Starting phenix.real_space_refine on Wed Jan 22 06:57:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmr_19368/01_2025/8rmr_19368.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmr_19368/01_2025/8rmr_19368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rmr_19368/01_2025/8rmr_19368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmr_19368/01_2025/8rmr_19368.map" model { file = "/net/cci-nas-00/data/ceres_data/8rmr_19368/01_2025/8rmr_19368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmr_19368/01_2025/8rmr_19368.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 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: 6 Type Number sf(0) Gaussians Mg 1 5.21 5 S 242 5.16 5 C 21574 2.51 5 N 5956 2.21 5 O 6441 1.98 5 H 34252 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 68466 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 11437 Classifications: {'peptide': 708} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 11376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 11376 Classifications: {'peptide': 714} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 683} Chain breaks: 4 Chain: "C" Number of atoms: 12186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 12186 Classifications: {'peptide': 759} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 29, 'TRANS': 729} Chain: "D" Number of atoms: 11417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 11417 Classifications: {'peptide': 707} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 674} Chain breaks: 1 Chain: "E" Number of atoms: 9700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 9700 Classifications: {'peptide': 613} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 584} Chain breaks: 3 Chain: "F" Number of atoms: 9821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 9821 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 25, 'TRANS': 589} Chain breaks: 1 Chain: "G" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2528 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.83, per 1000 atoms: 0.33 Number of scatterers: 68466 At special positions: 0 Unit cell: (115.08, 148.68, 201.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 242 16.00 Mg 1 11.99 O 6441 8.00 N 5956 7.00 C 21574 6.00 H 34252 1.00 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: 13.73 Conformation dependent library (CDL) restraints added in 4.1 seconds 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8044 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 50 sheets defined 47.7% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 32 through 49 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.694A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.678A pdb=" N GLU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 451 Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 529 through 538 Proline residue: A 534 - end of helix removed outlier: 3.986A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 582 through 604 removed outlier: 4.282A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET A 595 " --> pdb=" O GLN A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.561A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 716 removed outlier: 3.752A pdb=" N ARG A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.513A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.519A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 249 through 265 removed outlier: 3.760A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 292 removed outlier: 3.818A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.571A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.499A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.879A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.817A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 474 Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 687 through 694 Processing helix chain 'B' and resid 695 through 700 removed outlier: 4.006A pdb=" N PHE B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 706 removed outlier: 4.011A pdb=" N TYR B 705 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 733 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.748A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 24 through 31 removed outlier: 4.543A pdb=" N ALA C 29 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 removed outlier: 3.925A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.926A pdb=" N MET C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.660A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 4.442A pdb=" N LYS C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 4.295A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.763A pdb=" N LEU C 177 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 193 removed outlier: 3.525A pdb=" N LYS C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 254 through 272 removed outlier: 4.337A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 305 through 316 Processing helix chain 'C' and resid 390 through 406 Processing helix chain 'C' and resid 407 through 412 removed outlier: 3.877A pdb=" N ILE C 411 " --> pdb=" O GLU C 407 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 407 through 412' Processing helix chain 'C' and resid 429 through 441 Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 514 through 518 Processing helix chain 'C' and resid 540 through 556 removed outlier: 4.124A pdb=" N SER C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL C 547 " --> pdb=" O GLU C 543 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN C 556 " --> pdb=" O TRP C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 567 Processing helix chain 'C' and resid 567 through 573 removed outlier: 3.561A pdb=" N LEU C 571 " --> pdb=" O ASP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 576 No H-bonds generated for 'chain 'C' and resid 574 through 576' Processing helix chain 'C' and resid 577 through 584 removed outlier: 3.568A pdb=" N GLN C 581 " --> pdb=" O PHE C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 606 Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 623 removed outlier: 3.862A pdb=" N ALA C 623 " --> pdb=" O PRO C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 620 through 623' Processing helix chain 'C' and resid 709 through 716 removed outlier: 4.397A pdb=" N SER C 714 " --> pdb=" O ASN C 711 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN C 715 " --> pdb=" O GLU C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 759 Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 24 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 83 through 99 Processing helix chain 'D' and resid 126 through 138 removed outlier: 3.732A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 160 No H-bonds generated for 'chain 'D' and resid 158 through 160' Processing helix chain 'D' and resid 164 through 186 Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.824A pdb=" N GLU D 195 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 217 Processing helix chain 'D' and resid 225 through 235 Processing helix chain 'D' and resid 240 through 249 Processing helix chain 'D' and resid 302 through 313 Processing helix chain 'D' and resid 330 through 350 removed outlier: 4.072A pdb=" N TYR D 334 " --> pdb=" O ILE D 330 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 335 " --> pdb=" O ASN D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 372 through 375 Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 405 through 415 Processing helix chain 'D' and resid 433 through 451 Processing helix chain 'D' and resid 453 through 476 removed outlier: 3.700A pdb=" N GLU D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 537 Processing helix chain 'D' and resid 572 through 580 Processing helix chain 'D' and resid 582 through 604 removed outlier: 4.045A pdb=" N LEU D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL D 602 " --> pdb=" O ALA D 598 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 613 Processing helix chain 'D' and resid 632 through 650 Processing helix chain 'D' and resid 652 through 674 removed outlier: 3.621A pdb=" N GLU D 656 " --> pdb=" O SER D 652 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS D 664 " --> pdb=" O ALA D 660 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU D 665 " --> pdb=" O GLU D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 692 Processing helix chain 'D' and resid 697 through 715 removed outlier: 3.519A pdb=" N LEU D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 11 Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.730A pdb=" N ILE E 18 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N SER E 19 " --> pdb=" O ASN E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 removed outlier: 3.628A pdb=" N SER E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 99 Processing helix chain 'E' and resid 101 through 117 removed outlier: 4.537A pdb=" N GLU E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'E' and resid 138 through 153 Processing helix chain 'E' and resid 156 through 161 Processing helix chain 'E' and resid 162 through 176 Processing helix chain 'E' and resid 213 through 222 Processing helix chain 'E' and resid 248 through 266 removed outlier: 3.726A pdb=" N LYS E 265 " --> pdb=" O SER E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 291 removed outlier: 3.662A pdb=" N LEU E 282 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 