Starting phenix.real_space_refine on Sat Sep 28 06:56:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmr_19368/09_2024/8rmr_19368.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmr_19368/09_2024/8rmr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmr_19368/09_2024/8rmr_19368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmr_19368/09_2024/8rmr_19368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmr_19368/09_2024/8rmr_19368.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmr_19368/09_2024/8rmr_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-5461/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: 23.29, per 1000 atoms: 0.34 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: 13.15 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: 4.63 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: 25.66 Time building geometry restraints manager: 16.36 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: 7.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.870 Extract box with map and model: 1.970 Check model and map are aligned: 0.400 Set scattering table: 0.500 Process input model: 111.470 Find NCS groups from input model: 1.920 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.780 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 10 poor density : 910 time to evaluate : 4.002 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: 1.1138 time to fit residues: 1551.9328 Evaluate side-chains 633 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 630 time to evaluate : 3.961 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 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 fitting. rotamer outliers: 100 poor density : 631 time to evaluate : 3.999 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: 0.4074 (mtm180) cc_final: 0.3817 (mpt-90) REVERT: A 441 MET cc_start: 0.8065 (ttm) cc_final: 0.7775 (ttp) REVERT: B 134 ASN cc_start: 0.7446 (t0) cc_final: 0.7196 (t0) REVERT: B 317 MET cc_start: 0.4415 (mmp) cc_final: 0.4001 (mmp) REVERT: B 372 MET cc_start: 0.7489 (ptm) cc_final: 0.6383 (tmm) REVERT: B 522 ASP cc_start: 0.7886 (m-30) cc_final: 0.7180 (m-30) REVERT: C 318 ARG cc_start: 0.5452 (mmp80) cc_final: 0.4636 (mpp80) REVERT: C 332 ARG cc_start: 0.7662 (ttp-170) cc_final: 0.7149 (ptt-90) REVERT: C 365 MET cc_start: 0.4253 (mpp) cc_final: 0.3764 (ptp) REVERT: C 402 MET cc_start: -0.0376 (OUTLIER) cc_final: -0.0636 (ptt) REVERT: C 458 MET cc_start: 0.1497 (pmm) cc_final: -0.0489 (ptm) REVERT: C 536 MET cc_start: 0.2827 (mmm) cc_final: 0.1991 (ttm) REVERT: C 556 ASN cc_start: 0.6268 (OUTLIER) cc_final: 0.6036 (m110) REVERT: C 603 MET cc_start: 0.7009 (tpt) cc_final: 0.6684 (tpt) REVERT: C 739 ARG cc_start: 0.5637 (mtt-85) cc_final: 0.4593 (ttt90) REVERT: D 12 MET cc_start: 0.3079 (ppp) cc_final: 0.2813 (mmm) REVERT: D 368 TRP cc_start: 0.7597 (m100) cc_final: 0.7373 (m100) REVERT: D 393 TYR cc_start: 0.6719 (t80) cc_final: 0.6473 (t80) REVERT: D 477 MET cc_start: 0.5777 (mpp) cc_final: 0.5387 (mmm) REVERT: E 7 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7270 (tt) REVERT: E 27 ASP cc_start: 0.6885 (t70) cc_final: 0.5952 (p0) REVERT: E 92 MET cc_start: 0.7056 (ttm) cc_final: 0.6772 (mmm) REVERT: E 317 MET cc_start: 0.6153 (tpp) cc_final: 0.5448 (ttp) REVERT: E 376 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8044 (tt) REVERT: E 628 MET cc_start: 0.5935 (tpp) cc_final: 0.5609 (tpp) REVERT: F 51 MET cc_start: 0.6333 (mmm) cc_final: 0.5320 (mmm) REVERT: F 283 MET cc_start: 0.7862 (mtp) cc_final: 0.7610 (mtp) REVERT: F 365 MET cc_start: 0.2246 (mmp) cc_final: 0.1886 (mmt) REVERT: F 406 GLN cc_start: 0.7399 (mm110) cc_final: 0.7174 (mm110) REVERT: F 473 MET cc_start: 0.3241 (tpp) cc_final: 0.2960 (tpp) REVERT: F 610 PHE cc_start: 0.4283 (OUTLIER) cc_final: 0.3259 (t80) REVERT: F 735 MET cc_start: 0.8241 (ppp) cc_final: 0.7749 (ptm) REVERT: G 1 MET cc_start: 0.5662 (pmm) cc_final: 0.5120 (ptp) outliers start: 100 outliers final: 58 residues processed: 703 average time/residue: 1.0160 time to fit residues: 1128.0012 Evaluate side-chains 621 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 558 time to evaluate : 3.980 ------------------------------------------------------------------------------- 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 556 ASN 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 213 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 319 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 384 optimal weight: 9.9990 chunk 415 optimal weight: 5.9990 chunk 342 optimal weight: 3.9990 chunk 381 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 308 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 340 GLN E 476 ASN E 582 GLN F 100 ASN F 110 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 34866 Z= 0.259 Angle : 0.565 9.291 47027 Z= 0.301 Chirality : 0.040 0.181 5190 Planarity : 0.005 0.075 6075 Dihedral : 4.135 39.530 4655 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 2.45 % Allowed : 23.10 % 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: -0.42 (0.13), residues: 4239 helix: 1.05 (0.12), residues: 1857 sheet: -0.64 (0.23), residues: 503 loop : -1.56 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 309 HIS 0.007 0.001 HIS D 452 PHE 0.014 0.001 PHE A 646 TYR 0.014 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 676 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 583 time to evaluate : 4.006 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 144 HIS cc_start: 0.2199 (OUTLIER) cc_final: -0.0645 (t-170) REVERT: A 441 MET cc_start: 0.8026 (ttm) cc_final: 0.7762 (ttp) REVERT: B 171 MET cc_start: 0.4735 (mmm) cc_final: 0.4260 (mmm) REVERT: B 317 MET cc_start: 0.4535 (mmp) cc_final: 0.4289 (mmp) REVERT: B 372 MET cc_start: 0.7466 (ptm) cc_final: 0.6362 (tmm) REVERT: B 602 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7119 (mtp-110) REVERT: C 318 ARG cc_start: 0.5403 (mmp80) cc_final: 0.4657 (mpp80) REVERT: C 332 ARG cc_start: 0.7633 (ttp-170) cc_final: 0.7114 (ptt-90) REVERT: C 363 PHE cc_start: 0.6570 (m-80) cc_final: 0.6256 (m-80) REVERT: C 365 MET cc_start: 0.4434 (mpp) cc_final: 0.4020 (ptp) REVERT: C 402 MET cc_start: -0.0296 (ppp) cc_final: -0.0674 (ttp) REVERT: C 458 MET cc_start: 0.1669 (pmm) cc_final: -0.0370 (ptm) REVERT: C 536 MET cc_start: 0.2878 (mmm) cc_final: 0.1974 (ttm) REVERT: C 603 MET cc_start: 0.7135 (tpt) cc_final: 0.6832 (tpt) REVERT: C 641 ARG cc_start: 0.7073 (tpm170) cc_final: 0.6003 (tpp-160) REVERT: C 664 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7008 (ttt-90) REVERT: C 739 ARG cc_start: 0.5798 (mtt-85) cc_final: 0.4417 (ttt180) REVERT: C 756 MET cc_start: 0.4052 (mtp) cc_final: 0.3681 (mmm) REVERT: D 12 MET cc_start: 0.3198 (ppp) cc_final: 0.2914 (mmm) REVERT: D 490 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.6953 (mt) REVERT: D 611 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6320 (t80) REVERT: D 654 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7295 (tt0) REVERT: E 27 ASP cc_start: 0.7117 (t70) cc_final: 0.6271 (p0) REVERT: E 266 LEU cc_start: 0.8781 (mt) cc_final: 0.8571 (mm) REVERT: E 317 MET cc_start: 0.6155 (tpp) cc_final: 0.5492 (ttp) REVERT: E 376 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7939 (tt) REVERT: E 628 MET cc_start: 0.6128 (tpp) cc_final: 0.5644 (tpp) REVERT: F 51 MET cc_start: 0.6278 (mmm) cc_final: 0.5293 (mmm) REVERT: F 257 GLN cc_start: 0.8514 (tt0) cc_final: 0.8148 (tm-30) REVERT: F 365 MET cc_start: 0.2217 (mmp) cc_final: 0.1860 (mmt) REVERT: F 610 PHE cc_start: 0.4138 (OUTLIER) cc_final: 0.3055 (t80) REVERT: F 731 VAL cc_start: 0.5618 (OUTLIER) cc_final: 0.5389 (t) REVERT: F 735 MET cc_start: 0.8271 (ppp) cc_final: 0.7828 (ptm) REVERT: G 1 MET cc_start: 0.5640 (pmm) cc_final: 0.5058 (ptp) outliers start: 93 outliers final: 61 residues processed: 649 average time/residue: 0.9397 time to fit residues: 974.9634 Evaluate side-chains 624 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 555 time to evaluate : 5.191 ------------------------------------------------------------------------------- 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 151 THR 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 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 434 THR 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 692 CYS Chi-restraints excluded: chain B residue 702 SER 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 344 VAL Chi-restraints excluded: chain C residue 613 VAL 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 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 487 SER Chi-restraints excluded: chain D residue 490 ILE 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 32 HIS Chi-restraints excluded: chain E residue 128 THR 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 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 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 400 VAL Chi-restraints excluded: chain F residue 553 ILE 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 731 VAL Chi-restraints excluded: chain F residue 740 ASP 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 380 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 258 optimal weight: 1.9990 chunk 386 optimal weight: 4.9990 chunk 408 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 ASN C 265 ASN D 146 HIS D 340 GLN D 703 ASN E 124 GLN E 582 GLN F 100 ASN F 110 HIS ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34866 Z= 0.280 Angle : 0.576 7.877 47027 Z= 0.309 Chirality : 0.040 0.151 5190 Planarity : 0.005 0.061 6075 Dihedral : 4.306 41.219 4655 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.85 % Favored : 94.08 % Rotamer: Outliers : 3.43 % Allowed : 22.96 % Favored : 73.61 % 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: -0.64 (0.13), residues: 4239 helix: 0.90 (0.12), residues: 1846 sheet: -0.80 (0.23), residues: 503 loop : -1.68 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 309 HIS 0.006 0.001 HIS D 452 PHE 0.021 0.002 PHE D 710 TYR 0.015 0.002 TYR B 559 ARG 0.009 0.001 ARG E 560 *********************** 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 687 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 557 time to evaluate : 4.042 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: A 144 HIS cc_start: 0.2140 (OUTLIER) cc_final: -0.0646 (t-170) REVERT: A 151 THR cc_start: 0.7057 (OUTLIER) cc_final: 0.6799 (m) REVERT: A 441 MET cc_start: 0.7963 (ttm) cc_final: 0.7706 (ttp) REVERT: A 549 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7185 (pp) REVERT: B 8 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7932 (tt) REVERT: B 317 MET cc_start: 0.4496 (mmp) cc_final: 0.4016 (mmm) REVERT: B 372 MET cc_start: 0.7523 (ptm) cc_final: 0.6343 (tmm) REVERT: C 318 ARG cc_start: 0.5499 (mmp80) cc_final: 0.4707 (mpp80) REVERT: C 332 ARG cc_start: 0.7624 (ttp-170) cc_final: 0.7122 (ptt-90) REVERT: C 363 PHE cc_start: 0.6774 (m-80) cc_final: 0.6409 (m-80) REVERT: C 365 MET cc_start: 0.4528 (mpp) cc_final: 0.3842 (ptp) REVERT: C 402 MET cc_start: -0.0299 (OUTLIER) cc_final: -0.0596 (ptt) REVERT: C 458 MET cc_start: 0.2200 (pmm) cc_final: -0.0083 (ptm) REVERT: C 547 VAL cc_start: 0.7010 (t) cc_final: 0.6709 (p) REVERT: C 603 MET cc_start: 0.7197 (tpt) cc_final: 0.6908 (tpt) REVERT: C 641 ARG cc_start: 0.7042 (tpm170) cc_final: 0.5966 (tpp-160) REVERT: C 664 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6996 (ttt-90) REVERT: D 12 MET cc_start: 0.3116 (ppp) cc_final: 0.2818 (mmm) REVERT: D 21 MET cc_start: -0.3958 (OUTLIER) cc_final: -0.5751 (ttt) REVERT: D 294 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: D 490 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6952 (mt) REVERT: D 611 