_25924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjf_25924/09_2026/7tjf_25924.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tjf_25924/09_2026/7tjf_25924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjf_25924/09_2026/7tjf_25924.map" } 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-2.2.1-6174/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: 4.41, per 1000 atoms: 0.21 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: 1.56 Conformation dependent library (CDL) restraints added in 771.9 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: 2.49 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: 4.11 Time building geometry restraints manager: 2.08 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: 29000 3.39 - 6.78: 255 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: 1.840 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.580 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.140 ------------------------------------------------------------------------------- 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 : 0.896 16.948 29298 Z= 0.554 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 0.89610 / 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 : 0.905 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: 0.7852 (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: 0.7790 time to fit residues: 333.3576 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 : 0.737 ------------------------------------------------------------------------------- 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 D 155 GLN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.097861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.071831 restraints weight = 35727.874| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.10 r_work: 0.2780 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21411 Z= 0.167 Angle : 0.617 10.012 29298 Z= 0.335 Chirality : 0.044 0.232 3322 Planarity : 0.004 0.057 3392 Dihedral : 18.216 72.311 3481 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.43 % Allowed : 19.45 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.32 (0.16), residues: 2283 helix: 0.14 (0.14), residues: 1293 sheet: 0.16 (0.32), residues: 222 loop : -0.72 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 271 TYR 0.020 0.002 TYR C 528 PHE 0.018 0.001 PHE F 292 TRP 0.014 0.001 TRP C 494 HIS 0.009 0.001 HIS E 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (21411) covalent geometry : angle 0.61658 / 0.34 (29298) hydrogen bonds : bond 0.04766 / 3.21 ( 1029) hydrogen bonds : angle 4.41391 / 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 281 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7815 (mm-30) REVERT: B 390 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8302 (ttt90) REVERT: C 130 GLU cc_start: 0.8634 (mp0) cc_final: 0.8420 (mt-10) REVERT: C 454 HIS cc_start: 0.8049 (t70) cc_final: 0.7479 (t70) REVERT: C 568 GLU cc_start: 0.9074 (tt0) cc_final: 0.8827 (pp20) REVERT: C 592 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8436 (tm-30) REVERT: E 212 ASP cc_start: 0.8657 (t70) cc_final: 0.8364 (t0) REVERT: E 277 ASN cc_start: 0.8180 (m-40) cc_final: 0.7824 (m-40) REVERT: E 414 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8314 (ttt) REVERT: E 437 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7633 (ppp) REVERT: E 441 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7836 (tp) REVERT: F 277 TYR cc_start: 0.8400 (m-80) cc_final: 0.7980 (m-80) REVERT: F 284 GLU cc_start: 0.8350 (tp30) cc_final: 0.8051 (tp30) REVERT: F 344 HIS cc_start: 0.7829 (t-90) cc_final: 0.7476 (m-70) REVERT: F 350 MET cc_start: 0.8911 (tpt) cc_final: 0.8685 (tpt) REVERT: F 364 GLU cc_start: 0.8438 (tt0) cc_final: 0.8065 (tm-30) REVERT: F 400 ARG cc_start: 0.9028 (mtp180) cc_final: 0.8805 (mtm180) outliers start: 52 outliers final: 17 residues processed: 266 average time/residue: 0.7632 time to fit residues: 226.1419 Evaluate side-chains 220 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 94 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 HIS ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 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 = 0.3473 r_free = 0.3473 target = 0.098461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.072527 restraints weight = 36953.722| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.16 r_work: 0.2847 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9169 moved from start: 0.1968 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= 0.158 Angle : 0.569 8.442 29298 Z= 0.310 Chirality : 0.043 0.212 3322 Planarity : 0.004 0.053 3392 Dihedral : 18.207 74.051 3467 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.47 % Allowed : 18.94 % Favored : 78.59 % 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: 0.69 (0.14), residues: 1300 sheet: 0.29 (0.33), residues: 204 loop : -0.60 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 287 TYR 0.018 0.001 TYR C 483 PHE 0.027 0.001 PHE C 412 TRP 0.013 0.001 TRP D 526 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (21411) covalent geometry : angle 0.56942 / 0.31 (29298) hydrogen bonds : bond 0.04258 / 2.86 ( 1029) hydrogen bonds : angle 4.09403 / 2.92 ( 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 267 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 214 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7808 (mm-30) REVERT: A 429 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8631 (mm-40) REVERT: A 576 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7535 (pp30) REVERT: B 390 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8505 (ttt90) REVERT: C 454 HIS cc_start: 0.7987 (t70) cc_final: 0.7464 (t70) REVERT: D 186 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9349 (mp) REVERT: D 425 ARG cc_start: 0.6532 (ppt90) cc_final: 0.6272 (ppt170) REVERT: E 141 LEU cc_start: 0.8249 (tp) cc_final: 0.7952 (mt) REVERT: E 212 ASP cc_start: 0.8730 (t70) cc_final: 0.8387 (t0) REVERT: E 245 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8439 (mp10) REVERT: E 277 ASN cc_start: 0.8240 (m-40) cc_final: 0.7908 (m-40) REVERT: E 437 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7383 (ppp) REVERT: E 438 ASN cc_start: 0.7530 (m-40) cc_final: 0.7214 (t0) REVERT: E 441 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7862 (tp) REVERT: F 277 TYR cc_start: 0.8550 (m-80) cc_final: 0.8182 (m-80) REVERT: F 344 HIS cc_start: 0.8058 (t-90) cc_final: 0.7538 (m-70) REVERT: F 364 GLU cc_start: 0.8461 (tt0) cc_final: 0.7936 (tm-30) REVERT: F 368 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8472 (mt) outliers start: 53 outliers final: 17 residues processed: 255 average time/residue: 0.7187 time to fit residues: 205.4748 Evaluate side-chains 218 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 576 GLN 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 562 SER 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 D residue 453 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 Chi-restraints excluded: chain F residue 368 LEU 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: 2.9990 chunk 102 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 198 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 470 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.095690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.069339 restraints weight = 37396.719| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.03 r_work: 0.2814 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9198 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 21411 Z= 0.236 Angle : 0.617 8.409 29298 Z= 0.331 Chirality : 0.046 0.223 3322 Planarity : 0.004 0.054 3392 Dihedral : 18.356 75.422 3466 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.85 % Allowed : 18.28 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.53 (0.17), residues: 2283 helix: 0.92 (0.14), residues: 1299 sheet: 0.32 (0.34), residues: 205 loop : -0.46 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 271 TYR 0.023 0.002 TYR C 483 PHE 0.022 0.002 PHE C 412 TRP 0.012 0.002 TRP D 526 HIS 0.013 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (21411) covalent geometry : angle 0.61694 / 0.33 (29298) hydrogen bonds : bond 0.04692 / 3.15 ( 1029) hydrogen bonds : angle 4.08993 / 2.91 ( 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 261 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 200 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8136 (pmtt) REVERT: A 416 HIS cc_start: 0.8291 (m90) cc_final: 0.7892 (m-70) REVERT: A 420 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7723 (mp0) REVERT: A 429 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8576 (mm-40) REVERT: A 576 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7577 (pp30) REVERT: B 390 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8610 (ttt90) REVERT: B 496 MET cc_start: 0.8553 (mmm) cc_final: 0.7155 (tmt) REVERT: C 417 LEU cc_start: 0.9201 (mt) cc_final: 0.9000 (mt) REVERT: C 454 HIS cc_start: 0.7959 (t70) cc_final: 0.7534 (t70) REVERT: C 552 GLU cc_start: 0.8274 (mp0) cc_final: 0.8045 (mp0) REVERT: C 592 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8445 (tm-30) REVERT: D 186 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9341 (mp) REVERT: D 425 ARG cc_start: 0.6497 (ppt90) cc_final: 0.6242 (ppt170) REVERT: E 212 ASP cc_start: 0.8742 (t70) cc_final: 0.8377 (t0) REVERT: E 245 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8491 (mp10) REVERT: E 277 ASN cc_start: 0.8202 (m-40) cc_final: 0.7827 (m-40) REVERT: E 441 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7884 (tp) REVERT: F 277 TYR cc_start: 0.8607 (m-80) cc_final: 0.8259 (m-80) REVERT: F 280 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7257 (ptm) REVERT: F 344 HIS cc_start: 0.8152 (t-90) cc_final: 0.7657 (m-70) REVERT: F 364 GLU cc_start: 0.8424 (tt0) cc_final: 0.7894 (tm-30) REVERT: F 368 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8375 (mp) outliers start: 61 outliers final: 28 residues processed: 246 average time/residue: 0.7100 time to fit residues: 196.6215 Evaluate side-chains 227 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 560 THR 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 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 114 THR Chi-restraints excluded: chain C residue 341 VAL 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 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 294 SER 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 280 MET 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: 0.0970 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 155 GLN E 438 ASN 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 = 0.3465 r_free = 0.3465 target = 0.097903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.071477 restraints weight = 36927.630| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.06 r_work: 0.2859 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9164 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21411 Z= 0.120 Angle : 0.537 7.344 29298 Z= 0.293 Chirality : 0.041 0.202 3322 Planarity : 0.003 0.050 3392 Dihedral : 18.263 77.492 3465 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.01 % Allowed : 19.31 % Favored : 78.68 % 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: 0.80 (0.17), residues: 2283 helix: 1.19 (0.15), residues: 1299 sheet: 0.15 (0.34), residues: 206 loop : -0.37 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 607 TYR 0.014 0.001 TYR C 483 PHE 0.025 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 0.00263 / 0.12 (21411) covalent geometry : angle 0.53703 / 0.29 (29298) hydrogen bonds : bond 0.03792 / 2.54 ( 1029) hydrogen bonds : angle 3.90153 / 2.78 ( 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 240 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8141 (pmtt) REVERT: A 416 HIS cc_start: 0.8324 (m90) cc_final: 0.7983 (m-70) REVERT: A 420 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7821 (mm-30) REVERT: A 429 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8601 (mm-40) REVERT: A 504 GLU cc_start: 0.8350 (mp0) cc_final: 0.8092 (mp0) REVERT: A 576 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.7566 (pp30) REVERT: B 390 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8564 (ttt90) REVERT: B 496 MET cc_start: 0.8423 (mmm) cc_final: 0.7130 (tmt) REVERT: C 454 HIS cc_start: 0.7978 (t70) cc_final: 0.7574 (t70) REVERT: C 488 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8592 (mt-10) REVERT: C 592 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: D 186 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9289 (mp) REVERT: E 141 LEU cc_start: 0.8389 (tp) cc_final: 0.8117 (mt) REVERT: E 172 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8658 (mm-30) REVERT: E 212 ASP cc_start: 0.8750 (t70) cc_final: 0.8346 (t0) REVERT: E 217 LYS cc_start: 0.7223 (mmpt) cc_final: 0.6753 (mtpm) REVERT: E 245 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8460 (mp10) REVERT: E 277 ASN cc_start: 0.7995 (m-40) cc_final: 0.7636 (m-40) REVERT: E 441 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7961 (tp) REVERT: F 277 TYR cc_start: 0.8570 (m-80) cc_final: 0.8251 (m-80) REVERT: F 364 GLU cc_start: 0.8416 (tt0) cc_final: 0.8102 (tm-30) outliers start: 43 outliers final: 16 residues processed: 229 average time/residue: 0.7212 time to fit residues: 185.1180 Evaluate side-chains 214 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 415 LYS 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 390 ARG 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 461 ILE 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 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 206 CYS Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 441 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 9 