326 Processing helix chain 'E' and resid 330 through 345 removed outlier: 4.508A pdb=" N ALA E 340 " --> pdb=" O VAL E 336 " (cutoff:3.500A) Proline residue: E 341 - end of helix Processing helix chain 'E' and resid 371 through 373 No H-bonds generated for 'chain 'E' and resid 371 through 373' Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 394 through 396 No H-bonds generated for 'chain 'E' and resid 394 through 396' Processing helix chain 'E' and resid 412 through 426 Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'E' and resid 455 through 474 removed outlier: 3.511A pdb=" N VAL E 473 " --> pdb=" O THR E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 536 Processing helix chain 'E' and resid 540 through 560 Processing helix chain 'E' and resid 572 through 583 Processing helix chain 'E' and resid 585 through 589 Processing helix chain 'E' and resid 590 through 594 Processing helix chain 'E' and resid 607 through 612 Processing helix chain 'E' and resid 617 through 625 Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'F' and resid 60 through 66 removed outlier: 3.534A pdb=" N ILE F 63 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 103 removed outlier: 3.685A pdb=" N VAL F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 115 Processing helix chain 'F' and resid 117 through 128 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 253 through 271 Processing helix chain 'F' and resid 275 through 286 Processing helix chain 'F' and resid 294 through 301 Processing helix chain 'F' and resid 305 through 316 Processing helix chain 'F' and resid 390 through 406 removed outlier: 3.835A pdb=" N GLN F 406 " --> pdb=" O MET F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 413 Processing helix chain 'F' and resid 429 through 441 Processing helix chain 'F' and resid 442 through 447 removed outlier: 4.411A pdb=" N GLN F 447 " --> pdb=" O LYS F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 518 Processing helix chain 'F' and resid 541 through 556 Processing helix chain 'F' and resid 556 through 567 Processing helix chain 'F' and resid 567 through 572 removed outlier: 3.731A pdb=" N LEU F 571 " --> pdb=" O ASP F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 576 removed outlier: 5.947A pdb=" N GLU F 576 " --> pdb=" O ASN F 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 573 through 576' Processing helix chain 'F' and resid 577 through 584 Processing helix chain 'F' and resid 585 through 588 Processing helix chain 'F' and resid 589 through 607 removed outlier: 3.731A pdb=" N LEU F 607 " --> pdb=" O MET F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 619 Processing helix chain 'F' and resid 620 through 623 removed outlier: 3.693A pdb=" N ALA F 623 " --> pdb=" O PRO F 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 620 through 623' Processing helix chain 'F' and resid 711 through 716 Processing helix chain 'G' and resid 2 through 12 removed outlier: 3.515A pdb=" N ARG G 12 " --> pdb=" O HIS G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 33 removed outlier: 3.726A pdb=" N GLY G 32 " --> pdb=" O SER G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 87 Processing helix chain 'G' and resid 102 through 107 removed outlier: 3.632A pdb=" N ILE G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 112 Processing helix chain 'G' and resid 124 through 128 Processing helix chain 'G' and resid 130 through 139 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 removed outlier: 4.320A pdb=" N LYS A 73 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 259 removed outlier: 4.679A pdb=" N ASP B 305 " --> pdb=" O SER B 478 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N LYS B 480 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N THR B 303 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N SER B 482 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N THR B 301 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 10.248A pdb=" N ILE B 484 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N SER B 299 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 448 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 292 removed outlier: 7.362A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY A 555 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG A 551 " --> pdb=" O GLY A 555 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 542 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 292 removed outlier: 5.358A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 380 removed outlier: 4.079A pdb=" N GLN B 367 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.954A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB2, first strand: chain 'B' and resid 178 through 185 removed outlier: 3.752A pdb=" N PHE B 185 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 206 " --> pdb=" O PHE B 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 243 through 244 removed outlier: 6.597A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB5, first strand: chain 'B' and resid 642 through 643 Processing sheet with id=AB6, first strand: chain 'C' and resid 57 through 58 removed outlier: 3.828A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.116A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB9, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AC1, first strand: chain 'C' and resid 319 through 320 removed outlier: 4.729A pdb=" N ILE C 319 " --> pdb=" O VAL C 494 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 494 " --> pdb=" O ILE C 319 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.856A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA C 370 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C 371 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL C 386 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE C 373 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU C 384 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG C 375 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLY C 388 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL C 478 " --> pdb=" O ILE C 463 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE C 463 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 337 through 345 Processing sheet with id=AC4, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AC5, first strand: chain 'C' and resid 496 through 498 removed outlier: 6.293A pdb=" N VAL C 504 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 635 through 639 Processing sheet with id=AC7, first strand: chain 'C' and resid 657 through 659 removed outlier: 5.534A pdb=" N VAL C 667 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASP C 671 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 694 through 699 removed outlier: 5.012A pdb=" N LEU C 733 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS C 699 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL C 731 " --> pdb=" O LYS C 699 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.720A pdb=" N PHE D 117 " --> pdb=" O HIS D 144 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N HIS D 146 " --> pdb=" O PHE D 117 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU D 119 " --> pdb=" O HIS D 146 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE D 148 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY D 121 " --> pdb=" O PHE D 148 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET D 155 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 258 through 259 Processing sheet with id=AD3, first strand: chain 'D' and resid 290 through 292 removed outlier: 6.854A pdb=" N MET D 485 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE D 503 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE D 483 " --> pdb=" O PHE D 503 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE D 505 " --> pdb=" O GLN D 481 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN D 481 " --> pdb=" O ILE D 505 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE D 480 " --> pdb=" O MET D 360 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 322 through 324 removed outlier: 6.375A pdb=" N ILE D 322 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU D 544 " --> pdb=" O ILE D 322 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 324 " --> pdb=" O VAL D 542 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL D 542 " --> pdb=" O VAL D 565 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL D 565 " --> pdb=" O VAL D 542 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU D 544 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU D 563 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY D 546 " --> pdb=" O MET D 561 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N TYR D 501 " --> pdb=" O PHE D 525 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET D 485 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE D 503 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE D 483 " --> pdb=" O PHE D 503 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE D 505 " --> pdb=" O GLN D 481 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN D 481 " --> pdb=" O ILE D 505 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 377 through 378 removed outlier: 5.820A pdb=" N GLU D 377 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLN E 367 " --> pdb=" O GLU D 377 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 627 through 629 Processing sheet with