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6380 (t80) REVERT: D 654 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7368 (tt0) REVERT: E 7 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7498 (tt) REVERT: E 27 ASP cc_start: 0.7180 (t70) cc_final: 0.6318 (p0) REVERT: E 92 MET cc_start: 0.7208 (ttm) cc_final: 0.6945 (mmm) REVERT: E 266 LEU cc_start: 0.8861 (mt) cc_final: 0.8656 (mm) REVERT: E 317 MET cc_start: 0.6166 (tpp) cc_final: 0.5628 (ttp) REVERT: E 376 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8018 (tt) REVERT: E 628 MET cc_start: 0.6309 (tpp) cc_final: 0.5781 (tpp) REVERT: F 51 MET cc_start: 0.6231 (mmm) cc_final: 0.5113 (mmm) REVERT: F 365 MET cc_start: 0.2319 (mmp) cc_final: 0.1783 (mmp) REVERT: F 610 PHE cc_start: 0.4137 (OUTLIER) cc_final: 0.2992 (t80) REVERT: F 731 VAL cc_start: 0.5656 (OUTLIER) cc_final: 0.5415 (t) REVERT: F 735 MET cc_start: 0.8201 (ppp) cc_final: 0.7805 (ptm) REVERT: G 1 MET cc_start: 0.5552 (pmm) cc_final: 0.4956 (ptp) REVERT: G 136 PHE cc_start: 0.6962 (m-80) cc_final: 0.6424 (m-10) outliers start: 130 outliers final: 92 residues processed: 658 average time/residue: 0.9393 time to fit residues: 998.6643 Evaluate side-chains 638 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 532 time to evaluate : 4.093 ------------------------------------------------------------------------------- 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 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 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 223 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 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 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 750 ILE Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 94 LEU 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 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 733 LEU 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 155 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 348 ILE Chi-restraints excluded: chain D residue 363 THR 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 528 THR 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 644 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 70 ASP 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 285 VAL 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 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 491 GLU Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 572 ARG Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain F residue 96 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 393 SER Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 557 TRP 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 731 VAL Chi-restraints excluded: chain F residue 740 ASP 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 340 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 304 optimal weight: 0.4980 chunk 168 optimal weight: 3.9990 chunk 348 optimal weight: 0.3980 chunk 282 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 366 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN C 265 ASN D 146 HIS E 124 GLN E 456 HIS E 582 GLN F 110 HIS F 406 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34866 Z= 0.178 Angle : 0.518 5.736 47027 Z= 0.273 Chirality : 0.038 0.145 5190 Planarity : 0.004 0.067 6075 Dihedral : 4.095 41.502 4655 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 2.74 % Allowed : 23.75 % Favored : 73.50 % 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: -0.28 (0.13), residues: 4239 helix: 1.26 (0.12), residues: 1861 sheet: -0.72 (0.23), residues: 508 loop : -1.56 (0.14), residues: 1870 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 0.010 0.001 PHE B 505 TYR 0.012 0.001 TYR B 217 ARG 0.003 0.000 ARG F 124 *********************** 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 654 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 550 time to evaluate : 4.083 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: A 144 HIS cc_start: 0.2280 (OUTLIER) cc_final: -0.0559 (t-170) REVERT: A 441 MET cc_start: 0.7981 (ttm) cc_final: 0.7715 (ttp) REVERT: A 549 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7199 (pp) REVERT: B 8 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8062 (tt) REVERT: B 317 MET cc_start: 0.4471 (mmp) cc_final: 0.4064 (mmm) REVERT: B 372 MET cc_start: 0.7393 (ptm) cc_final: 0.6283 (tmm) REVERT: B 517 ILE cc_start: 0.8476 (mp) cc_final: 0.8252 (mt) REVERT: C 318 ARG cc_start: 0.5480 (mmp80) cc_final: 0.4775 (mpp80) REVERT: C 332 ARG cc_start: 0.7670 (ttp-170) cc_final: 0.7099 (ptt-90) REVERT: C 363 PHE cc_start: 0.6824 (m-80) cc_final: 0.6495 (m-80) REVERT: C 365 MET cc_start: 0.4535 (mpp) cc_final: 0.3886 (ptp) REVERT: C 402 MET cc_start: -0.0148 (ppp) cc_final: -0.0558 (ttp) REVERT: C 458 MET cc_start: 0.2263 (pmm) cc_final: -0.0045 (ptm) REVERT: C 603 MET cc_start: 0.7098 (tpt) cc_final: 0.6834 (tpt) REVERT: C 641 ARG cc_start: 0.7007 (tpm170) cc_final: 0.5922 (tpp-160) REVERT: C 664 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6977 (ttt-90) REVERT: D 12 MET cc_start: 0.3125 (ppp) cc_final: 0.2863 (mmm) REVERT: D 21 MET cc_start: -0.3835 (OUTLIER) cc_final: -0.5595 (ttt) REVERT: D 294 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: D 490 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.7050 (mt) REVERT: D 611 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6360 (t80) REVERT: D 654 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7307 (tt0) REVERT: E 27 ASP cc_start: 0.7161 (t70) cc_final: 0.6322 (p0) REVERT: E 376 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8089 (tt) REVERT: E 578 LYS cc_start: 0.6317 (OUTLIER) cc_final: 0.5650 (mmmt) REVERT: E 612 LYS cc_start: 0.5497 (mmtt) cc_final: 0.5171 (mmtp) REVERT: E 628 MET cc_start: 0.6304 (tpp) cc_final: 0.5777 (tpp) REVERT: F 51 MET cc_start: 