Starting phenix.real_space_refine on Sat Aug 23 12:50:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gi0_40056/08_2025/8gi0_40056.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gi0_40056/08_2025/8gi0_40056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gi0_40056/08_2025/8gi0_40056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gi0_40056/08_2025/8gi0_40056.map" model { file = "/net/cci-nas-00/data/ceres_data/8gi0_40056/08_2025/8gi0_40056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gi0_40056/08_2025/8gi0_40056.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 7734 2.51 5 N 2124 2.21 5 O 2266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12189 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2333 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 293} Chain breaks: 1 Chain: "B" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2333 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 293} Chain breaks: 1 Chain: "C" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2333 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 293} Chain breaks: 1 Chain: "D" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2333 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 293} Chain breaks: 1 Chain: "E" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2402 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 15, 'TRANS': 287} Chain breaks: 1 Time building chain proxies: 2.38, per 1000 atoms: 0.20 Number of scatterers: 12189 At special positions: 0 Unit cell: (104.06, 124.7, 133.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2266 8.00 N 2124 7.00 C 7734 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: 0.96 Conformation dependent library (CDL) restraints added in 431.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2990 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 12 sheets defined 57.4% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'F' and resid 25 through 38 removed outlier: 3.521A pdb=" N ARG F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 4.416A pdb=" N ILE F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 56 removed outlier: 3.610A pdb=" N LYS F 50 " --> pdb=" O PRO F 46 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 71 Processing helix chain 'F' and resid 76 through 82 Processing helix chain 'A' and resid 11 through 23 removed outlier: 4.173A pdb=" N SER A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 99 through 116 removed outlier: 4.290A pdb=" N GLY A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 Proline residue: A 135 - end of helix removed outlier: 3.659A pdb=" N ILE A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 removed outlier: 4.213A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 194 through 197 removed outlier: 3.633A pdb=" N ILE A 197 " --> pdb=" O TYR A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.895A pdb=" N GLN A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.679A pdb=" N GLU A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.562A pdb=" N HIS A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 317 removed outlier: 3.828A pdb=" N GLY A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 25 removed outlier: 4.234A pdb=" N SER B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.502A pdb=" N VAL B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 98 through 116 removed outlier: 3.764A pdb=" N GLY B 105 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 145 Proline residue: B 135 - end of helix removed outlier: 3.512A pdb=" N ILE B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 171 removed outlier: 4.200A pdb=" N GLY B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 194 through 197 removed outlier: 3.556A pdb=" N ILE B 197 " --> pdb=" O TYR B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 203 through 225 removed outlier: 3.579A pdb=" N GLU B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY B 218 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU B 220 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 252 Processing helix chain 'B' and resid 294 through 323 removed outlier: 3.878A pdb=" N GLY B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 25 removed outlier: 4.234A pdb=" N SER C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 47 removed outlier: 3.582A pdb=" N ASP C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.790A pdb=" N GLY C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 156 through 171 removed outlier: 4.498A pdb=" N GLY C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 203 through 225 removed outlier: 3.660A pdb=" N GLU C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLY C 218 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL C 222 " --> pdb=" O GLY C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 252 Processing helix chain 'C' and resid 294 through 321 removed outlier: 3.622A pdb=" N GLU C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 25 removed outlier: 4.215A pdb=" N SER D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.703A pdb=" N ILE D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 145 Proline residue: D 135 - end of helix removed outlier: 3.520A pdb=" N ILE D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 172 removed outlier: 4.255A pdb=" N GLY D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 170 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 