id=AD7, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AD8, first strand: chain 'E' and resid 128 through 130 removed outlier: 3.664A pdb=" N ARG E 135 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 179 through 183 Processing sheet with id=AE1, first strand: chain 'E' and resid 242 through 244 removed outlier: 6.682A pdb=" N LEU E 224 " --> pdb=" O ARG E 350 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 489 through 490 removed outlier: 4.180A pdb=" N PHE E 496 " --> pdb=" O ALA E 503 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 57 through 59 removed outlier: 3.839A pdb=" N MET F 90 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 133 through 134 Processing sheet with id=AE5, first strand: chain 'F' and resid 292 through 293 removed outlier: 3.726A pdb=" N GLN F 288 " --> pdb=" O THR F 530 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR F 530 " --> pdb=" O GLN F 288 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 319 through 320 Processing sheet with id=AE7, first strand: chain 'F' and resid 323 through 325 removed outlier: 5.746A pdb=" N PHE F 330 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL F 366 " --> pdb=" O PHE F 330 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG F 332 " --> pdb=" O THR F 364 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR F 364 " --> pdb=" O ARG F 332 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER F 334 " --> pdb=" O GLU F 362 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR F 371 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL F 386 " --> pdb=" O THR F 371 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE F 373 " --> pdb=" O LEU F 384 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU F 384 " --> pdb=" O ILE F 373 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG F 375 " --> pdb=" O ILE F 382 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE F 382 " --> pdb=" O ARG F 375 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ARG F 479 " --> pdb=" O ILE F 382 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU F 384 " --> pdb=" O ARG F 479 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER F 481 " --> pdb=" O LEU F 384 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL F 386 " --> pdb=" O SER F 481 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 338 through 345 Processing sheet with id=AE9, first strand: chain 'F' and resid 497 through 498 removed outlier: 3.702A pdb=" N SER F 497 " --> pdb=" O ARG F 505 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG F 505 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL F 504 " --> pdb=" O LEU F 512 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 635 through 639 Processing sheet with id=AF2, first strand: chain 'F' and resid 656 through 659 removed outlier: 7.336A pdb=" N LEU F 665 " --> pdb=" O ALA F 672 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 694 through 699 removed outlier: 5.436A pdb=" N LEU F 733 " --> pdb=" O LEU F 697 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LYS F 699 " --> pdb=" O VAL F 731 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL F 731 " --> pdb=" O LYS F 699 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 694 through 699 removed outlier: 5.436A pdb=" N LEU F 733 " --> pdb=" O LEU F 697 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LYS F 699 " --> pdb=" O VAL F 731 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL F 731 " --> pdb=" O LYS F 699 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY F 727 " --> pdb=" O ASP F 730 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL F 732 " --> pdb=" O LEU F 725 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU F 725 " --> pdb=" O VAL F 732 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 22 through 25 removed outlier: 3.718A pdb=" N GLU G 70 " --> pdb=" O LEU G 47 " (cutoff:3.500A) 1648 hydrogen bonds defined for protein. 4539 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: 25.32 Time building geometry restraints manager: 16.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 34190 1.03 - 1.23: 77 1.23 - 1.42: 14295 1.42 - 1.62: 20134 1.62 - 1.81: 422 Bond restraints: 69118 Sorted by residual: bond pdb=" N GLU C 543 " pdb=" CA GLU C 543 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.16e-02 7.43e+03 7.25e+00 bond pdb=" N GLU C 681 " pdb=" H GLU C 681 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.74e+00 bond pdb=" N GLY C 682 " pdb=" H GLY C 682 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.56e+00 bond pdb=" N GLU C 543 " pdb=" H GLU C 543 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" N GLU C 681 " pdb=" CA GLU C 681 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.33e-02 5.65e+03 6.35e+00 ... (remaining 69113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 124389 2.05 - 4.11: 557 4.11 - 6.16: 29 6.16 - 8.21: 5 8.21 - 10.27: 1 Bond angle restraints: 124981 Sorted by residual: angle pdb=" CA PRO C 579 " pdb=" N PRO C 579 " pdb=" CD PRO C 579 " ideal model delta sigma weight residual 112.00 105.51 6.49 1.40e+00 5.10e-01 2.15e+01 angle pdb=" N ILE A 79 " pdb=" CA ILE A 79 " pdb=" C ILE A 79 " ideal model delta sigma weight residual 113.53 109.93 3.60 9.80e-01 1.04e+00 1.35e+01 angle pdb=" CA PRO F 579 " pdb=" N PRO F 579 " pdb=" CD PRO F 579 " ideal model delta sigma weight residual 112.00 107.27 4.73 1.40e+00 5.10e-01 1.14e+01 angle pdb=" N ILE A 30 " pdb=" CA ILE A 30 " pdb=" C ILE A 30 " ideal model delta sigma weight residual 111.81 108.91 2.90 8.60e-01 1.35e+00 1.14e+01 angle pdb=" N PRO F 579 " pdb=" CD PRO F 579 " pdb=" CG PRO F 579 " ideal model delta sigma weight residual 103.20 98.15 5.05 1.50e+00 4.44e-01 1.13e+01 ... (remaining 124976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 28186 17.99 - 35.98: 2996 35.98 - 53.97: 930 53.97 - 71.96: 177 71.96 - 89.94: 61 Dihedral angle restraints: 32350 sinusoidal: 17982 harmonic: 14368 Sorted by residual: dihedral pdb=" CA LEU A 261 " pdb=" C LEU A 261 " pdb=" N ARG A 262 " pdb=" CA ARG A 262 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA GLY F 685 " pdb=" C GLY F 685 " pdb=" N VAL F 686 " pdb=" CA VAL F 686 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU B 695 " pdb=" C LEU B 695 " pdb=" N PHE B 696 " pdb=" CA PHE B 696 " ideal model delta harmonic sigma weight residual 180.00 161.63 18.37 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 32347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3794 0.035 - 0.070: 987 0.070 - 0.105: 273 0.105 - 0.140: 131 0.140 - 0.175: 5 Chirality restraints: 5190 Sorted by residual: chirality pdb=" CB ILE E 147 " pdb=" CA ILE E 147 " pdb=" CG1 ILE E 147 " pdb=" CG2 ILE E 147 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CA ILE B 735 " pdb=" N ILE B 735 " pdb=" C ILE B 735 " pdb=" CB ILE B 735 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA VAL E 451 " pdb=" N VAL E 451 " pdb=" C VAL E 451 " pdb=" CB VAL E 451 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 5187 not shown) Planarity restraints: 10148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 578 " -0.057 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO C 579 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 579 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 579 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 464 " -0.050 5.00e-02 4.00e+02 7.50e-02 8.99e+00 pdb=" N PRO C 465 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 465 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 465 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 625 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO F 626 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO F 626 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 626 " -0.031 5.00e-02 4.00e+02 ... (remaining 10145 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.83: 230 1.83 - 2.53: 58488 2.53 - 3.22: 211444 3.22 - 3.91: 266590 3.91 - 4.60: 423492 Nonbonded interactions: 960244 Sorted by model distance: nonbonded pdb=" HB3 GLU B 636 " pdb=" HZ1 LYS C 32 " model vdw 1.142 2.270 nonbonded pdb=" HB3 SER C 225 " pdb=" HD2 TYR C 228 " model vdw 1.241 2.270 nonbonded pdb=" HG1 THR C 530 " pdb=" OE1 GLN C 551 " model vdw 1.248 2.450 nonbonded pdb="HG21 VAL D 450 " pdb="HD22 LEU D 641 " model vdw 1.318 2.440 nonbonded pdb=" OE2 GLU C 525 " pdb=" HZ1 LYS C 670 " model vdw 1.507 2.450 ... (remaining 960239 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' and (resid 1 through 63 or (resid 73 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 74 through 715 or (r \ esid 716 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name \ HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or na \ me HH11 or name HH12 or name HH21 or name HH22)))) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 1 through 184 or (resid 207 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 208 through 633 or \ (resid 656 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 o \ r name HG3)) or resid 657 through 669)) selection = (chain 'E' and (resid 1 through 227 or (resid 241 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name H \ B or name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 \ or name HD12 or name HD13)) or resid 242 through 669)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.590 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: 0.500 Extract box with map and model: 1.720 Check model and map are aligned: 0.400 Set scattering table: 0.490 Process input model: 109.420 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 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 : 0.002 0.081 34866 Z= 0.155 Angle : 0.499 10.266 47027 Z= 0.267 Chirality : 0.038 0.175 5190 Planarity : 0.004 0.083 6075 Dihedral : 17.461 89.945 13332 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.20 % Favored : 95.73 % Rotamer: Outliers : 0.26 % Allowed : 23.44 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.13), residues: 4239 helix: 1.60 (0.13), residues: 1826 sheet: -0.34 (0.24), residues: 529 loop : -1.21 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 78 HIS 0.006 0.001 HIS A 74 PHE 0.010 0.001 PHE B 730 TYR 0.010 0.001 TYR B 555 ARG 0.006 0.000 ARG B 706 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 910 time to evaluate : 4.