0.6092 (mmm) cc_final: 0.5194 (mmm) REVERT: F 283 MET cc_start: 0.7480 (mtp) cc_final: 0.7254 (mpp) REVERT: F 365 MET cc_start: 0.2324 (mmp) cc_final: 0.1985 (mmt) REVERT: F 536 MET cc_start: 0.5938 (mmp) cc_final: 0.5684 (mmp) REVERT: F 610 PHE cc_start: 0.4234 (OUTLIER) cc_final: 0.3146 (t80) REVERT: F 731 VAL cc_start: 0.5572 (OUTLIER) cc_final: 0.5273 (t) REVERT: F 735 MET cc_start: 0.8186 (ppp) cc_final: 0.7809 (ptm) REVERT: G 1 MET cc_start: 0.5532 (pmm) cc_final: 0.4926 (ptp) REVERT: G 136 PHE cc_start: 0.6860 (m-80) cc_final: 0.6221 (m-10) outliers start: 104 outliers final: 69 residues processed: 624 average time/residue: 0.9083 time to fit residues: 915.8298 Evaluate side-chains 617 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 536 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 223 THR Chi-restraints excluded: chain B residue 261 SER 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 702 SER Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 94 LEU 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 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 211 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 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 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 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 572 ARG 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 236 GLN Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 393 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 137 optimal weight: 9.9990 chunk 368 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 100 optimal weight: 0.0370 chunk 409 optimal weight: 0.9990 chunk 339 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 HIS D 340 GLN D 713 HIS E 84 GLN E 124 GLN E 306 ASN E 456 HIS E 582 GLN F 110 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34866 Z= 0.226 Angle : 0.541 7.224 47027 Z= 0.286 Chirality : 0.039 0.148 5190 Planarity : 0.004 0.067 6075 Dihedral : 4.170 42.469 4655 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.50 % Favored : 94.43 % Rotamer: Outliers : 3.14 % Allowed : 23.89 % Favored : 72.98 % 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: -0.35 (0.13), residues: 4239 helix: 1.21 (0.12), residues: 1864 sheet: -0.81 (0.24), residues: 479 loop : -1.57 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 309 HIS 0.007 0.001 HIS F 110 PHE 0.024 0.001 PHE E 551 TYR 0.016 0.001 TYR A 48 ARG 0.008 0.000 ARG F 136 *********************** 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 645 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 526 time to evaluate : 4.087 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 144 HIS cc_start: 0.2251 (OUTLIER) cc_final: -0.0470 (t-170) REVERT: A 441 MET cc_start: 0.7990 (ttm) cc_final: 0.7698 (ttp) REVERT: A 549 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7188 (pp) REVERT: B 8 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7914 (tt) REVERT: B 317 MET cc_start: 0.4384 (mmp) cc_final: 0.4174 (mmp) REVERT: B 372 MET cc_start: 0.7300 (ptm) cc_final: 0.6223 (tmm) REVERT: B 517 ILE cc_start: 0.8473 (mp) cc_final: 0.8229 (mt) REVERT: B 602 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7220 (mtp-110) REVERT: C 11 MET cc_start: 0.4859 (mmt) cc_final: 0.4571 (tpt) REVERT: C 172 VAL cc_start: 0.7282 (OUTLIER) cc_final: 0.7079 (t) REVERT: C 318 ARG cc_start: 0.5500 (mmp80) cc_final: 0.4811 (mpp80) REVERT: C 332 ARG cc_start: 0.7673 (ttp-170) cc_final: 0.7122 (ptt-90) REVERT: C 363 PHE cc_start: 0.6886 (m-80) cc_final: 0.6543 (m-80) REVERT: C 365 MET cc_start: 0.4575 (mpp) cc_final: 0.3923 (ptp) REVERT: C 402 MET cc_start: 0.0027 (ppp) cc_final: -0.0386 (ptt) REVERT: C 458 MET cc_start: 0.2404 (pmm) cc_final: 0.0082 (ptm) REVERT: C 603 MET cc_start: 0.7119 (tpt) cc_final: 0.6860 (tpt) REVERT: C 641 ARG cc_start: 0.7058 (tpm170) cc_final: 0.5967 (tpp-160) REVERT: C 664 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6999 (ttt-90) REVERT: D 21 MET cc_start: -0.3914 (OUTLIER) cc_final: -0.5601 (ttt) REVERT: D 490 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7071 (mt) REVERT: D 611 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6356 (t80) REVERT: D 654 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7315 (tt0) REVERT: E 7 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7511 (tt) REVERT: E 27 ASP cc_start: 0.7191 (t70) cc_final: 0.6350 (p0) REVERT: E 376 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8096 (tt) REVERT: E 578 LYS cc_start: 0.6293 (OUTLIER) cc_final: 0.5538 (mmmt) REVERT: E 612 LYS cc_start: 0.5523 (mmtt) cc_final: 0.5218 (mmtp) REVERT: E 628 MET cc_start: 0.6278 (tpp) cc_final: 0.5834 (tpp) REVERT: F 51 MET cc_start: 0.6093 (mmm) cc_final: 0.5186 (mmm) REVERT: F 283 MET cc_start: 0.7507 (mtp) cc_final: 0.7262 (mpp) REVERT: F 365 MET cc_start: 0.2335 (mmp) cc_final: 0.2002 (mmt) REVERT: F 536 MET cc_start: 0.5769 (mmp) cc_final: 0.5514 (mmp) REVERT: F 610 PHE cc_start: 0.4229 (OUTLIER) cc_final: 0.3064 (t80) REVERT: F 731 VAL cc_start: 0.5520 (OUTLIER) cc_final: 0.5225 (t) REVERT: F 735 MET cc_start: 0.8199 (ppp) cc_final: 0.7869 (ptm) REVERT: G 1 MET cc_start: 0.5512 (pmm) cc_final: 0.4917 (ptp) outliers start: 119 outliers final: 85 residues processed: 616 average time/residue: 0.9362 time to fit residues: 933.9507 Evaluate side-chains 614 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 515 time to evaluate : 4.075 ------------------------------------------------------------------------------- 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 211 MET 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 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 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 172 VAL 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 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 733 LEU 