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 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: 0.6980 chunk 81 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.096171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.069667 restraints weight = 37176.433| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.06 r_work: 0.2826 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9191 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 : 0.005 0.053 21411 Z= 0.195 Angle : 0.576 7.804 29298 Z= 0.310 Chirality : 0.044 0.212 3322 Planarity : 0.004 0.073 3392 Dihedral : 18.286 77.411 3465 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.33 % Allowed : 19.03 % 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: 0.90 (0.17), residues: 2283 helix: 1.26 (0.15), residues: 1301 sheet: 0.18 (0.34), residues: 206 loop : -0.30 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 271 TYR 0.019 0.001 TYR C 483 PHE 0.026 0.002 PHE C 392 TRP 0.011 0.001 TRP C 494 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (21411) covalent geometry : angle 0.57581 / 0.31 (29298) hydrogen bonds : bond 0.04193 / 2.81 ( 1029) hydrogen bonds : angle 3.92131 / 2.79 ( 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 245 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8118 (pmtt) REVERT: A 416 HIS cc_start: 0.8297 (m90) cc_final: 0.7912 (m-70) REVERT: A 420 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 425 LYS cc_start: 0.9079 (mmmm) cc_final: 0.8829 (mmpt) REVERT: A 432 SER cc_start: 0.8702 (m) cc_final: 0.8499 (t) REVERT: A 504 GLU cc_start: 0.8318 (mp0) cc_final: 0.8094 (mp0) REVERT: A 576 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7598 (pp30) REVERT: B 390 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8616 (ttt90) REVERT: C 454 HIS cc_start: 0.8044 (t70) cc_final: 0.7352 (t70) REVERT: C 592 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8402 (tm-30) REVERT: D 186 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9338 (mp) REVERT: D 242 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7347 (mtm-85) REVERT: E 172 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8698 (mm-30) REVERT: E 217 LYS cc_start: 0.7270 (mmpt) cc_final: 0.6723 (mttm) REVERT: E 245 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8507 (mp10) REVERT: E 277 ASN cc_start: 0.7953 (m-40) cc_final: 0.7608 (m-40) REVERT: E 441 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7969 (tp) REVERT: F 277 TYR cc_start: 0.8605 (m-80) cc_final: 0.8234 (m-80) REVERT: F 312 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7765 (ptt180) REVERT: F 364 GLU cc_start: 0.8437 (tt0) cc_final: 0.7985 (tm-30) REVERT: F 368 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8445 (mt) outliers start: 50 outliers final: 21 residues processed: 232 average time/residue: 0.7474 time to fit residues: 194.5368 Evaluate side-chains 219 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 609 LEU 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 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 130 GLU 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 242 ARG 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 206 CYS 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 F residue 312 ARG 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: 6.9990 chunk 173 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 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: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN D 155 GLN E 438 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 = 0.3408 r_free = 0.3408 target = 0.094614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.067414 restraints weight = 35976.388| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.09 r_work: 0.2737 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.2572 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= 0.172 Angle : 0.569 9.290 29298 Z= 0.307 Chirality : 0.043 0.206 3322 Planarity : 0.003 0.051 3392 Dihedral : 18.304 78.307 3465 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.38 % Allowed : 19.64 % Favored : 77.99 % 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: 0.99 (0.17), residues: 2283 helix: 1.34 (0.15), residues: 1302 sheet: 0.25 (0.34), residues: 204 loop : -0.28 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 297 TYR 0.018 0.001 TYR F 306 PHE 0.038 0.001 PHE C 412 TRP 0.011 0.001 TRP C 494 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (21411) covalent geometry : angle 0.56879 / 0.31 (29298) hydrogen bonds : bond 0.04022 / 2.69 ( 1029) hydrogen bonds : angle 3.89801 / 2.77 ( 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 