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6163 (mm-30) cc_final: 0.5566 (mt-10) REVERT: A 125 ARG cc_start: 0.3657 (mtm180) cc_final: 0.3262 (mtt90) REVERT: A 441 MET cc_start: 0.8049 (ttm) cc_final: 0.7681 (ttp) REVERT: B 317 MET cc_start: 0.3836 (mmp) cc_final: 0.3580 (mmp) REVERT: B 372 MET cc_start: 0.7445 (ptm) cc_final: 0.6439 (tmm) REVERT: C 1 MET cc_start: 0.6298 (mmp) cc_final: 0.5707 (mmp) REVERT: C 241 GLU cc_start: 0.6692 (tt0) cc_final: 0.6352 (tt0) REVERT: C 332 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7189 (ptt-90) REVERT: C 365 MET cc_start: 0.4013 (mpp) cc_final: 0.3646 (ptp) REVERT: C 402 MET cc_start: -0.0188 (ppp) cc_final: -0.0795 (ttp) REVERT: C 458 MET cc_start: 0.1159 (pmm) cc_final: -0.0659 (ptm) REVERT: C 536 MET cc_start: 0.3187 (mmm) cc_final: 0.2094 (ttp) REVERT: C 739 ARG cc_start: 0.5465 (mtt-85) cc_final: 0.4282 (ttt90) REVERT: D 12 MET cc_start: 0.3122 (ppp) cc_final: 0.2828 (mmt) REVERT: D 393 TYR cc_start: 0.6686 (t80) cc_final: 0.6433 (t80) REVERT: D 477 MET cc_start: 0.5886 (mpp) cc_final: 0.5668 (mmm) REVERT: E 46 THR cc_start: 0.5988 (m) cc_final: 0.5780 (m) REVERT: E 92 MET cc_start: 0.6701 (ttm) cc_final: 0.6332 (mmm) REVERT: F 241 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6667 (tm-30) REVERT: F 283 MET cc_start: 0.7751 (mtp) cc_final: 0.7517 (mtp) REVERT: F 365 MET cc_start: 0.2368 (mmp) cc_final: 0.2010 (mmt) REVERT: F 735 MET cc_start: 0.8121 (ppp) cc_final: 0.7716 (ptm) REVERT: G 1 MET cc_start: 0.5449 (pmm) cc_final: 0.5123 (ptp) REVERT: G 109 LEU cc_start: 0.6164 (mt) cc_final: 0.5865 (tt) outliers start: 10 outliers final: 3 residues processed: 916 average time/residue: 1.1012 time to fit residues: 1530.8477 Evaluate side-chains 633 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 630 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain E residue 32 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 357 optimal weight: 6.9990 chunk 320 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 216 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 201 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 384 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 425 ASN B 694 ASN C 306 GLN C 425 ASN D 365 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN E 314 ASN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 545 GLN E 582 GLN F 100 ASN F 102 ASN F 110 HIS G 26 ASN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.173859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.135639 restraints weight = 208450.211| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 3.63 r_work: 0.3860 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 34866 Z= 0.301 Angle : 0.617 7.501 47027 Z= 0.331 Chirality : 0.041 0.201 5190 Planarity : 0.005 0.080 6075 Dihedral : 4.182 38.048 4659 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 2.64 % Allowed : 22.91 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 4239 helix: 1.05 (0.12), residues: 1856 sheet: -0.67 (0.23), residues: 516 loop : -1.46 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 309 HIS 0.009 0.001 HIS D 452 PHE 0.018 0.002 PHE B 333 TYR 0.015 0.002 TYR E 30 ARG 0.007 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 631 time to evaluate : 4.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.4224 (mtm180) cc_final: 0.3406 (mpt-90) REVERT: A 441 MET cc_start: 0.8473 (ttm) cc_final: 0.8246 (ttp) REVERT: B 284 ASN cc_start: 0.8216 (m-40) cc_final: 0.7919 (m110) REVERT: B 317 MET cc_start: 0.4736 (mmp) cc_final: 0.4210 (mmp) REVERT: B 372 MET cc_start: 0.7901 (ptm) cc_final: 0.6284 (tmm) REVERT: B 522 ASP cc_start: 0.8368 (m-30) cc_final: 0.7656 (m-30) REVERT: B 743 ILE cc_start: 0.7587 (mm) cc_final: 0.7327 (tp) REVERT: C 184 THR cc_start: 0.7985 (t) cc_final: 0.7645 (t) REVERT: C 318 ARG cc_start: 0.5765 (mmp80) cc_final: 0.4874 (mpp80) REVERT: C 332 ARG cc_start: 0.7762 (ttp-170) cc_final: 0.7169 (ptt-90) REVERT: C 365 MET cc_start: 0.3990 (mpp) cc_final: 0.3559 (ptp) REVERT: C 402 MET cc_start: -0.0160 (OUTLIER) cc_final: -0.0378 (ptt) REVERT: C 458 MET cc_start: 0.1796 (pmm) cc_final: -0.0283 (ptm) REVERT: C 536 MET cc_start: 0.3030 (mmm) cc_final: 0.2451 (ttm) REVERT: C 603 MET cc_start: 0.7281 (tpt) cc_final: 0.6974 (tpt) REVERT: C 739 ARG cc_start: 0.6466 (mtt-85) cc_final: 0.4628 (ttt90) REVERT: D 12 MET cc_start: 0.3508 (ppp) cc_final: 0.3133 (mmm) REVERT: D 204 ARG cc_start: 0.8409 (ptt-90) cc_final: 0.8120 (ptt90) REVERT: D 368 TRP cc_start: 0.7636 (m100) cc_final: 0.7433 (m100) REVERT: D 393 TYR cc_start: 0.6823 (t80) cc_final: 0.6610 (t80) REVERT: D 477 MET cc_start: 0.5675 (mpp) cc_final: 0.5298 (mmm) REVERT: D 604 GLU cc_start: 0.8413 (tt0) cc_final: 0.8153 (mt-10) REVERT: E 7 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7069 (tt) REVERT: E 27 ASP cc_start: 0.6714 (t70) cc_final: 0.5990 (p0) REVERT: E 92 MET cc_start: 0.7194 (ttm) cc_final: 0.6992 (mmm) REVERT: E 317 MET cc_start: 0.6182 (tpp) cc_final: 0.5577 (ttp) REVERT: E 376 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7933 (tt) REVERT: E 628 MET cc_start: 0.5896 (tpp) cc_final: 0.5562 (tpp) REVERT: F 51 MET cc_start: 0.6681 (mmm) cc_final: 0.5587 (mmm) REVERT: F 283 MET cc_start: 0.8093 (mtp) cc_final: 0.7828 (mtp) REVERT: F 365 MET cc_start: 0.1751 (mmp) cc_final: 0.1441 (mmt) REVERT: F 406 GLN cc_start: 0.7567 (mm110) cc_final: 0.7326 (mm110) REVERT: F 473 MET cc_start: 0.3693 (tpp) cc_final: 0.3412 (tpp) REVERT: F 610 PHE cc_start: 0.4358 (OUTLIER) cc_final: 0.3276 (t80) REVERT: F 735 MET cc_start: 0.8260 (ppp) cc_final: 0.7791 (ptm) REVERT: G 1 MET cc_start: 0.5351 (pmm) cc_final: 0.4725 (ptp) outliers start: 100 outliers final: 58 residues processed: 703 average time/residue: 0.9616 time to fit residues: 1058.0119 Evaluate side-chains 621 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 559 time to evaluate : 4.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 405 CYS Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 495 ARG Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 640 VAL Chi-restraints excluded: chain F residue 740 ASP Chi-restraints excluded: chain F residue 743 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 202 optimal weight: 0.9990 chunk 187 optimal weight: 0.0070 chunk 336 optimal weight: 0.9980 chunk 212 optimal weight: 8.9990 chunk 258 optimal weight: 1.9990 chunk 343 optimal weight: 4.9990 chunk 341 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 chunk 207 optimal weight: 7.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN D 41 HIS D 340 GLN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN F 110 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.174419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.136202 restraints weight = 207572.036| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 3.86 r_work: 0.3868 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34866 Z= 0.205 Angle : 0.538 8.315 47027 Z= 0.285 Chirality : 0.039 0.159 5190 Planarity : 0.004 0.072 6075 Dihedral : 3.999 38.679 4655 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 1.92 % Allowed : 23.49 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 4239 helix: 1.26 (0.12), residues: 1861 sheet: -0.55 (0.23), residues: 507 loop : -1.45 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 309 HIS 0.005 0.001 HIS F 110 PHE 0.014 0.001 PHE A 4 TYR 0.013 0.001 TYR C 360 ARG 0.005 0.000 ARG F 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 583 time to evaluate : 4.