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 211 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 363 THR 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 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 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 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 572 ARG 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 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 393 SER 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 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 688 SER 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 394 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 chunk 231 optimal weight: 8.9990 chunk 344 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 chunk 407 optimal weight: 2.9990 chunk 255 optimal weight: 0.6980 chunk 248 optimal weight: 0.6980 chunk 188 optimal weight: 8.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN D 146 HIS D 340 GLN D 713 HIS ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 HIS E 582 GLN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34866 Z= 0.246 Angle : 0.549 7.491 47027 Z= 0.291 Chirality : 0.039 0.156 5190 Planarity : 0.004 0.076 6075 Dihedral : 4.259 43.493 4655 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.29 % Rotamer: Outliers : 3.43 % Allowed : 23.57 % Favored : 73.00 % 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: -0.48 (0.13), residues: 4239 helix: 1.12 (0.12), residues: 1865 sheet: -0.89 (0.24), residues: 478 loop : -1.67 (0.14), residues: 1896 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 0.027 0.001 PHE E 551 TYR 0.022 0.002 TYR B 217 ARG 0.007 0.000 ARG C 101 *********************** 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 fitting. rotamer outliers: 130 poor density : 528 time to evaluate : 4.011 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: A 144 HIS cc_start: 0.2144 (OUTLIER) cc_final: -0.0681 (t-170) REVERT: A 441 MET cc_start: 0.8007 (ttm) cc_final: 0.7714 (ttp) REVERT: A 549 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7230 (pp) REVERT: B 8 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7937 (tt) REVERT: B 217 TYR cc_start: 0.6611 (t80) cc_final: 0.6330 (t80) REVERT: B 317 MET cc_start: 0.4449 (mmp) cc_final: 0.4221 (mmp) REVERT: B 372 MET cc_start: 0.7320 (ptm) cc_final: 0.6226 (tmm) REVERT: B 517 ILE cc_start: 0.8464 (mp) cc_final: 0.8239 (mt) REVERT: B 602 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7315 (mtp-110) REVERT: C 11 MET cc_start: 0.4851 (mmt) cc_final: 0.4570 (tpt) REVERT: C 172 VAL cc_start: 0.7311 (OUTLIER) cc_final: 0.7088 (t) REVERT: C 318 ARG cc_start: 0.5498 (mmp80) cc_final: 0.4855 (mpp80) REVERT: C 332 ARG cc_start: 0.7689 (ttp-170) cc_final: 0.7098 (ptt-90) REVERT: C 357 HIS cc_start: -0.1028 (OUTLIER) cc_final: -0.2016 (m90) REVERT: C 363 PHE cc_start: 0.6927 (m-80) cc_final: 0.6538 (m-80) REVERT: C 365 MET cc_start: 0.4775 (mpp) cc_final: 0.4132 (ptp) REVERT: C 483 MET cc_start: 0.2983 (mmp) cc_final: 0.2746 (mmp) REVERT: C 603 MET cc_start: 0.7199 (tpt) cc_final: 0.6955 (tpt) REVERT: C 641 ARG cc_start: 0.7090 (tpm170) cc_final: 0.6015 (tpp-160) REVERT: C 664 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6853 (ttt-90) REVERT: D 21 MET cc_start: -0.3870 (OUTLIER) cc_final: -0.5580 (ttt) REVERT: D 490 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.7063 (mt) REVERT: D 611 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6390 (t80) REVERT: D 654 GLN cc_start: 0.8122 (tp-100) cc_final: 0.7368 (tt0) REVERT: E 1 MET cc_start: 0.5328 (tpt) cc_final: 0.5077 (tpt) REVERT: E 7 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7478 (tt) REVERT: E 27 ASP cc_start: 0.7204 (t70) cc_final: 0.6342 (p0) REVERT: E 267 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: E 317 MET cc_start: 0.5742 (ttm) cc_final: 0.5405 (ttm) REVERT: E 376 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8108 (tt) REVERT: E 578 LYS cc_start: 0.6339 (OUTLIER) cc_final: 0.5550 (mmmt) REVERT: E 612 LYS cc_start: 0.5607 (mmtt) cc_final: 0.5279 (mmtp) REVERT: E 628 MET cc_start: 0.6323 (tpp) cc_final: 0.5911 (tpp) REVERT: F 51 MET cc_start: 0.6138 (mmm) cc_final: 0.5191 (mmm) REVERT: F 257 GLN cc_start: 0.8463 (tt0) cc_final: 0.8129 (tm-30) REVERT: F 283 MET cc_start: 0.7523 (mtp) cc_final: 0.7254 (mpp) REVERT: F 365 MET cc_start: 0.2352 (mmp) cc_final: 0.2004 (mmt) REVERT: F 610 PHE cc_start: 0.4235 (OUTLIER) cc_final: 0.3014 (t80) REVERT: F 731 VAL cc_start: 0.5495 (OUTLIER) cc_final: 0.5237 (t) REVERT: F 735 MET cc_start: 0.8128 (ppp) cc_final: 0.7842 (ptm) REVERT: G 1 MET cc_start: 0.5484 (pmm) cc_final: 0.4943 (ptp) REVERT: G 142 LEU cc_start: 0.8191 (tt) cc_final: 0.7722 (mm) outliers start: 130 outliers final: 97 residues processed: 623 average time/residue: 0.9151 time to fit residues: 927.1022 Evaluate side-chains 630 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 517 time to evaluate : 4.037 ------------------------------------------------------------------------------- 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 211 MET Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 451 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 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 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 120 GLU 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 357 HIS 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 613 VAL 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 733 LEU 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 291 SER Chi-restraints excluded: chain D residue 323 ILE 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 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 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 42 THR 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 267 GLU 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 309 TRP 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 572 ARG 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 115 TYR 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 373 ILE Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 393 SER 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 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 688 SER 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 252 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 chunk 201 optimal weight: 0.0370 chunk 37 optimal weight: 0.9990 chunk 320 optimal weight: 3.