250 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8116 (pmtt) REVERT: A 416 HIS cc_start: 0.8314 (m90) cc_final: 0.7996 (m-70) REVERT: A 420 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 425 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8809 (mmpt) REVERT: A 576 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7586 (pp30) REVERT: A 653 LYS cc_start: 0.8810 (ptpt) cc_final: 0.8539 (mptt) REVERT: B 390 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8579 (ttt90) REVERT: B 496 MET cc_start: 0.8375 (mmm) cc_final: 0.7145 (tmt) REVERT: C 454 HIS cc_start: 0.8086 (t70) cc_final: 0.7362 (t70) REVERT: C 552 GLU cc_start: 0.8458 (mp0) cc_final: 0.7993 (mp0) REVERT: C 592 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8443 (tm-30) REVERT: D 186 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9289 (mp) REVERT: D 242 ARG cc_start: 0.8086 (pmt170) cc_final: 0.7351 (mtm-85) REVERT: E 172 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8675 (mm-30) REVERT: E 217 LYS cc_start: 0.7223 (mmpt) cc_final: 0.6675 (mttm) REVERT: E 245 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8525 (mp10) REVERT: E 277 ASN cc_start: 0.7898 (m-40) cc_final: 0.7502 (m-40) REVERT: E 441 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7960 (tp) REVERT: F 277 TYR cc_start: 0.8511 (m-80) cc_final: 0.8145 (m-80) REVERT: F 281 THR cc_start: 0.9333 (p) cc_final: 0.9002 (p) REVERT: F 312 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7721 (ptt180) REVERT: F 364 GLU cc_start: 0.8429 (tt0) cc_final: 0.7960 (tm-30) REVERT: F 368 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8391 (mt) outliers start: 51 outliers final: 24 residues processed: 238 average time/residue: 0.7556 time to fit residues: 201.6187 Evaluate side-chains 222 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 615 SER 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 390 ARG 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 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 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 195 ASP 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 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=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: 0.8980 chunk 211 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 210 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 370 GLN C 470 ASN D 155 GLN E 438 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 = 0.3414 r_free = 0.3414 target = 0.094943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.067723 restraints weight = 35913.713| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.09 r_work: 0.2742 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21411 Z= 0.155 Angle : 0.571 8.767 29298 Z= 0.308 Chirality : 0.043 0.199 3322 Planarity : 0.003 0.082 3392 Dihedral : 18.274 78.662 3465 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.38 % Allowed : 20.06 % Favored : 77.57 % 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: 1.07 (0.17), residues: 2283 helix: 1.42 (0.15), residues: 1301 sheet: 0.23 (0.34), residues: 204 loop : -0.27 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 271 TYR 0.018 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 0.00358 / 0.16 (21411) covalent geometry : angle 0.57138 / 0.31 (29298) hydrogen bonds : bond 0.03913 / 2.62 ( 1029) hydrogen bonds : angle 3.87195 / 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 244 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8009 (pmtt) REVERT: A 416 HIS cc_start: 0.8340 (m90) cc_final: 0.7742 (m-70) REVERT: A 420 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7547 (mm-30) REVERT: A 425 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8794 (mmpt) REVERT: A 504 GLU cc_start: 0.8211 (mp0) cc_final: 0.7949 (mp0) REVERT: A 576 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7562 (pp30) REVERT: A 647 PHE cc_start: 0.8419 (m-80) cc_final: 0.8217 (m-80) REVERT: A 653 LYS cc_start: 0.8786 (ptpt) cc_final: 0.8526 (mptt) REVERT: B 390 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8564 (ttt90) REVERT: B 496 MET cc_start: 0.8486 (mmm) cc_final: 0.7120 (tmt) REVERT: C 454 HIS cc_start: 0.8100 (t70) cc_final: 0.7390 (t70) REVERT: C 592 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8473 (tm-30) REVERT: D 186 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9321 (mp) REVERT: E 217 LYS cc_start: 0.7127 (mmpt) cc_final: 0.6619 (mttm) REVERT: E 245 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8539 (mp10) REVERT: E 277 ASN cc_start: 0.7798 (m-40) cc_final: 0.7352 (m-40) REVERT: E 441 