194 through 197 removed outlier: 3.606A pdb=" N ILE D 197 " --> pdb=" O TYR D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 194 through 197' Processing helix chain 'D' and resid 203 through 225 removed outlier: 3.959A pdb=" N GLU D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLY D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D 222 " --> pdb=" O GLY D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 252 Processing helix chain 'D' and resid 294 through 320 removed outlier: 3.840A pdb=" N GLU D 303 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA D 319 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 344 removed outlier: 3.533A pdb=" N GLU E 334 " --> pdb=" O ARG E 330 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN E 340 " --> pdb=" O GLN E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 359 removed outlier: 4.302A pdb=" N TYR E 358 " --> pdb=" O PRO E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 373 removed outlier: 3.685A pdb=" N GLU E 365 " --> pdb=" O LYS E 361 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA E 368 " --> pdb=" O GLU E 364 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN E 371 " --> pdb=" O ILE E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 377 removed outlier: 3.597A pdb=" N GLU E 377 " --> pdb=" O ASN E 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 374 through 377' Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.733A pdb=" N CYS E 386 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN E 387 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS E 388 " --> pdb=" O ALA E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 406 removed outlier: 3.778A pdb=" N TRP E 396 " --> pdb=" O ASN E 392 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA E 404 " --> pdb=" O GLY E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 423 removed outlier: 4.410A pdb=" N ILE E 414 " --> pdb=" O CYS E 410 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ALA E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS E 418 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 439 removed outlier: 3.750A pdb=" N HIS E 430 " --> pdb=" O ASP E 426 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA E 431 " --> pdb=" O ILE E 427 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN E 439 " --> pdb=" O VAL E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 456 removed outlier: 3.711A pdb=" N LEU E 454 " --> pdb=" O LEU E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 501 removed outlier: 4.400A pdb=" N LEU E 499 " --> pdb=" O ASP E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 524 removed outlier: 3.979A pdb=" N HIS E 514 " --> pdb=" O ASP E 510 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 541 removed outlier: 3.801A pdb=" N ALA E 531 " --> pdb=" O PHE E 527 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LYS E 532 " --> pdb=" O ASP E 528 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN E 533 " --> pdb=" O GLU E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 558 removed outlier: 4.102A pdb=" N TRP E 548 " --> pdb=" O ASP E 544 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS E 550 " --> pdb=" O HIS E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 575 removed outlier: 3.908A pdb=" N LEU E 565 " --> pdb=" O PRO E 561 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU E 566 " --> pdb=" O GLN E 562 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA E 567 " --> pdb=" O GLU E 563 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP E 573 " --> pdb=" O ASN E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 592 removed outlier: 3.709A pdb=" N MET E 582 " --> pdb=" O TYR E 578 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN E 591 " --> pdb=" O VAL E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 609 removed outlier: 4.202A pdb=" N LYS E 600 " --> pdb=" O PRO E 596 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG E 604 " --> pdb=" O LYS E 600 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU E 608 " --> pdb=" O ARG E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 625 removed outlier: 4.108A pdb=" N THR E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.674A pdb=" N LEU E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 648 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 60 removed outlier: 6.737A pdb=" N SER A 29 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LYS A 57 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A 31 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA A 59 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 33 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 4 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N TYR A 34 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 6 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN A 3 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL A 83 " --> pdb=" O ASN A 3 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA A 5 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE A 123 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 263 removed outlier: 5.197A pdb=" N ARG A 287 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL A 278 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 283 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 54 through 60 removed outlier: 6.833A pdb=" N SER B 29 