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 HIS D 340 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 HIS ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34866 Z= 0.169 Angle : 0.517 8.209 47027 Z= 0.271 Chirality : 0.038 0.161 5190 Planarity : 0.004 0.067 6075 Dihedral : 4.083 43.467 4655 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.79 % Favored : 95.14 % Rotamer: Outliers : 2.72 % Allowed : 24.36 % Favored : 72.92 % 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: -0.20 (0.13), residues: 4239 helix: 1.38 (0.12), residues: 1867 sheet: -0.76 (0.24), residues: 487 loop : -1.54 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 309 HIS 0.007 0.001 HIS F 110 PHE 0.025 0.001 PHE D 710 TYR 0.015 0.001 TYR B 217 ARG 0.007 0.000 ARG F 136 *********************** 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 640 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 537 time to evaluate : 4.747 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: A 144 HIS cc_start: 0.2354 (OUTLIER) cc_final: -0.0414 (t-170) REVERT: A 335 LEU cc_start: 0.6958 (tp) cc_final: 0.6621 (tp) REVERT: A 441 MET cc_start: 0.7989 (ttm) cc_final: 0.7674 (ttp) REVERT: A 549 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7290 (pp) REVERT: B 8 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7883 (tt) REVERT: B 372 MET cc_start: 0.7314 (ptm) cc_final: 0.6222 (tmm) REVERT: B 517 ILE cc_start: 0.8483 (mp) cc_final: 0.8256 (mt) REVERT: C 172 VAL cc_start: 0.7282 (OUTLIER) cc_final: 0.7056 (t) REVERT: C 318 ARG cc_start: 0.5407 (mmp80) cc_final: 0.4828 (mpp80) REVERT: C 363 PHE cc_start: 0.6971 (m-80) cc_final: 0.6566 (m-80) REVERT: C 365 MET cc_start: 0.4790 (mpp) cc_final: 0.4168 (ptp) REVERT: C 483 MET cc_start: 0.2695 (mmp) cc_final: 0.2484 (mmp) REVERT: C 603 MET cc_start: 0.7101 (tpt) cc_final: 0.6856 (tpt) REVERT: C 641 ARG cc_start: 0.7032 (tpm170) cc_final: 0.5994 (tpp-160) REVERT: C 664 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6951 (ttt-90) REVERT: D 21 MET cc_start: -0.3859 (OUTLIER) cc_final: -0.5536 (ttt) REVERT: D 490 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7039 (mt) REVERT: D 611 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6403 (t80) REVERT: D 654 GLN cc_start: 0.8065 (tp-100) cc_final: 0.7340 (tt0) REVERT: E 7 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7484 (tt) REVERT: E 27 ASP cc_start: 0.7087 (t70) cc_final: 0.6203 (p0) REVERT: E 317 MET cc_start: 0.5691 (ttm) cc_final: 0.5361 (ttm) REVERT: E 376 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8106 (tt) REVERT: E 578 LYS cc_start: 0.6303 (OUTLIER) cc_final: 0.5513 (mmmt) REVERT: E 612 LYS cc_start: 0.5517 (mmtt) cc_final: 0.5182 (mmtp) REVERT: E 628 MET cc_start: 0.6340 (tpp) cc_final: 0.5949 (tpp) REVERT: F 51 MET cc_start: 0.6030 (mmm) cc_final: 0.5122 (mmm) REVERT: F 118 TYR cc_start: 0.7219 (m-80) cc_final: 0.6970 (m-80) REVERT: F 283 MET cc_start: 0.7441 (mtp) cc_final: 0.7111 (mpp) REVERT: F 365 MET cc_start: 0.2424 (mmp) cc_final: 0.2073 (mmt) REVERT: F 610 PHE cc_start: 0.4254 (OUTLIER) cc_final: 0.3035 (t80) REVERT: F 731 VAL cc_start: 0.5517 (OUTLIER) cc_final: 0.5252 (t) REVERT: F 735 MET cc_start: 0.8110 (ppp) cc_final: 0.7830 (ptm) REVERT: G 1 MET cc_start: 0.5484 (pmm) cc_final: 0.4935 (ptp) outliers start: 103 outliers final: 78 residues processed: 613 average time/residue: 0.8881 time to fit residues: 882.3885 Evaluate side-chains 613 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 522 time to evaluate : 4.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 451 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 223 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 SER 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 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 94 LEU 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 407 GLU 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 276 CYS Chi-restraints excluded: chain D residue 291 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 490 ILE Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 500 LEU 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 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 98 SER Chi-restraints excluded: chain E residue 113 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 572 ARG Chi-restraints excluded: chain E residue 578 LYS Chi-restraints excluded: chain E residue 660 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 409 CYS Chi-restraints excluded: chain F residue 410 MET 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 640 VAL Chi-restraints excluded: chain F residue 647 ILE Chi-restraints excluded: chain F residue 688 SER Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 743 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 370 optimal weight: 10.0000 chunk 390 optimal weight: 1.9990 chunk 356 optimal weight: 6.9990 chunk 379 optimal weight: 0.2980 chunk 228 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 343 optimal weight: 3.9990 chunk 359 optimal weight: 7.9990 chunk 378 optimal weight: 5.