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7854 (tp) REVERT: F 277 TYR cc_start: 0.8497 (m-80) cc_final: 0.8119 (m-80) REVERT: F 312 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7694 (ptt180) REVERT: F 364 GLU cc_start: 0.8404 (tt0) cc_final: 0.7965 (tm-30) REVERT: F 368 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8387 (mt) outliers start: 51 outliers final: 26 residues processed: 234 average time/residue: 0.7276 time to fit residues: 191.4453 Evaluate side-chains 223 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 609 LEU 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 259 SER Chi-restraints excluded: chain B residue 390 ARG 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 88 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 470 ASN 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 453 LYS Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain E residue 96 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 56 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 227 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 155 GLN E 2 ASN E 438 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 = 0.3426 r_free = 0.3426 target = 0.095666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.068578 restraints weight = 35842.017| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.09 r_work: 0.2762 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21411 Z= 0.125 Angle : 0.558 8.936 29298 Z= 0.301 Chirality : 0.042 0.186 3322 Planarity : 0.003 0.050 3392 Dihedral : 18.232 79.089 3465 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.77 % Allowed : 20.71 % Favored : 77.52 % 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: 1.14 (0.18), residues: 2283 helix: 1.51 (0.15), residues: 1301 sheet: 0.14 (0.34), residues: 206 loop : -0.26 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 442 TYR 0.017 0.001 TYR F 306 PHE 0.036 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 0.00278 / 0.12 (21411) covalent geometry : angle 0.55845 / 0.30 (29298) hydrogen bonds : bond 0.03680 / 2.47 ( 1029) hydrogen bonds : angle 3.82408 / 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: 38 poor density : 187 time to evaluate : 0.851 Fit side-chains REVERT: A 415 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7980 (pmtt) REVERT: A 416 HIS cc_start: 0.8309 (m90) cc_final: 0.7721 (m-70) REVERT: A 420 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 425 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8788 (mmpt) REVERT: A 504 GLU cc_start: 0.8175 (mp0) cc_final: 0.7854 (mp0) REVERT: A 576 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7540 (pp30) REVERT: A 647 PHE cc_start: 0.8408 (m-80) cc_final: 0.8171 (m-80) REVERT: A 653 LYS cc_start: 0.8776 (ptpt) cc_final: 0.8516 (mptt) REVERT: B 496 MET cc_start: 0.8359 (mmm) cc_final: 0.7116 (tmt) REVERT: C 454 HIS cc_start: 0.8100 (t70) cc_final: 0.7401 (t70) REVERT: C 592 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8439 (tm-30) REVERT: D 186 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9304 (mp) REVERT: D 242 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7198 (mtm-85) REVERT: E 217 LYS cc_start: 0.7190 (mmpt) cc_final: 0.6667 (mttm) REVERT: E 245 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8521 (mp10) REVERT: E 277 ASN cc_start: 0.7700 (m-40) cc_final: 0.7274 (m-40) REVERT: E 437 MET cc_start: 0.8072 (pmm) cc_final: 0.7677 (pmm) REVERT: E 441 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7876 (tp) REVERT: F 277 TYR cc_start: 0.8478 (m-80) cc_final: 0.8047 (m-80) REVERT: F 312 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7697 (ptt180) REVERT: F 364 GLU cc_start: 0.8446 (tt0) cc_final: 0.8143 (tm-30) outliers start: 38 outliers final: 22 residues processed: 220 average time/residue: 0.7344 time to fit residues: 181.2835 Evaluate side-chains 215 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain B residue 259 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 88 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 130 GLU 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 359 LYS Chi-restraints excluded: chain D residue 453 LYS Chi-restraints excluded: chain D residue 454 LYS Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain E residue 96 ASP 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 236 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 493 GLN D 155 GLN D 491 GLN E 2 ASN E 438 ASN F 307 ASN F 318 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.067295 restraints weight = 36160.223| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.09 r_work: 0.2735 