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N LYS B 57 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU B 31 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ALA B 59 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 33 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASN B 3 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL B 83 " --> pdb=" O ASN B 3 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA B 5 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'B' and resid 257 through 263 removed outlier: 5.245A pdb=" N ARG B 287 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 278 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 55 through 60 removed outlier: 6.444A pdb=" N LEU C 31 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA C 59 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU C 33 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 4 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N TYR C 34 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 6 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'C' and resid 257 through 263 removed outlier: 5.067A pdb=" N ARG C 287 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C 278 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 55 through 60 removed outlier: 3.715A pdb=" N ASP D 35 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB3, first strand: chain 'D' and resid 257 through 263 removed outlier: 5.223A pdb=" N ARG D 287 " --> pdb=" O PRO D 276 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL D 278 " --> pdb=" O GLU D 285 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2882 1.33 - 1.45: 2141 1.45 - 1.57: 7275 1.57 - 1.69: 0 1.69 - 1.81: 109 Bond restraints: 12407 Sorted by residual: bond pdb=" CA GLU F 66 " pdb=" C GLU F 66 " ideal model delta sigma weight residual 1.522 1.488 0.034 1.39e-02 5.18e+03 5.92e+00 bond pdb=" CA LYS F 26 " pdb=" C LYS F 26 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.39e-02 5.18e+03 5.77e+00 bond pdb=" CA SER E 647 " pdb=" C SER E 647 " ideal model delta sigma weight residual 1.522 1.491 0.031 1.36e-02 5.41e+03 5.22e+00 bond pdb=" CA CYS F 65 " pdb=" C CYS F 65 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.27e-02 6.20e+03 4.76e+00 bond pdb=" CA ALA E 646 " pdb=" C ALA E 646 " ideal model delta sigma weight residual 1.523 1.493 0.030 1.37e-02 5.33e+03 4.76e+00 ... (remaining 12402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 16486 1.97 - 3.94: 361 3.94 - 5.92: 33 5.92 - 7.89: 3 7.89 - 9.86: 1 Bond angle restraints: 16884 Sorted by residual: angle pdb=" C TRP E 648 " pdb=" N GLN E 649 " pdb=" CA GLN E 649 " ideal model delta sigma weight residual 121.54 111.68 9.86 1.91e+00 2.74e-01 2.66e+01 angle pdb=" N SER E 647 " pdb=" CA SER E 647 " pdb=" C SER E 647 " ideal model delta sigma weight residual 111.71 106.88 4.83 1.15e+00 7.56e-01 1.76e+01 angle pdb=" N SER A 321 " pdb=" CA SER A 321 " pdb=" C SER A 321 " ideal model delta sigma weight residual 108.96 115.51 -6.55 1.59e+00 3.96e-01 1.70e+01 angle pdb=" N LYS A 322 " pdb=" CA LYS A 322 " pdb=" C LYS A 322 " ideal model delta sigma weight residual 109.15 114.78 -5.63 1.44e+00 4.82e-01 1.53e+01 angle pdb=" C LYS F 26 " pdb=" N ARG F 27 " pdb=" CA ARG F 27 " ideal model delta sigma weight residual 120.28 114.89 5.39 1.44e+00 4.82e-01 1.40e+01 ... (remaining 16879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 6813 16.88 - 33.76: 529 33.76 - 50.64: 177 50.64 - 67.52: 41 67.52 - 84.39: 14 Dihedral angle restraints: 7574 sinusoidal: 2934 harmonic: 4640 Sorted by residual: dihedral pdb=" CA ASN E 636 " pdb=" C ASN E 636 " pdb=" N LEU E 637 " pdb=" CA LEU E 637 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP E 651 " pdb=" C ASP E 651 " pdb=" N LEU E 652 " pdb=" CA LEU E 652 " ideal model delta harmonic sigma weight residual 180.00 154.14 25.86 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA THR B 127 " pdb=" C THR B 127 " pdb=" N ASN B 128 " pdb=" CA ASN B 128 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 7571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1218 0.036 - 0.071: 549 0.071 - 0.107: 167 0.107 - 0.142: 82 0.142 - 0.178: 5 Chirality restraints: 2021 Sorted by residual: chirality pdb=" CG LEU E 523 " pdb=" CB LEU E 523 " pdb=" CD1 LEU E 523 " pdb=" CD2 LEU E 523 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA ASP E 651 " pdb=" N ASP E 651 " pdb=" C ASP E 651 " pdb=" CB ASP E 651 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA GLU F 63 " pdb=" N GLU F 63 " pdb=" C GLU F 63 " pdb=" CB GLU F 63 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 2018 not shown) Planarity restraints: 2190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 510 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" CG ASP E 510 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP E 510 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP E 510 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 176 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO D 177 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 177 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 177 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 134 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO B 135 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 135 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 135 " -0.024 5.00e-02 4.00e+02 ... (remaining 2187 