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN C 728 GLN D 340 GLN D 713 HIS ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34866 Z= 0.278 Angle : 0.572 8.595 47027 Z= 0.304 Chirality : 0.040 0.235 5190 Planarity : 0.004 0.065 6075 Dihedral : 4.299 44.561 4655 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.32 % Favored : 93.61 % Rotamer: Outliers : 3.11 % Allowed : 24.31 % Favored : 72.58 % 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: -0.53 (0.13), residues: 4239 helix: 1.08 (0.12), residues: 1867 sheet: -0.97 (0.24), residues: 478 loop : -1.69 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 309 HIS 0.044 0.002 HIS F 110 PHE 0.035 0.002 PHE E 551 TYR 0.018 0.002 TYR B 253 ARG 0.008 0.000 ARG F 136 *********************** 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 636 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 518 time to evaluate : 4.064 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: A 144 HIS cc_start: 0.2094 (OUTLIER) cc_final: -0.0658 (t-170) REVERT: A 441 MET cc_start: 0.8033 (ttm) cc_final: 0.7756 (ttp) REVERT: A 549 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7246 (pp) REVERT: B 8 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7960 (tt) REVERT: B 372 MET cc_start: 0.7402 (ptm) cc_final: 0.6274 (tmm) REVERT: B 517 ILE cc_start: 0.8493 (mp) cc_final: 0.8273 (mt) REVERT: B 602 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7293 (mtp-110) REVERT: C 172 VAL cc_start: 0.7526 (OUTLIER) cc_final: 0.7304 (t) REVERT: C 318 ARG cc_start: 0.5398 (mmp80) cc_final: 0.4900 (mpp80) REVERT: C 332 ARG cc_start: 0.7677 (ttp-170) cc_final: 0.7109 (ptt-90) REVERT: C 357 HIS cc_start: -0.1194 (OUTLIER) cc_final: -0.2149 (m90) REVERT: C 363 PHE cc_start: 0.6998 (m-80) cc_final: 0.6617 (m-80) REVERT: C 365 MET cc_start: 0.4849 (mpp) cc_final: 0.4331 (ptp) REVERT: C 483 MET cc_start: 0.3083 (mmp) cc_final: 0.2864 (mmp) REVERT: C 603 MET cc_start: 0.7177 (tpt) cc_final: 0.6948 (tpt) REVERT: C 641 ARG cc_start: 0.7091 (tpm170) cc_final: 0.6028 (tpp-160) REVERT: C 664 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6901 (ttt-90) REVERT: C 756 MET cc_start: 0.4616 (mtp) cc_final: 0.3960 (mmm) REVERT: D 21 MET cc_start: -0.3859 (OUTLIER) cc_final: -0.5567 (ttt) REVERT: D 490 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7106 (mt) REVERT: D 604 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7835 (mt-10) REVERT: D 611 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6361 (t80) REVERT: D 654 GLN cc_start: 0.8112 (tp-100) cc_final: 0.7380 (tt0) REVERT: E 7 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7466 (tt) REVERT: E 27 ASP cc_start: 0.7237 (t70) cc_final: 0.6374 (p0) REVERT: E 267 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: E 317 MET cc_start: 0.5771 (ttm) cc_final: 0.5402 (ttm) REVERT: E 376 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8136 (tt) REVERT: E 578 LYS cc_start: 0.6281 (OUTLIER) cc_final: 0.5420 (mmmt) REVERT: E 612 LYS cc_start: 0.5634 (mmtt) cc_final: 0.5311 (mmtp) REVERT: E 628 MET cc_start: 0.6477 (tpp) cc_final: 0.6034 (tpp) REVERT: F 51 MET cc_start: 0.6141 (mmm) cc_final: 0.5222 (mmm) REVERT: F 257 GLN cc_start: 0.8508 (tt0) cc_final: 0.8162 (tm-30) REVERT: F 283 MET cc_start: 0.7564 (mtp) cc_final: 0.7238 (mpp) REVERT: F 365 MET cc_start: 0.2437 (mmp) cc_final: 0.2081 (mmt) REVERT: F 610 PHE cc_start: 0.4272 (OUTLIER) cc_final: 0.3027 (t80) REVERT: F 731 VAL cc_start: 0.5425 (OUTLIER) cc_final: 0.5182 (t) REVERT: F 735 MET cc_start: 0.8033 (ppp) cc_final: 0.7759 (ptm) REVERT: G 95 LEU cc_start: 0.5142 (OUTLIER) cc_final: 0.4665 (mt) outliers start: 118 outliers final: 94 residues processed: 610 average time/residue: 0.9080 time to fit residues: 899.5063 Evaluate side-chains 623 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 512 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET 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 211 MET Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 451 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 223 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 269 SER 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 489 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 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 120 GLU 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 357 HIS Chi-restraints excluded: chain C residue 407 GLU 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 733 LEU 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 157 THR Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 323 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 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 500 LEU Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 644 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 42 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 309 TRP 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 572 ARG 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 115 TYR Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 409 CYS Chi-restraints excluded: chain F residue 410 MET 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 688 SER Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain G residue 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 249 optimal weight: 2.9990 chunk 401 optimal weight: 8.9990 chunk 245 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 279 optimal weight: 2.9990 chunk 421 optimal weight: 4.9990 chunk 387 optimal weight: 0.9990 chunk 335 optimal weight: 0.3980 chunk 34 optimal weight: 9.9990 chunk 259 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 HIS D 340 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.4786 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 : 0.526 9.037 47027 Z= 0.275 Chirality : 0.039 0.190 5190 Planarity : 0.004 0.066 6075 Dihedral : 4.112 44.724 4655 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 2.48 % Allowed : 24.62 % Favored : 72.90 % 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: 