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.4291 (mtm180) cc_final: 0.3536 (mpt-90) REVERT: A 174 ARG cc_start: 0.4906 (tpt170) cc_final: 0.4558 (tpp80) REVERT: A 441 MET cc_start: 0.8438 (ttm) cc_final: 0.8214 (ttp) REVERT: B 284 ASN cc_start: 0.8212 (m-40) cc_final: 0.7912 (m110) REVERT: B 317 MET cc_start: 0.4817 (mmp) cc_final: 0.4428 (mmp) REVERT: B 372 MET cc_start: 0.7795 (ptm) cc_final: 0.6264 (tmm) REVERT: B 501 PHE cc_start: 0.7622 (t80) cc_final: 0.7335 (t80) REVERT: B 743 ILE cc_start: 0.7481 (mm) cc_final: 0.7261 (tp) REVERT: C 318 ARG cc_start: 0.5725 (mmp80) cc_final: 0.4891 (mpp80) REVERT: C 332 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7141 (ptt-90) REVERT: C 363 PHE cc_start: 0.6921 (m-80) cc_final: 0.6557 (m-80) REVERT: C 365 MET cc_start: 0.4133 (mpp) cc_final: 0.3793 (ptp) REVERT: C 402 MET cc_start: -0.0120 (ppp) cc_final: -0.0481 (ttp) REVERT: C 458 MET cc_start: 0.1787 (pmm) cc_final: -0.0291 (ptm) REVERT: C 536 MET cc_start: 0.3082 (mmm) cc_final: 0.2385 (ttm) REVERT: C 603 MET cc_start: 0.7394 (tpt) cc_final: 0.7085 (tpt) REVERT: C 641 ARG cc_start: 0.7087 (tpm170) cc_final: 0.5982 (tpp-160) REVERT: C 664 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7107 (ttt-90) REVERT: C 739 ARG cc_start: 0.6470 (mtt-85) cc_final: 0.4395 (ttt90) REVERT: C 756 MET cc_start: 0.4135 (mtp) cc_final: 0.3866 (mmm) REVERT: D 12 MET cc_start: 0.3573 (ppp) cc_final: 0.3219 (mmm) REVERT: D 21 MET cc_start: -0.4103 (OUTLIER) cc_final: -0.5711 (ttt) REVERT: D 146 HIS cc_start: 0.8455 (t70) cc_final: 0.8242 (t-90) REVERT: D 204 ARG cc_start: 0.8435 (ptt-90) cc_final: 0.8105 (ptt90) REVERT: D 604 GLU cc_start: 0.8441 (tt0) cc_final: 0.8117 (mt-10) REVERT: D 654 GLN cc_start: 0.7733 (tp-100) cc_final: 0.7168 (tt0) REVERT: E 27 ASP cc_start: 0.6748 (t70) cc_final: 0.6000 (p0) REVERT: E 266 LEU cc_start: 0.8674 (mt) cc_final: 0.8466 (mm) REVERT: E 317 MET cc_start: 0.6064 (tpp) cc_final: 0.5502 (ttp) REVERT: E 376 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7885 (tt) REVERT: E 628 MET cc_start: 0.5855 (tpp) cc_final: 0.5402 (tpp) REVERT: F 51 MET cc_start: 0.6689 (mmm) cc_final: 0.5614 (mmm) REVERT: F 283 MET cc_start: 0.8154 (mtp) cc_final: 0.7884 (mtp) REVERT: F 365 MET cc_start: 0.1900 (mmp) cc_final: 0.1591 (mmt) REVERT: F 610 PHE cc_start: 0.4164 (OUTLIER) cc_final: 0.3040 (t80) REVERT: F 731 VAL cc_start: 0.5516 (OUTLIER) cc_final: 0.5276 (t) REVERT: F 735 MET cc_start: 0.8298 (ppp) cc_final: 0.7863 (ptm) REVERT: G 1 MET cc_start: 0.5286 (pmm) cc_final: 0.4603 (ptp) outliers start: 73 outliers final: 50 residues processed: 636 average time/residue: 0.9768 time to fit residues: 989.7072 Evaluate side-chains 609 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 554 time to evaluate : 4.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 692 CYS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 664 ARG Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 405 CYS Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 743 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 1 optimal weight: 10.0000 chunk 347 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 281 optimal weight: 0.8980 chunk 304 optimal weight: 0.9990 chunk 283 optimal weight: 0.7980 chunk 408 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN C 265 ASN D 340 GLN E 124 GLN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.174773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.136531 restraints weight = 207324.226| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 3.70 r_work: 0.3882 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34866 Z= 0.177 Angle : 0.512 6.648 47027 Z= 0.270 Chirality : 0.038 0.141 5190 Planarity : 0.004 0.063 6075 Dihedral : 3.926 39.031 4655 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 2.27 % Allowed : 23.10 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.13), residues: 4239 helix: 1.40 (0.12), residues: 1867 sheet: -0.55 (0.23), residues: 508 loop : -1.42 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 309 HIS 0.005 0.001 HIS F 110 PHE 0.014 0.001 PHE A 236 TYR 0.011 0.001 TYR B 559 ARG 0.007 0.000 ARG F 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 571 time to evaluate : 4.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.4166 (mtm180) cc_final: 0.3435 (mpt-90) REVERT: A 131 TYR cc_start: 0.7725 (t80) cc_final: 0.7425 (t80) REVERT: A 144 HIS cc_start: 0.2419 (OUTLIER) cc_final: -0.0157 (t-170) REVERT: A 174 ARG cc_start: 0.4883 (tpt170) cc_final: 0.4575 (tpp80) REVERT: A 441 MET cc_start: 0.8431 (ttm) cc_final: 0.8204 (ttp) REVERT: A 549 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6971 (pp) REVERT: B 284 ASN cc_start: 0.8142 (m-40) cc_final: 0.7854 (m110) REVERT: B 317 MET cc_start: 0.4839 (mmp) cc_final: 0.3809 (mmm) REVERT: B 372 MET cc_start: 0.7796 (ptm) cc_final: 0.6240 (tmm) REVERT: B 501 PHE cc_start: 0.7614 (t80) cc_final: 0.7346 (t80) REVERT: B 602 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7388 (mtp-110) REVERT: B 743 ILE cc_start: 0.7565 (mm) cc_final: 0.7317 (tp) REVERT: C 241 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: C 318 ARG cc_start: 0.5726 (mmp80) cc_final: 0.4905 (mpp80) REVERT: C 332 ARG cc_start: 0.7806 (ttp-170) cc_final: 0.7130 (ptt-90) REVERT: C 363 PHE cc_start: 0.6879 (m-80) cc_final: 0.6468 (m-80) REVERT: C 365 MET cc_start: 0.4304 (mpp) cc_final: 0.3689 (ptp) REVERT: C 402 MET cc_start: -0.0151 (OUTLIER) cc_final: -0.0695 (ttp) REVERT: C 458 MET cc_start: 0.1904 (pmm) cc_final: -0.0183 (ptm) REVERT: C 536 MET cc_start: 0.3339 (mmm) cc_final: 0.2513 (ttm) REVERT: C 603 MET cc_start: 0.7341 (tpt) cc_final: 0.7096 (tpt) REVERT: C 641 ARG cc_start: 0.7071 (tpm170) cc_final: 0.5998 (tpp-160) REVERT: C 664 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7146 (ttt-90) REVERT: C 756 MET cc_start: 0.4301 (mtp) cc_final: 0.3893 (mmm) REVERT: D 12 MET cc_start: 0.3354 (ppp) cc_final: 0.3010 (mmm) REVERT: D 146 HIS cc_start: 0.8270 (t70) cc_final: 0.8051 (t-90) REVERT: D 204 ARG cc_start: 0.8512 (ptt-90) cc_final: 0.8163 (ptt90) REVERT: D 294 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: D 490 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7059 (mt) REVERT: D 611 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6137 (t80) REVERT: D 654 GLN cc_start: 0.7719 (tp-100) cc_final: 0.7174 (tt0) REVERT: E 27 ASP cc_start: 0.6773 (t70) cc_final: 0.6035 (p0) REVERT: E 317 MET cc_start: 0.6067 (tpp) cc_final: 0.5669 (ttp) REVERT: E 376 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7818 (tt) REVERT: E 628 MET cc_start: 0.5922 (tpp) cc_final: 0.5440 (tpp) REVERT: F 51 MET cc_start: 0.6629 (mmm) cc_final: 0.5563 (mmm) REVERT: F 283 MET cc_start: 0.8001 (mtp) cc_final: 0.7707 (mtp) REVERT: F 365 MET cc_start: 0.2303 (mmp) cc_final: 0.1919 (mmt) REVERT: F 610 PHE cc_start: 0.4229 (OUTLIER) cc_final: 0.3089 (t80) REVERT: F 731 VAL cc_start: 0.5552 (OUTLIER) cc_final: 0.5309 (t) REVERT: F 735 MET cc_start: 0.8230 (ppp) cc_final: 0.7811 (ptm) REVERT: G 1 MET cc_start: 0.5317 (pmm) cc_final: 0.4662 (ptp) outliers start: 86 outliers final: 61 residues processed: 637 average time/residue: 0.9195 time to fit residues: 937.4596 Evaluate side-chains 626 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 553 time to evaluate : 4.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 548 ASN Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 664 ARG Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 405 CYS Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 375 ARG Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 640 VAL Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 743 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 128 optimal weight: 2.9990 chunk 375 optimal weight: 10.0000 chunk 348 optimal weight: 10.0000 chunk 158 optimal weight: 0.6980 chunk 309 optimal weight: 0.1980 chunk 372 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 326 optimal weight: 0.8980 chunk 181 optimal weight: 20.0000 chunk 44 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN B 642 ASN E 124 GLN E 310 ASN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.175325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.137154 restraints weight = 206744.451| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 3.66 r_work: 0.3893 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 34866 Z= 0.159 Angle : 0.497 6.194 47027 Z= 0.261 Chirality : 0.038 0.145 5190 Planarity : 0.004 0.060 6075 Dihedral : 3.829 39.199 4655 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.82 % Rotamer: Outliers : 2.16 % Allowed : 23.28 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.13), residues: 4239 helix: 1.61 (0.12), residues: 1871 sheet: -0.48 (0.23), residues: 518 loop : -1.32 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 309 HIS 0.007 0.001 HIS F 110 PHE 0.012 0.001 PHE A 236 TYR 0.010 0.001 TYR B 559 ARG 0.009 0.000 ARG C 737 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 587 time to evaluate : 4.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.4219 (mtm180) cc_final: 0.3482 (mpt-90) REVERT: A 131 TYR cc_start: 0.7753 (t80) cc_final: 0.7381 (t80) REVERT: A 144 HIS cc_start: 0.2365 (OUTLIER) cc_final: -0.0171 (t-170) REVERT: A 174 ARG cc_start: 0.4850 (tpt170) cc_final: 0.4566 (tpp80) REVERT: A 441 MET cc_start: 0.8440 (ttm) cc_final: 0.8197 (ttp) REVERT: A 549 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6985 (pp) REVERT: A 561 MET cc_start: 0.4805 (ttp) cc_final: 0.4399 (ttp) REVERT: A 599 GLU cc_start: 0.8103 (tp30) cc_final: 0.7852 (tp30) REVERT: B 284 ASN cc_start: 0.8096 (m-40) cc_final: 0.7815 (m110) REVERT: B 317 MET cc_start: 0.4775 (mmp) cc_final: 0.3820 (mmm) REVERT: B 372 MET cc_start: 0.7737 (ptm) cc_final: 0.6178 (tmm) REVERT: B 438 TRP cc_start: 0.5837 (p90) cc_final: 0.5499 (p90) REVERT: B 501 PHE cc_start: 0.7617 (t80) cc_final: 0.7334 (t80) REVERT: B 602 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7493 (mtp-110) REVERT: C 318 ARG cc_start: 0.5779 (mmp80) cc_final: 0.4930 (mpp80) REVERT: C 332 ARG cc_start: 0.7798 (ttp-170) cc_final: 0.7336 (ptm-80) REVERT: C 363 PHE cc_start: 0.7144 (m-80) cc_final: 0.6690 (m-80) REVERT: C 365 MET cc_start: 0.4219 (mpp) cc_final: 0.3613 (ptp) REVERT: C 402 MET cc_start: -0.0147 (ppp) cc_final: -0.0557 (ttp) REVERT: C 458 MET cc_start: 0.2020 (pmm) cc_final: -0.0153 (ptm) REVERT: C 603 MET cc_start: 0.7373 (tpt) cc_final: 0.7095 (tpt) REVERT: C 641 ARG cc_start: 0.7082 (tpm170) cc_final: 0.6009 (tpp-160) REVERT: C 664 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7127 (ttt-90) REVERT: C 756 MET cc_start: 0.4358 (mtp) cc_final: 0.3985 (mmm) REVERT: D 12 MET cc_start: 0.3657 (ppp) cc_final: 0.3272 (mmm) REVERT: D 21 MET cc_start: -0.3818 (OUTLIER) cc_final: -0.5436 (ttt) REVERT: D 146 HIS cc_start: 0.8571 (t70) cc_final: 0.8189 (t-90) REVERT: D 204 ARG cc_start: 0.8474 (ptt-90) cc_final: 0.8127 (ptt90) REVERT: D 294 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: D 490 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7086 (mt) REVERT: D 611 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6117 (t80) REVERT: E 27 ASP cc_start: 0.6764 (t70) cc_final: 0.5955 (p0) REVERT: E 376 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7900 (tt) REVERT: E 612 LYS cc_start: 0.5240 (mmtt) cc_final: 0.4802 (mmtp) REVERT: E 628 MET cc_start: 0.6048 (tpp) cc_final: 0.5551 (tpp) REVERT: F 51 MET cc_start: 0.6535 (mmm) cc_final: 0.5451 (mmm) REVERT: F 283 MET cc_start: 0.8039 (mtp) cc_final: 0.7792 (mtp) REVERT: F 365 MET cc_start: 0.1844 (mmp) cc_final: 0.1402 (mmp) REVERT: F 610 PHE cc_start: 0.4044 (OUTLIER) cc_final: 0.2907 (t80) REVERT: F 731 VAL cc_start: 0.5486 (OUTLIER) cc_final: 0.5114 (t) REVERT: F 735 MET cc_start: 0.8217 (ppp) cc_final: 0.7812 (ptm) REVERT: G 1 MET cc_start: 0.5356 (pmm) cc_final: 0.4672 (ptp) REVERT: G 65 LYS cc_start: 0.7176 (tppt) cc_final: 0.6928 (tppt) outliers start: 82 outliers final: 54 residues processed: 646 average time/residue: 0.9173 time to fit residues: 949.3685 Evaluate side-chains 628 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 563 time to evaluate : 4.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 548 ASN Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 664 ARG Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 405 CYS Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 375 ARG Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 640 VAL Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 743 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 250 optimal weight: 0.8980 chunk 350 optimal weight: 9.9990 chunk 370 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 324 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 380 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN E 84 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN E 476 ASN E 582 GLN F 100 ASN F 110 HIS ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.172709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.133609 restraints weight = 207279.695| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 3.29 r_work: 0.3867 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34866 Z= 0.229 Angle : 0.532 6.074 47027 Z= 0.282 Chirality : 0.039 0.194 5190 Planarity : 0.004 0.057 6075 Dihedral : 4.013 40.576 4655 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 2.82 % Allowed : 23.44 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.13), residues: 4239 helix: 1.40 (0.12), residues: 1871 sheet: -0.56 (0.23), residues: 511 loop : -1.42 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 309 HIS 0.007 0.001 HIS F 110 PHE 0.023 0.001 PHE E 551 TYR 0.015 0.001 TYR B 559 ARG 0.005 0.000 ARG E 572 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 554 time to evaluate : 4.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.4264 (mtm180) cc_final: 0.3458 (mpt-90) REVERT: A 131 TYR cc_start: 0.7733 (t80) cc_final: 0.7419 (t80) REVERT: A 144 HIS cc_start: 0.2457 (OUTLIER) cc_final: -0.0033 (t-170) REVERT: A 174 ARG cc_start: 0.4925 (tpt170) cc_final: 0.4629 (tpt-90) REVERT: A 549 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6985 (pp) REVERT: B 8 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7923 (tt) REVERT: B 131 TRP cc_start: 0.6493 (p-90) cc_final: 0.5164 (p-90) REVERT: B 284 ASN cc_start: 0.8091 (m-40) cc_final: 0.7819 (m110) REVERT: B 317 MET cc_start: 0.4818 (mmp) cc_final: 0.4492 (mmp) REVERT: B 372 MET cc_start: 0.7922 (ptm) cc_final: 0.6226 (tmm) REVERT: B 475 ILE cc_start: 0.7278 (mm) cc_final: 0.6774 (tt) REVERT: B 602 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7294 (mtp-110) REVERT: C 101 ARG cc_start: 0.7996 (ptt90) cc_final: 0.7741 (ptm-80) REVERT: C 318 ARG cc_start: 0.5718 (mmp80) cc_final: 0.4915 (mpp80) REVERT: C 332 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7176 (ptt-90) REVERT: C 363 PHE cc_start: 0.7128 (m-80) cc_final: 0.6736 (m-80) REVERT: C 365 MET cc_start: 0.4340 (mpp) cc_final: 0.3959 (ptp) REVERT: C 371 THR cc_start: 0.5990 (m) cc_final: 0.5672 (p) REVERT: C 402 MET cc_start: 0.0019 (OUTLIER) cc_final: -0.0442 (ttp) REVERT: C 458 MET cc_start: 0.2245 (pmm) cc_final: 0.0029 (ptm) REVERT: C 603 MET cc_start: 0.7447 (tpt) cc_final: 0.7201 (tpt) REVERT: C 641 ARG cc_start: 0.7159 (tpm170) cc_final: 0.6059 (tpp-160) REVERT: C 664 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7142 (ttt-90) REVERT: D 12 MET cc_start: 0.3553 (ppp) cc_final: 0.3184 (mmm) REVERT: D 21 MET cc_start: -0.3763 (OUTLIER) cc_final: -0.5410 (ttt) REVERT: D 204 ARG cc_start: 0.8389 (ptt-90) cc_final: 0.8133 (ptt90) REVERT: D 294 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: D 490 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7163 (mt) REVERT: D 611 PHE cc_start: 0.7035 (OUTLIER) cc_final: 0.6236 (t80) REVERT: E 7 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7215 (tt) REVERT: E 27 ASP cc_start: 0.6813 (t70) cc_final: 0.6083 (p0) REVERT: E 75 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6801 (tm-30) REVERT: E 317 MET cc_start: 0.5787 (ttm) cc_final: 0.5050 (ttp) REVERT: E 376 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7961 (tt) REVERT: E 612 LYS cc_start: 0.5422 (mmtt) cc_final: 0.4992 (mmtp) REVERT: E 628 MET cc_start: 0.6119 (tpp) cc_final: 0.5647 (tpp) REVERT: F 51 MET cc_start: 0.6530 (mmm) cc_final: 0.5330 (mmm) REVERT: F 283 MET cc_start: 0.7985 (mtp) cc_final: 0.7750 (mtp) REVERT: F 365 MET cc_start: 0.2037 (mmp) cc_final: 0.1717 (mmt) REVERT: F 463 ILE cc_start: 0.7971 (mt) cc_final: 0.7754 (mp) REVERT: F 610 PHE cc_start: 0.4220 (OUTLIER) cc_final: 0.3043 (t80) REVERT: F 731 VAL cc_start: 0.5427 (OUTLIER) cc_final: 0.5185 (t) REVERT: F 735 MET cc_start: 0.8149 (ppp) cc_final: 0.7804 (ptm) REVERT: G 1 MET cc_start: 0.5439 (pmm) cc_final: 0.4753 (ptp) REVERT: G 65 LYS cc_start: 0.7256 (tppt) cc_final: 0.7027 (tppt) REVERT: G 136 PHE cc_start: 0.6595 (m-80) cc_final: 0.5999 (m-10) outliers start: 107 outliers final: 75 residues processed: 633 average time/residue: 0.9296 time to fit residues: 945.5511 Evaluate side-chains 636 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 547 time to evaluate : 4.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 548 ASN Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 664 ARG Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 405 CYS Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 508 GLU Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 375 ARG Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 640 VAL Chi-restraints excluded: chain F residue 647 ILE Chi-restraints excluded: chain F residue 731 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 375 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 377 optimal weight: 0.9990 chunk 350 optimal weight: 7.9990 chunk 297 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 354 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 HIS ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 728 GLN D 713 HIS ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 HIS E 582 GLN F 110 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.170522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.132583 restraints weight = 207688.374| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 3.59 r_work: 0.3848 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 34866 Z= 0.279 Angle : 0.570 7.382 47027 Z= 0.305 Chirality : 0.040 0.161 5190 Planarity : 0.004 0.062 6075 Dihedral : 4.259 42.439 4655 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.59 % Favored : 94.34 % Rotamer: Outliers : 3.08 % Allowed : 23.39 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.13), residues: 4239 helix: 1.08 (0.12), residues: 1868 sheet: -0.79 (0.24), residues: 473 loop : -1.62 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 309 HIS 0.007 0.001 HIS F 110 PHE 0.020 0.002 PHE E 344 TYR 0.018 0.002 TYR B 253 ARG 0.005 0.001 ARG E 572 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 541 time to evaluate : 4.