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 431 2.72 - 3.26: 12075 3.26 - 3.81: 17816 3.81 - 4.35: 22853 4.35 - 4.90: 39237 Nonbonded interactions: 92412 Sorted by model distance: nonbonded pdb=" O ARG D 320 " pdb=" OG SER D 321 " model vdw 2.170 3.040 nonbonded pdb=" O ASP E 510 " pdb=" OD1 ASP E 510 " model vdw 2.221 3.040 nonbonded pdb=" O GLN E 649 " pdb=" NE2 GLN E 650 " model vdw 2.273 3.120 nonbonded pdb=" OD1 ASP E 426 " pdb=" N ALA E 428 " model vdw 2.274 3.120 nonbonded pdb=" O ARG A 165 " pdb=" OD1 ASN A 169 " model vdw 2.304 3.040 ... (remaining 92407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.370 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12407 Z= 0.211 Angle : 0.701 9.859 16884 Z= 0.393 Chirality : 0.047 0.178 2021 Planarity : 0.006 0.044 2190 Dihedral : 14.688 84.395 4584 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.14 % Allowed : 11.99 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 aren not related in a simple way. whole: -0.53 (0.20), residues: 1603 helix: 0.39 (0.18), residues: 788 sheet: -0.32 (0.36), residues: 181 loop : -1.22 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 621 TYR 0.014 0.002 TYR E 568 PHE 0.020 0.002 PHE A 27 TRP 0.017 0.002 TRP E 328 HIS 0.006 0.002 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00437 (12407) covalent geometry : angle 0.70134 (16884) hydrogen bonds : bond 0.19924 ( 611) hydrogen bonds : angle 6.00056 ( 1815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.429 Fit side-chains REVERT: A 317 THR cc_start: 0.8109 (t) cc_final: 0.7869 (p) REVERT: C 143 LYS cc_start: 0.6822 (ttpp) cc_final: 0.6451 (tttt) REVERT: C 212 LYS cc_start: 0.7951 (tttp) cc_final: 0.7513 (tptp) REVERT: E 633 MET cc_start: 0.8231 (ttp) cc_final: 0.7790 (ttp) REVERT: E 645 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7256 (mm-30) outliers start: 15 outliers final: 8 residues processed: 163 average time/residue: 0.0970 time to fit residues: 22.9158 Evaluate side-chains 143 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 LYS Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 645 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN D 139 GLN E 546 HIS E 549 ASN E 584 ASN E 601 HIS E 614 ASN E 650 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.134473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.107923 restraints weight = 139729.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.109397 restraints weight = 100953.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.109272 restraints weight = 85731.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.109312 restraints weight = 86300.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.109444 restraints weight = 82366.166| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12407 Z= 0.126 Angle : 0.570 6.586 16884 Z= 0.300 Chirality : 0.045 0.191 2021 Planarity : 0.005 0.047 2190 Dihedral : 6.086 65.404 1750 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.19 % Allowed : 12.22 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 aren not related in a simple way. whole: 0.16 (0.21), residues: 1603 helix: 1.02 (0.18), residues: 821 sheet: 0.10 (0.35), residues: 192 loop : -1.14 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 398 TYR 0.007 0.001 TYR E 460 PHE 0.012 0.001 PHE D 27 TRP 0.007 0.001 TRP E 328 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00266 (12407) covalent geometry : angle 0.57007 (16884) hydrogen bonds : bond 0.04858 ( 611) hydrogen bonds : angle 4.05832 ( 1815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.465 Fit side-chains REVERT: A 157 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8077 (tt) REVERT: C 1 MET cc_start: 0.6041 (ttp) cc_final: 0.5823 (ttp) REVERT: C 143 LYS cc_start: 0.7329 (ttpp) cc_final: 0.6982 (tttt) REVERT: C 212 LYS cc_start: 0.8131 (tttp) cc_final: 0.7891 (tptp) REVERT: D 77 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6463 (mt-10) REVERT: D 285 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6236 (tp30) REVERT: E 555 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7910 (mt) REVERT: E 633 MET cc_start: 0.7991 (ttp) cc_final: 0.7577 (ttt) REVERT: E 645 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7331 (mp0) outliers start: 42 outliers final: 21 residues processed: 167 average time/residue: 0.0914 time to fit residues: 22.7090 Evaluate side-chains 154 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 0.0170 chunk 35 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 79 optimal weight: 0.0170 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 584 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.135115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.108789 restraints weight = 138512.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.109855 restraints weight = 99040.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.110102 restraints weight = 87581.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.110359 restraints weight = 87620.