1.40 (0.12), residues: 1857 sheet: -0.80 (0.24), residues: 485 loop : -1.57 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 309 HIS 0.005 0.001 HIS F 110 PHE 0.028 0.001 PHE D 710 TYR 0.016 0.001 TYR E 436 ARG 0.006 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 629 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 535 time to evaluate : 4.045 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 144 HIS cc_start: 0.2289 (OUTLIER) cc_final: -0.0512 (t-170) REVERT: A 335 LEU cc_start: 0.6954 (tp) cc_final: 0.6624 (tp) REVERT: A 441 MET cc_start: 0.8080 (ttm) cc_final: 0.7740 (ttp) REVERT: A 549 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7281 (pp) REVERT: B 8 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7960 (tt) REVERT: B 217 TYR cc_start: 0.6584 (t80) cc_final: 0.6323 (t80) REVERT: B 372 MET cc_start: 0.7293 (ptm) cc_final: 0.6210 (tmm) REVERT: B 517 ILE cc_start: 0.8459 (mp) cc_final: 0.8230 (mt) REVERT: B 602 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7322 (mtp-110) REVERT: C 172 VAL cc_start: 0.7500 (OUTLIER) cc_final: 0.7269 (t) REVERT: C 318 ARG cc_start: 0.5387 (mmp80) cc_final: 0.4878 (mpp80) REVERT: C 357 HIS cc_start: -0.1320 (OUTLIER) cc_final: -0.2269 (m90) REVERT: C 363 PHE cc_start: 0.7004 (m-80) cc_final: 0.6601 (m-80) REVERT: C 365 MET cc_start: 0.4984 (mpp) cc_final: 0.4371 (ptp) REVERT: C 483 MET cc_start: 0.2861 (mmp) cc_final: 0.2638 (mmp) REVERT: C 603 MET cc_start: 0.7100 (tpt) cc_final: 0.6879 (tpt) REVERT: C 641 ARG cc_start: 0.7040 (tpm170) cc_final: 0.6012 (tpp-160) REVERT: C 664 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6979 (ttt-90) REVERT: C 756 MET cc_start: 0.4565 (mtp) cc_final: 0.3943 (mmm) REVERT: D 21 MET cc_start: -0.3852 (OUTLIER) cc_final: -0.5530 (ttt) REVERT: D 490 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.7038 (mt) REVERT: D 611 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6427 (t80) REVERT: D 654 GLN cc_start: 0.8072 (tp-100) cc_final: 0.7354 (tt0) REVERT: E 7 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7584 (tt) REVERT: E 27 ASP cc_start: 0.7109 (t70) cc_final: 0.6227 (p0) REVERT: E 376 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8102 (tt) REVERT: E 578 LYS cc_start: 0.6207 (OUTLIER) cc_final: 0.5354 (mmmt) REVERT: E 612 LYS cc_start: 0.5536 (mmtt) cc_final: 0.5187 (mmtp) REVERT: E 628 MET cc_start: 0.6439 (tpp) cc_final: 0.6025 (tpp) REVERT: F 51 MET cc_start: 0.6005 (mmm) cc_final: 0.5157 (mmm) REVERT: F 257 GLN cc_start: 0.8466 (tt0) cc_final: 0.8143 (tm-30) REVERT: F 283 MET cc_start: 0.7487 (mtp) cc_final: 0.7138 (mpp) REVERT: F 365 MET cc_start: 0.2405 (mmp) cc_final: 0.2068 (mmt) REVERT: F 460 MET cc_start: 0.4729 (tpp) cc_final: 0.4321 (tpp) REVERT: F 610 PHE cc_start: 0.4266 (OUTLIER) cc_final: 0.2984 (t80) REVERT: F 731 VAL cc_start: 0.5388 (OUTLIER) cc_final: 0.5137 (t) REVERT: F 735 MET cc_start: 0.8020 (ppp) cc_final: 0.7758 (ptm) REVERT: G 1 MET cc_start: 0.5450 (pmm) cc_final: 0.4904 (ptp) outliers start: 94 outliers final: 74 residues processed: 604 average time/residue: 0.8960 time to fit residues: 872.4829 Evaluate side-chains 612 residues out of total 3793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 523 time to evaluate : 3.976 ------------------------------------------------------------------------------- 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 211 MET Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 451 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 223 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 SER 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 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 94 LEU 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 357 HIS Chi-restraints excluded: chain C residue 407 GLU 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 157 THR Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 291 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 500 LEU Chi-restraints excluded: chain D residue 538 GLU 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 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 98 SER Chi-restraints excluded: chain E residue 113 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 236 GLN Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 409 CYS Chi-restraints excluded: chain F residue 410 MET 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 647 ILE Chi-restraints excluded: chain F residue 688 SER Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 743 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 266 optimal weight: 0.6980 chunk 357 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 309 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 336 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 345 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN D 340 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.172603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.134212 restraints weight = 206406.408| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 3.27 r_work: 0.3903 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 34866 Z= 0.156 Angle : 0.517 9.512 47027 Z= 0.269 Chirality : 0.039 0.278 5190 Planarity : 0.004 0.065 6075 Dihedral : 3.980 44.842 4655 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.51 % Favored : 95.42 % Rotamer: Outliers : 2.14 % Allowed : 25.10 % Favored : 72.77 % 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: 0.01 (0.13), residues: 4239 helix: 1.59 (0.12), residues: 1858 sheet: -0.71 (0.24), residues: 485 loop : -1.44 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 666 HIS 0.004 0.001 HIS A 128 PHE 0.028 0.001 PHE D 710 TYR 0.014 0.001 TYR E 436 ARG 0.005 0.000 ARG C 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17378.90 seconds wall clock time: 296 minutes 27.65 seconds (17787.65 seconds total)