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.4476 (mtm180) cc_final: 0.3538 (mpt-90) REVERT: A 131 TYR cc_start: 0.7802 (t80) cc_final: 0.7461 (t80) REVERT: A 144 HIS cc_start: 0.2419 (OUTLIER) cc_final: 0.0063 (t-170) REVERT: A 549 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6962 (pp) REVERT: B 8 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7983 (tt) REVERT: B 131 TRP cc_start: 0.6673 (p-90) cc_final: 0.5247 (p-90) REVERT: B 284 ASN cc_start: 0.8101 (m-40) cc_final: 0.7828 (m110) REVERT: B 317 MET cc_start: 0.4906 (mmp) cc_final: 0.4582 (mmp) REVERT: B 372 MET cc_start: 0.7738 (ptm) cc_final: 0.6181 (tmm) REVERT: B 475 ILE cc_start: 0.7359 (mm) cc_final: 0.6832 (tt) REVERT: B 602 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7371 (mtp-110) REVERT: C 101 ARG cc_start: 0.8032 (ptt90) cc_final: 0.7789 (ptm-80) REVERT: C 318 ARG cc_start: 0.5763 (mmp80) cc_final: 0.5011 (mpp80) REVERT: C 332 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7191 (ptt-90) REVERT: C 363 PHE cc_start: 0.7314 (m-80) cc_final: 0.6867 (m-80) REVERT: C 365 MET cc_start: 0.4424 (mpp) cc_final: 0.3827 (ptp) REVERT: C 402 MET cc_start: 0.0111 (OUTLIER) cc_final: -0.0175 (ptt) REVERT: C 458 MET cc_start: 0.2552 (pmm) cc_final: 0.0156 (ptm) REVERT: C 483 MET cc_start: 0.3397 (mmp) cc_final: 0.3163 (mmp) REVERT: C 603 MET cc_start: 0.7606 (tpt) cc_final: 0.7369 (tpt) REVERT: C 641 ARG cc_start: 0.7189 (tpm170) cc_final: 0.6051 (tpp-160) REVERT: C 664 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6917 (ttt-90) REVERT: D 12 MET cc_start: 0.3419 (ppp) cc_final: 0.3137 (mmm) REVERT: D 21 MET cc_start: -0.3725 (OUTLIER) cc_final: -0.5379 (ttt) REVERT: D 204 ARG cc_start: 0.8508 (ptt-90) cc_final: 0.8204 (ptt90) REVERT: D 294 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: D 490 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7146 (mt) REVERT: D 611 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6373 (t80) REVERT: D 654 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7266 (tt0) REVERT: E 7 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7200 (tt) REVERT: E 27 ASP cc_start: 0.7021 (t70) cc_final: 0.6328 (p0) REVERT: E 40 MET cc_start: 0.7494 (mmp) cc_final: 0.6988 (mmp) REVERT: E 337 LEU cc_start: 0.8500 (tp) cc_final: 0.8289 (tp) REVERT: E 376 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7990 (tt) REVERT: E 578 LYS cc_start: 0.6186 (OUTLIER) cc_final: 0.5460 (mmmt) REVERT: E 612 LYS cc_start: 0.5613 (mmtt) cc_final: 0.5215 (mmtp) REVERT: E 628 MET cc_start: 0.6058 (tpp) cc_final: 0.5664 (tpp) REVERT: F 51 MET cc_start: 0.6540 (mmm) cc_final: 0.5582 (mmm) REVERT: F 283 MET cc_start: 0.8050 (mtp) cc_final: 0.7824 (mtp) REVERT: F 365 MET cc_start: 0.1871 (mmp) cc_final: 0.1593 (mmt) REVERT: F 463 ILE cc_start: 0.8002 (mt) cc_final: 0.7798 (mp) REVERT: F 610 PHE cc_start: 0.4265 (OUTLIER) cc_final: 0.3004 (t80) REVERT: F 731 VAL cc_start: 0.5456 (OUTLIER) cc_final: 0.5201 (t) REVERT: F 735 MET cc_start: 0.8150 (ppp) cc_final: 0.7870 (ptm) REVERT: G 1 MET cc_start: 0.5282 (pmm) cc_final: 0.4629 (ptp) outliers start: 117 outliers final: 85 residues processed: 628 average time/residue: 0.8925 time to fit residues: 898.4597 Evaluate side-chains 625 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 525 time to evaluate : 4.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 548 ASN Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 664 ARG Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 405 CYS Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 84 GLN Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 508 GLU Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 578 LYS Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 409 CYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 557 TRP Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 640 VAL Chi-restraints excluded: chain F residue 647 ILE Chi-restraints excluded: chain F residue 731 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 291 optimal weight: 0.8980 chunk 268 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 229 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 299 optimal weight: 4.9990 chunk 420 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 ASN E 310 ASN F 110 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.172795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.134694 restraints weight = 206734.531| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.62 r_work: 0.3853 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34866 Z= 0.164 Angle : 0.519 8.659 47027 Z= 0.272 Chirality : 0.038 0.142 5190 Planarity : 0.004 0.061 6075 Dihedral : 4.047 42.477 4655 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 2.45 % Allowed : 24.23 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.13), residues: 4239 helix: 1.42 (0.12), residues: 1869 sheet: -0.72 (0.23), residues: 508 loop : -1.48 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 309 HIS 0.006 0.001 HIS F 110 PHE 0.028 0.001 PHE E 551 TYR 0.021 0.001 TYR A 48 ARG 0.006 0.000 ARG C 737 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 544 time to evaluate : 4.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.4275 (mtm180) cc_final: 0.3533 (mpt-90) REVERT: A 131 TYR cc_start: 0.7760 (t80) cc_final: 0.7407 (t80) REVERT: A 144 HIS cc_start: 0.2373 (OUTLIER) cc_final: -0.0048 (t-170) REVERT: A 174 ARG cc_start: 0.4879 (tpt170) cc_final: 0.4571 (tpp80) REVERT: A 549 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6982 (pp) REVERT: B 8 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7911 (tt) REVERT: B 131 TRP cc_start: 0.6605 (p-90) cc_final: 0.5196 (p-90) REVERT: B 217 TYR cc_start: 0.8112 (t80) cc_final: 0.7663 (t80) REVERT: B 284 ASN cc_start: 0.8077 (m-40) cc_final: 0.7800 (m110) REVERT: B 317 MET cc_start: 0.4916 (mmp) cc_final: 0.4594 (mmp) REVERT: B 372 MET cc_start: 0.7713 (ptm) cc_final: 0.6092 (tmm) REVERT: B 475 ILE cc_start: 0.7345 (mm) cc_final: 0.6773 (tt) REVERT: B 602 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7465 (mtp-110) REVERT: C 172 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7440 (t) REVERT: C 318 ARG cc_start: 0.5649 (mmp80) cc_final: 0.4978 (mpp80) REVERT: C 332 ARG cc_start: 0.7816 (ttp-170) cc_final: 0.7127 (ptt-90) REVERT: C 363 PHE cc_start: 0.7345 (m-80) cc_final: 0.6958 (m-80) REVERT: C 365 MET cc_start: 0.4405 (mpp) cc_final: 0.3813 (ptp) REVERT: C 402 MET cc_start: 0.0231 (ppp) cc_final: -0.0027 (ptt) REVERT: C 458 MET cc_start: 0.2398 (pmm) cc_final: -0.0078 (ptm) REVERT: C 603 MET cc_start: 0.7528 (tpt) cc_final: 0.7309 (tpt) REVERT: C 641 ARG cc_start: 0.7149 (tpm170) cc_final: 0.6087 (tpp-160) REVERT: C 664 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7039 (ttt-90) REVERT: D 12 MET cc_start: 0.3473 (ppp) cc_final: 0.3198 (mmm) REVERT: D 21 MET cc_start: -0.3792 (OUTLIER) cc_final: -0.5368 (ttt) REVERT: D 204 ARG cc_start: 0.8506 (ptt-90) cc_final: 0.8198 (ptt90) REVERT: D 294 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: D 490 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7134 (mt) REVERT: D 611 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6366 (t80) REVERT: D 654 GLN cc_start: 0.7851 (tp-100) cc_final: 0.7199 (tt0) REVERT: E 7 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7201 (tt) REVERT: E 27 ASP cc_start: 0.6866 (t70) cc_final: 0.6181 (p0) REVERT: E 40 MET cc_start: 0.7421 (mmp) cc_final: 0.7112 (mmp) REVERT: E 376 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7978 (tt) REVERT: E 578 LYS cc_start: 0.6147 (OUTLIER) cc_final: 0.5411 (mmmt) REVERT: E 612 LYS cc_start: 0.5486 (mmtt) cc_final: 0.5041 (mmtp) REVERT: E 628 MET cc_start: 0.6126 (tpp) cc_final: 0.5734 (tpp) REVERT: F 51 MET cc_start: 0.6359 (mmm) cc_final: 0.5183 (mmm) REVERT: F 283 MET cc_start: 0.8045 (mtp) cc_final: 0.7841 (mtp) REVERT: F 365 MET cc_start: 0.1763 (mmp) cc_final: 0.1499 (mmt) REVERT: F 610 PHE cc_start: 0.4274 (OUTLIER) cc_final: 0.3044 (t80) REVERT: F 731 VAL cc_start: 0.5395 (OUTLIER) cc_final: 0.5117 (t) REVERT: F 735 MET cc_start: 0.8100 (ppp) cc_final: 0.7826 (ptm) REVERT: G 1 MET cc_start: 0.5220 (pmm) cc_final: 0.4543 (ptp) REVERT: G 136 PHE cc_start: 0.6622 (m-80) cc_final: 0.6007 (m-10) outliers start: 93 outliers final: 70 residues processed: 612 average time/residue: 0.9173 time to fit residues: 904.7233 Evaluate side-chains 615 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 530 time to evaluate : 4.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 548 ASN Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 664 ARG Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 405 CYS Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 578 LYS Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 409 CYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 640 VAL Chi-restraints excluded: chain F residue 647 ILE Chi-restraints excluded: chain F residue 731 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 356 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 359 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 188 optimal weight: 20.0000 chunk 413 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN C 657 ASN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.171393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.133315 restraints weight = 207820.196| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.63 r_work: 0.3835 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34866 Z= 0.234 Angle : 0.546 8.600 47027 Z= 0.288 Chirality : 0.039 0.225 5190 Planarity : 0.004 0.078 6075 Dihedral : 4.138 43.111 4655 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.29 % Rotamer: Outliers : 2.61 % Allowed : 24.33 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.13), residues: 4239 helix: 1.30 (0.12), residues: 1868 sheet: -0.79 (0.23), residues: 487 loop : -1.56 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 368 HIS 0.038 0.001 HIS F 110 PHE 0.026 0.001 PHE E 551 TYR 0.015 0.001 TYR B 559 ARG 0.009 0.000 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 526 time to evaluate : 4.