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.110661 restraints weight = 81283.612| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12407 Z= 0.112 Angle : 0.530 7.384 16884 Z= 0.275 Chirality : 0.044 0.182 2021 Planarity : 0.005 0.045 2190 Dihedral : 5.210 65.324 1738 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.41 % Allowed : 12.29 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 aren not related in a simple way. whole: 0.54 (0.21), residues: 1603 helix: 1.45 (0.18), residues: 825 sheet: 0.25 (0.39), residues: 156 loop : -1.10 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.008 0.001 TYR E 358 PHE 0.012 0.001 PHE A 27 TRP 0.006 0.001 TRP E 328 HIS 0.002 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00237 (12407) covalent geometry : angle 0.52971 (16884) hydrogen bonds : bond 0.04422 ( 611) hydrogen bonds : angle 3.74683 ( 1815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 157 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8106 (tt) REVERT: B 74 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6880 (tp30) REVERT: B 157 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7652 (tt) REVERT: B 232 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7891 (p) REVERT: C 143 LYS cc_start: 0.7302 (ttpp) cc_final: 0.7023 (tttt) REVERT: C 212 LYS cc_start: 0.8086 (tttp) cc_final: 0.7836 (tptp) REVERT: C 223 LYS cc_start: 0.7479 (mttt) cc_final: 0.7069 (ttmm) REVERT: D 77 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6358 (mt-10) REVERT: D 285 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.6273 (tp30) REVERT: E 555 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7966 (mt) REVERT: E 633 MET cc_start: 0.8103 (ttp) cc_final: 0.7786 (ttt) REVERT: E 645 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7086 (mm-30) outliers start: 45 outliers final: 22 residues processed: 175 average time/residue: 0.0941 time to fit residues: 24.0930 Evaluate side-chains 154 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 25 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.132124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.105576 restraints weight = 140387.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.106829 restraints weight = 101237.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.106950 restraints weight = 87023.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.107222 restraints weight = 86755.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.107367 restraints weight = 82121.166| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12407 Z= 0.140 Angle : 0.573 9.362 16884 Z= 0.298 Chirality : 0.046 0.176 2021 Planarity : 0.005 0.051 2190 Dihedral : 5.291 65.083 1738 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.41 % Allowed : 12.75 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 aren not related in a simple way. whole: 0.59 (0.21), residues: 1603 helix: 1.54 (0.18), residues: 824 sheet: -0.10 (0.35), residues: 192 loop : -1.08 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 51 TYR 0.007 0.001 TYR E 358 PHE 0.015 0.002 PHE A 27 TRP 0.008 0.001 TRP E 328 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00317 (12407) covalent geometry : angle 0.57323 (16884) hydrogen bonds : bond 0.05377 ( 611) hydrogen bonds : angle 3.82446 ( 1815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 0.373 Fit side-chains REVERT: A 157 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8236 (tt) REVERT: A 265 ASP cc_start: 0.7961 (t0) cc_final: 0.7723 (t0) REVERT: B 74 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7027 (tp30) REVERT: C 212 LYS cc_start: 0.8200 (tttp) cc_final: 0.7891 (tptp) REVERT: D 74 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6564 (tp30) REVERT: D 77 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6386 (mt-10) REVERT: D 285 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6244 (tp30) REVERT: E 457 GLN cc_start: 0.8237 (mt0) cc_final: 0.7942 (mt0) REVERT: E 555 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8049 (mt) REVERT: E 633 MET cc_start: 0.7891 (ttp) cc_final: 0.7610 (ttt) REVERT: E 645 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7078 (mm-30) outliers start: 45 outliers final: 26 residues processed: 159 average time/residue: 0.0866 time to fit residues: 20.3515 Evaluate side-chains 158 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 122 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 3 optimal weight: 0.0030 chunk 23 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 430 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.132741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.105977 restraints weight = 139887.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.107050 restraints weight = 98494.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.106969 restraints weight = 85813.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.107515 restraints weight = 89098.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.107831 restraints weight = 82244.514| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12407 Z= 0.132 Angle : 0.550 8.249 16884 Z= 0.286 Chirality : 0.045 0.174 2021 Planarity : 0.005 0.051 2190 Dihedral : 5.193 65.105 1738 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.57 % Allowed : 13.35 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 aren not related in a simple way. whole: 0.64 (0.21), residues: 1603 helix: 1.60 (0.18), residues: 829 sheet: -0.17 (0.35), residues: 192 loop : -1.08 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 51 TYR 0.006 0.001 TYR E 358 PHE 0.014 0.002 PHE A 27 TRP 0.006 0.001 TRP E 328 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00296 (12407) covalent geometry : angle 0.55044 (16884) hydrogen bonds : bond 0.04987 ( 611) hydrogen bonds : angle 3.74294 ( 1815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 