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9177 moved from start: 0.2705 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= 0.178 Angle : 0.590 11.933 29298 Z= 0.315 Chirality : 0.043 0.194 3322 Planarity : 0.003 0.051 3392 Dihedral : 18.257 78.761 3464 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.96 % Allowed : 20.57 % Favored : 77.47 % 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: 1.15 (0.18), residues: 2283 helix: 1.49 (0.15), residues: 1301 sheet: 0.25 (0.34), residues: 204 loop : -0.25 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 297 TYR 0.018 0.001 TYR F 306 PHE 0.027 0.001 PHE C 392 TRP 0.011 0.001 TRP C 494 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (21411) covalent geometry : angle 0.58958 / 0.31 (29298) hydrogen bonds : bond 0.04005 / 2.69 ( 1029) hydrogen bonds : angle 3.86673 / 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 231 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8002 (pmtt) REVERT: A 416 HIS cc_start: 0.8306 (m90) cc_final: 0.7718 (m-70) REVERT: A 420 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7571 (mm-30) REVERT: A 425 LYS cc_start: 0.9078 (mmmm) cc_final: 0.8804 (mmpt) REVERT: A 504 GLU cc_start: 0.8142 (mp0) cc_final: 0.7887 (mp0) REVERT: A 576 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7610 (pp30) REVERT: A 653 LYS cc_start: 0.8782 (ptpt) cc_final: 0.8529 (mptt) REVERT: B 496 MET cc_start: 0.8351 (mmm) cc_final: 0.7136 (tmt) REVERT: C 417 LEU cc_start: 0.9336 (mt) cc_final: 0.9122 (mp) REVERT: C 454 HIS cc_start: 0.8060 (t70) cc_final: 0.7345 (t70) REVERT: C 592 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8468 (tm-30) REVERT: D 186 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9323 (mp) REVERT: D 242 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7232 (mtm-85) REVERT: E 141 LEU cc_start: 0.8435 (tp) cc_final: 0.8182 (mt) REVERT: E 217 LYS cc_start: 0.7183 (mmpt) cc_final: 0.6649 (mttm) REVERT: E 245 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8536 (mp10) REVERT: E 277 ASN cc_start: 0.7672 (m-40) cc_final: 0.7248 (m-40) REVERT: E 437 MET cc_start: 0.8045 (pmm) cc_final: 0.7656 (pmm) REVERT: E 441 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7912 (tp) REVERT: F 277 TYR cc_start: 0.8503 (m-80) cc_final: 0.8016 (m-80) REVERT: F 312 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7735 (ptt180) REVERT: F 364 GLU cc_start: 0.8415 (tt0) cc_final: 0.7973 (tm-30) REVERT: F 368 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8392 (mt) outliers start: 42 outliers final: 20 residues processed: 224 average time/residue: 0.7324 time to fit residues: 184.5017 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 : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain B residue 259 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 88 SER Chi-restraints excluded: chain C residue 114 THR 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 242 ARG 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 D residue 470 THR 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 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=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: 0.9980 chunk 92 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 135 optimal weight: 0.0770 chunk 117 optimal weight: 5.9990 chunk 177 optimal weight: 0.3980 overall best weight: 1.4340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 493 GLN 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 = 0.3422 r_free = 0.3422 target = 0.095364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.068282 restraints weight = 36032.335| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.09 r_work: 0.2755 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.2722 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= 0.138 Angle : 0.574 9.406 29298 Z= 0.306 Chirality : 0.042 0.177 3322 Planarity : 0.003 0.090 3392 Dihedral : 18.237 79.405 3464 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.59 % Allowed : 21.08 % Favored : 77.33 % 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: 1.20 (0.18), residues: 2283 helix: 1.56 (0.15), residues: 1308 sheet: 0.14 (0.34), residues: 206 loop : -0.25 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 271 TYR 0.017 0.001 TYR B 372 PHE 0.039 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 0.00314 / 0.14 (21411) covalent geometry : angle 0.57363 / 0.31 (29298) hydrogen bonds : bond 0.03711 / 2.49 ( 1029) hydrogen bonds : angle 3.82542 / 2.71 ( 2860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8326.75 seconds wall clock time: 142 minutes 49.15 seconds (8569.15 seconds total)