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.4342 (mtm180) cc_final: 0.3302 (mtt90) REVERT: A 131 TYR cc_start: 0.7795 (t80) cc_final: 0.7434 (t80) REVERT: A 144 HIS cc_start: 0.2333 (OUTLIER) cc_final: -0.0078 (t-170) REVERT: A 549 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7000 (pp) REVERT: B 8 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7956 (tt) REVERT: B 131 TRP cc_start: 0.6638 (p-90) cc_final: 0.5224 (p-90) REVERT: B 284 ASN cc_start: 0.8109 (m-40) cc_final: 0.7781 (m110) REVERT: B 317 MET cc_start: 0.4794 (mmp) cc_final: 0.4260 (mmp) REVERT: B 372 MET cc_start: 0.7715 (ptm) cc_final: 0.6106 (tmm) REVERT: B 602 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7295 (mtp-110) REVERT: C 11 MET cc_start: 0.6143 (mmm) cc_final: 0.5918 (mmm) REVERT: C 172 VAL cc_start: 0.7791 (OUTLIER) cc_final: 0.7471 (t) REVERT: C 283 MET cc_start: 0.7353 (mmm) cc_final: 0.6707 (mmm) REVERT: C 318 ARG cc_start: 0.5722 (mmp80) cc_final: 0.5069 (mpp80) REVERT: C 332 ARG cc_start: 0.7857 (ttp-170) cc_final: 0.7178 (ptt-90) REVERT: C 363 PHE cc_start: 0.7398 (m-80) cc_final: 0.6960 (m-80) REVERT: C 365 MET cc_start: 0.4465 (mpp) cc_final: 0.4155 (ptp) REVERT: C 371 THR cc_start: 0.5899 (m) cc_final: 0.5556 (p) REVERT: C 402 MET cc_start: 0.0160 (OUTLIER) cc_final: -0.0103 (ptt) REVERT: C 603 MET cc_start: 0.7537 (tpt) cc_final: 0.7323 (tpt) REVERT: C 641 ARG cc_start: 0.7161 (tpm170) cc_final: 0.6084 (tpp-160) REVERT: D 12 MET cc_start: 0.3462 (ppp) cc_final: 0.3181 (mmm) REVERT: D 21 MET cc_start: -0.3775 (OUTLIER) cc_final: -0.5358 (ttt) REVERT: D 204 ARG cc_start: 0.8505 (ptt-90) cc_final: 0.8209 (ptt90) REVERT: D 294 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: D 490 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7180 (mt) REVERT: D 611 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6352 (t80) REVERT: D 654 GLN cc_start: 0.7903 (tp-100) cc_final: 0.7228 (tt0) REVERT: D 710 PHE cc_start: 0.8103 (t80) cc_final: 0.7812 (t80) REVERT: E 7 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7251 (tt) REVERT: E 27 ASP cc_start: 0.7021 (t70) cc_final: 0.6334 (p0) REVERT: E 376 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7987 (tt) REVERT: E 578 LYS cc_start: 0.6148 (OUTLIER) cc_final: 0.5406 (mmmt) REVERT: E 612 LYS cc_start: 0.5559 (mmtt) cc_final: 0.5109 (mmtp) REVERT: E 628 MET cc_start: 0.6085 (tpp) cc_final: 0.5705 (tpp) REVERT: F 51 MET cc_start: 0.6299 (mmm) cc_final: 0.5164 (mmm) REVERT: F 354 ILE cc_start: 0.6954 (mp) cc_final: 0.6674 (mt) REVERT: F 365 MET cc_start: 0.1889 (mmp) cc_final: 0.1624 (mmt) REVERT: F 610 PHE cc_start: 0.4325 (OUTLIER) cc_final: 0.3038 (t80) REVERT: F 731 VAL cc_start: 0.5430 (OUTLIER) cc_final: 0.5172 (t) REVERT: F 735 MET cc_start: 0.8095 (ppp) cc_final: 0.7850 (ptm) REVERT: G 1 MET cc_start: 0.5223 (pmm) cc_final: 0.4618 (ptp) outliers start: 99 outliers final: 77 residues processed: 601 average time/residue: 0.9058 time to fit residues: 877.9524 Evaluate side-chains 614 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 522 time to evaluate : 4.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 548 ASN Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 405 CYS Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 578 LYS Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 409 CYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 640 VAL Chi-restraints excluded: chain F residue 647 ILE Chi-restraints excluded: chain F residue 731 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 290 optimal weight: 2.9990 chunk 355 optimal weight: 6.9990 chunk 368 optimal weight: 10.0000 chunk 285 optimal weight: 3.9990 chunk 376 optimal weight: 1.9990 chunk 279 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 419 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.171746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.133522 restraints weight = 207800.526| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.79 r_work: 0.3827 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34866 Z= 0.205 Angle : 0.537 8.982 47027 Z= 0.283 Chirality : 0.039 0.167 5190 Planarity : 0.004 0.070 6075 Dihedral : 4.122 43.739 4655 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.95 % Favored : 94.98 % Rotamer: Outliers : 2.53 % Allowed : 24.31 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 4239 helix: 1.33 (0.12), residues: 1866 sheet: -0.78 (0.23), residues: 487 loop : -1.55 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 309 HIS 0.003 0.001 HIS A 144 PHE 0.025 0.001 PHE E 551 TYR 0.015 0.001 TYR E 436 ARG 0.007 0.000 ARG C 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8478 Ramachandran restraints generated. 4239 Oldfield, 0 Emsley, 4239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 530 time to evaluate : 4.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.4320 (mtm180) cc_final: 0.3549 (mpt-90) REVERT: A 131 TYR cc_start: 0.7833 (t80) cc_final: 0.7438 (t80) REVERT: A 144 HIS cc_start: 0.2361 (OUTLIER) cc_final: -0.0037 (t-170) REVERT: A 335 LEU cc_start: 0.8188 (tp) cc_final: 0.7899 (tp) REVERT: A 549 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7005 (pp) REVERT: B 8 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7924 (tt) REVERT: B 131 TRP cc_start: 0.6634 (p-90) cc_final: 0.5219 (p-90) REVERT: B 217 TYR cc_start: 0.8089 (t80) cc_final: 0.7533 (t80) REVERT: B 284 ASN cc_start: 0.8137 (m-40) cc_final: 0.7804 (m110) REVERT: B 317 MET cc_start: 0.4946 (mmp) cc_final: 0.4621 (mmp) REVERT: B 372 MET cc_start: 0.7689 (ptm) cc_final: 0.6116 (tmm) REVERT: B 602 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7409 (mtp-110) REVERT: C 11 MET cc_start: 0.6014 (mmm) cc_final: 0.5788 (mmm) REVERT: C 172 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7532 (t) REVERT: C 318 ARG cc_start: 0.5759 (mmp80) cc_final: 0.5085 (mpp80) REVERT: C 332 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7128 (ptt-90) REVERT: C 363 PHE cc_start: 0.7466 (m-80) cc_final: 0.7042 (m-80) REVERT: C 365 MET cc_start: 0.4478 (mpp) cc_final: 0.4157 (ptp) REVERT: C 371 THR cc_start: 0.5842 (m) cc_final: 0.5503 (p) REVERT: C 402 MET cc_start: 0.0334 (OUTLIER) cc_final: 0.0115 (ptt) REVERT: C 603 MET cc_start: 0.7583 (tpt) cc_final: 0.7374 (tpt) REVERT: C 641 ARG cc_start: 0.7154 (tpm170) cc_final: 0.6079 (tpp-160) REVERT: D 12 MET cc_start: 0.3499 (ppp) cc_final: 0.3196 (mmm) REVERT: D 21 MET cc_start: -0.3717 (OUTLIER) cc_final: -0.5269 (ttt) REVERT: D 204 ARG cc_start: 0.8555 (ptt-90) cc_final: 0.8258 (ptt90) REVERT: D 294 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: D 490 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.7156 (mt) REVERT: D 611 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6354 (t80) REVERT: D 654 GLN cc_start: 0.7927 (tp-100) cc_final: 0.7243 (tt0) REVERT: E 7 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7275 (tt) REVERT: E 27 ASP cc_start: 0.7019 (t70) cc_final: 0.6297 (p0) REVERT: E 130 ASP cc_start: 0.8535 (t0) cc_final: 0.8332 (t0) REVERT: E 376 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7995 (tt) REVERT: E 578 LYS cc_start: 0.6123 (OUTLIER) cc_final: 0.5339 (mmmt) REVERT: E 612 LYS cc_start: 0.5501 (mmtt) cc_final: 0.5066 (mmtp) REVERT: E 628 MET cc_start: 0.6128 (tpp) cc_final: 0.5750 (tpp) REVERT: F 51 MET cc_start: 0.6258 (mmm) cc_final: 0.5086 (mmm) REVERT: F 365 MET cc_start: 0.1692 (mmp) cc_final: 0.1464 (mmt) REVERT: F 610 PHE cc_start: 0.4259 (OUTLIER) cc_final: 0.2918 (t80) REVERT: F 731 VAL cc_start: 0.5474 (OUTLIER) cc_final: 0.5225 (t) REVERT: F 735 MET cc_start: 0.8042 (ppp) cc_final: 0.7811 (ptm) REVERT: G 1 MET cc_start: 0.5134 (pmm) cc_final: 0.4527 (ptp) outliers start: 96 outliers final: 74 residues processed: 603 average time/residue: 0.9003 time to fit residues: 876.4754 Evaluate side-chains 611 residues out of total 3793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 522 time to evaluate : 4.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 548 ASN Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 405 CYS Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 84 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 578 LYS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 409 CYS Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 610 PHE Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 640 VAL Chi-restraints excluded: chain F residue 647 ILE Chi-restraints excluded: chain F residue 731 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 329 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 351 optimal weight: 0.9980 chunk 334 optimal weight: 0.9990 chunk 353 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 323 optimal weight: 2.9990 chunk 395 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.172580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.134629 restraints weight = 206881.060| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 3.62 r_work: 0.3854 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34866 Z= 0.175 Angle : 0.521 9.212 47027 Z= 0.272 Chirality : 0.039 0.274 5190 Planarity : 0.004 0.067 6075 Dihedral : 4.010 44.112 4655 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.69 % Favored : 95.23 % Rotamer: Outliers : 2.37 % Allowed : 24.55 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.13), residues: 4239 helix: 1.47 (0.12), residues: 1869 sheet: -0.73 (0.24), residues: 487 loop : -1.48 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 309 HIS 0.009 0.001 HIS F 110 PHE 0.030 0.001 PHE E 551 TYR 0.013 0.001 TYR E 436 ARG 0.007 0.000 ARG C 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32013.78 seconds wall clock time: 546 minutes 19.55 seconds (32779.55 seconds total)