157 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8299 (tt) REVERT: A 265 ASP cc_start: 0.7951 (t0) cc_final: 0.7720 (t0) REVERT: B 74 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7063 (tp30) REVERT: C 212 LYS cc_start: 0.8181 (tttp) cc_final: 0.7920 (tptp) REVERT: D 74 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6613 (tp30) REVERT: D 77 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6357 (mt-10) REVERT: D 223 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7139 (ttmt) REVERT: D 285 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6313 (tp30) REVERT: E 457 GLN cc_start: 0.8319 (mt0) cc_final: 0.8027 (mt0) REVERT: E 523 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8134 (tt) REVERT: E 555 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8056 (mt) REVERT: E 633 MET cc_start: 0.7863 (ttp) cc_final: 0.7597 (ttt) REVERT: E 645 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7014 (mm-30) outliers start: 47 outliers final: 32 residues processed: 158 average time/residue: 0.0884 time to fit residues: 20.8619 Evaluate side-chains 160 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 126 optimal weight: 0.7980 chunk 85 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 chunk 16 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.135656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.109056 restraints weight = 137976.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.110748 restraints weight = 98653.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.110339 restraints weight = 84044.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.110410 restraints weight = 84922.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.110428 restraints weight = 82334.529| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12407 Z= 0.103 Angle : 0.501 7.072 16884 Z= 0.260 Chirality : 0.043 0.169 2021 Planarity : 0.005 0.048 2190 Dihedral : 4.935 65.387 1738 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.88 % Allowed : 13.81 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 aren not related in a simple way. whole: 0.82 (0.22), residues: 1603 helix: 1.80 (0.18), residues: 836 sheet: 0.14 (0.40), residues: 156 loop : -1.15 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.006 0.001 TYR E 358 PHE 0.010 0.001 PHE A 27 TRP 0.006 0.001 TRP E 328 HIS 0.002 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00217 (12407) covalent geometry : angle 0.50126 (16884) hydrogen bonds : bond 0.03807 ( 611) hydrogen bonds : angle 3.55360 ( 1815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 157 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8065 (tt) REVERT: A 265 ASP cc_start: 0.7935 (t0) cc_final: 0.7712 (t0) REVERT: B 74 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7028 (tp30) REVERT: B 157 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7696 (tt) REVERT: B 176 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7480 (m) REVERT: C 212 LYS cc_start: 0.8045 (tttp) cc_final: 0.7817 (tptp) REVERT: D 74 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6647 (tp30) REVERT: D 77 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6357 (mt-10) REVERT: D 223 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7157 (ttmt) REVERT: D 285 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.6251 (tp30) REVERT: E 457 GLN cc_start: 0.8233 (mt0) cc_final: 0.7957 (mt0) REVERT: E 555 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7891 (mt) REVERT: E 633 MET cc_start: 0.7914 (ttp) cc_final: 0.7693 (ttt) REVERT: E 645 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6959 (mm-30) outliers start: 38 outliers final: 19 residues processed: 157 average time/residue: 0.0940 time to fit residues: 21.4429 Evaluate side-chains 152 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 114 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 636 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.129413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.103134 restraints weight = 142043.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.104149 restraints weight = 100713.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.104592 restraints weight = 87357.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.104754 restraints weight = 86152.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.104690 restraints weight = 82403.877| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12407 Z= 0.185 Angle : 0.627 9.313 16884 Z= 0.325 Chirality : 0.048 0.177 2021 Planarity : 0.006 0.069 2190 Dihedral : 5.344 64.983 1738 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.41 % Allowed : 13.51 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 aren not related in a simple way. whole: 0.43 (0.21), residues: 1603 helix: 1.49 (0.18), residues: 829 sheet: -0.38 (0.34), residues: 194 loop : -1.24 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 51 TYR 0.008 0.002 TYR A 259 PHE 0.019 0.002 PHE A 27 TRP 0.006 0.001 TRP E 628 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00442 (12407) covalent geometry : angle 0.62672 (16884) hydrogen bonds : bond 0.06504 ( 611) hydrogen bonds : angle 3.94130 ( 1815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 0.534 Fit side-chains REVERT: F 50 LYS cc_start: 0.7194 (mttt) cc_final: 0.6535 (ttmt) REVERT: A 157 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8218 (tt) REVERT: A 265 ASP cc_start: 0.7833 (t0) cc_final: 0.7587 (t0) REVERT: B 74 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7047 (tp30) REVERT: C 143 LYS cc_start: 0.7578 (ttpp) cc_final: 0.7142 (tttt) REVERT: D 77 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6431 (mt-10) REVERT: D 223 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7142 (ttmt) REVERT: D 285 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6330 (tp30) REVERT: E 523 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8245 (tt) REVERT: E 541 ARG cc_start: 0.7072 (ptm160) cc_final: 0.6763 (ptt180) REVERT: E 555 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8223 (mt) REVERT: E 633 MET cc_start: 0.7912 (ttp) cc_final: 0.7645 (ttt) REVERT: E 645 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7097 (mm-30) outliers start: 45 outliers final: 32 residues processed: 153 average time/residue: 0.1121 time to fit residues: 25.3286 Evaluate side-chains 158 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 579 VAL Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 140 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 52 optimal weight: 0.2980 chunk 154 optimal weight: 1.9990 chunk 150 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 636 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.132092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.105926 restraints weight = 141554.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.107446 restraints weight = 99393.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.107121 restraints weight = 84556.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.107244 restraints weight = 86029.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.107343 restraints weight = 82115.664| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12407 Z= 0.132 Angle : 0.552 8.046 16884 Z= 0.286 Chirality : 0.045 0.173 2021 Planarity : 0.005 0.051 2190 Dihedral : 5.188 65.496 1738 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.41 % Allowed : 13.88 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 aren not related in a simple way. whole: 0.57 (0.21), residues: 1603 helix: 1.63 (0.18), residues: 829 sheet: -0.33 (0.34), residues: 194 loop : -1.20 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 51 TYR 0.005 0.001 TYR E 358 PHE 0.014 0.001 PHE A 27 TRP 0.006 0.001 TRP E 328 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00297 (12407) covalent geometry : angle 0.55202 (16884) hydrogen bonds : bond 0.05033 ( 611) hydrogen bonds : angle 3.76773 ( 1815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8139 (tt) REVERT: A 265 ASP cc_start: 0.7909 (t0) cc_final: 0.7654 (t0) REVERT: B 74 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7044 (tp30) REVERT: B 176 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7485 (m) REVERT: C 143 LYS cc_start: 0.7457 (ttpp) cc_final: 0.7088 (tttt) REVERT: C 212 LYS cc_start: 0.8273 (tttp) cc_final: 0.7921 (tptp) REVERT: D 74 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6533 (tp30) REVERT: D 77 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6391 (mt-10) REVERT: D 176 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.7985 (m) REVERT: D 223 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7151 (ttmt) REVERT: D 285 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6323 (tp30) REVERT: E 457 GLN cc_start: 0.8356 (mt0) cc_final: 0.8069 (mt0) REVERT: E 523 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8107 (tt) REVERT: E 555 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8171 (mt) REVERT: E 633 MET cc_start: 0.7894 (ttp) cc_final: 0.7652 (ttt) REVERT: E 645 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.6956 (mm-30) outliers start: 45 outliers final: 31 residues processed: 152 average time/residue: 0.1130 time to fit residues: 25.3206 Evaluate side-chains 163 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 81 optimal weight: 0.0040 chunk 147 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 156 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.134289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.107976 restraints weight = 140159.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.109364 restraints weight = 101104.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.109244 restraints weight = 86440.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.109472 restraints weight = 86580.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.109367 restraints weight = 84295.450| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 12407 Z= 0.112 Angle : 0.525 8.218 16884 Z= 0.272 Chirality : 0.044 0.171 2021 Planarity : 0.005 0.049 2190 Dihedral : 5.021 67.839 1738 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.34 % Allowed : 14.04 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 aren not related in a simple way. whole: 0.65 (0.21), residues: 1603 helix: 1.71 (0.18), residues: 840 sheet: -0.08 (0.39), residues: 158 loop : -1.28 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.005 0.001 TYR E 358 PHE 0.011 0.001 PHE A 27 TRP 0.006 0.001 TRP E 328 HIS 0.002 0.001 HIS D 58 Details of bonding type rmsd covalent geometry : bond 0.00241 (12407) covalent geometry : angle 0.52526 (16884) hydrogen bonds : bond 0.04202 ( 611) hydrogen bonds : angle 3.62120 ( 1815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8195 (tt) REVERT: A 265 ASP cc_start: 0.8023 (t0) cc_final: 0.7770 (t0) REVERT: B 74 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6911 (tp30) REVERT: B 157 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7623 (tt) REVERT: B 176 VAL cc_start: 0.7862 (OUTLIER) cc_final: 0.7570 (m) REVERT: C 212 LYS cc_start: 0.8236 (tttp) cc_final: 0.7798 (tptp) REVERT: D 77 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6268 (mt-10) REVERT: D 101 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7573 (m-40) REVERT: D 176 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.7926 (m) REVERT: D 223 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7087 (ttmt) REVERT: E 455 LEU cc_start: 0.8427 (mt) cc_final: 0.8098 (mt) REVERT: E 523 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8081 (tt) REVERT: E 555 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8049 (mt) REVERT: E 633 MET cc_start: 0.7849 (ttp) cc_final: 0.7595 (ttt) REVERT: E 645 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.6948 (mm-30) outliers start: 44 outliers final: 28 residues processed: 155 average time/residue: 0.1155 time to fit residues: 26.2834 Evaluate side-chains 164 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 579 VAL Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 22 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 138 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.135477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.109215 restraints weight = 139608.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.110519 restraints weight = 99547.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.110751 restraints weight = 85079.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.110955 restraints weight = 81881.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.110903 restraints weight = 80809.140| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12407 Z= 0.106 Angle : 0.519 8.139 16884 Z= 0.267 Chirality : 0.043 0.175 2021 Planarity : 0.005 0.048 2190 Dihedral : 4.849 67.971 1738 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.88 % Allowed : 14.42 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 aren not related in a simple way. whole: 0.83 (0.22), residues: 1603 helix: 1.85 (0.18), residues: 840 sheet: -0.04 (0.40), residues: 158 loop : -1.18 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.005 0.001 TYR E 460 PHE 0.010 0.001 PHE A 27 TRP 0.006 0.001 TRP E 328 HIS 0.002 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00227 (12407) covalent geometry : angle 0.51942 (16884) hydrogen bonds : bond 0.03831 ( 611) hydrogen bonds : angle 3.52890 ( 1815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7841 (tppt) cc_final: 0.7405 (mmtm) REVERT: A 157 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8068 (tt) REVERT: B 74 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6933 (tp30) REVERT: B 157 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7589 (tt) REVERT: B 176 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7606 (m) REVERT: B 208 LYS cc_start: 0.7138 (ptmm) cc_final: 0.6934 (ptpp) REVERT: C 212 LYS cc_start: 0.8196 (tttp) cc_final: 0.7816 (tptp) REVERT: D 74 GLU cc_start: 0.7161 (tp30) cc_final: 0.6510 (mp0) REVERT: D 77 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6245 (mt-10) REVERT: D 101 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7473 (m-40) REVERT: D 176 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.7953 (m) REVERT: D 223 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7197 (ttmt) REVERT: E 523 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8077 (tt) REVERT: E 555 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7932 (mt) REVERT: E 633 MET cc_start: 0.7860 (ttp) cc_final: 0.7640 (ttt) REVERT: E 645 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.6886 (mm-30) outliers start: 38 outliers final: 25 residues processed: 158 average time/residue: 0.1161 time to fit residues: 26.6227 Evaluate side-chains 164 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 55 optimal weight: 0.0030 chunk 150 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.133982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.107683 restraints weight = 139938.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.108832 restraints weight = 101546.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.108635 restraints weight = 88612.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.109213 restraints weight = 87415.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.109240 restraints weight = 82381.096| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12407 Z= 0.120 Angle : 0.546 8.300 16884 Z= 0.279 Chirality : 0.044 0.173 2021 Planarity : 0.005 0.048 2190 Dihedral : 4.928 68.162 1738 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.96 % Allowed : 14.19 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 aren not related in a simple way. whole: 0.77 (0.22), residues: 1603 helix: 1.80 (0.18), residues: 840 sheet: -0.26 (0.35), residues: 194 loop : -1.19 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 51 TYR 0.006 0.001 TYR A 261 PHE 0.012 0.001 PHE A 27 TRP 0.007 0.001 TRP E 328 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00265 (12407) covalent geometry : angle 0.54552 (16884) hydrogen bonds : bond 0.04459 ( 611) hydrogen bonds : angle 3.62015 ( 1815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1726.51 seconds wall clock time: 30 minutes 35.02 seconds (1835.02 seconds total)