Starting phenix.real_space_refine on Tue Aug 26 10:22:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rn0_19382/08_2025/8rn0_19382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rn0_19382/08_2025/8rn0_19382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rn0_19382/08_2025/8rn0_19382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rn0_19382/08_2025/8rn0_19382.map" model { file = "/net/cci-nas-00/data/ceres_data/8rn0_19382/08_2025/8rn0_19382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rn0_19382/08_2025/8rn0_19382.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.050 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: 5 Type Number sf(0) Gaussians S 121 5.16 5 C 11305 2.51 5 N 3103 2.21 5 O 3374 1.98 5 H 17891 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35794 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2328 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 9, 'TRANS': 137} 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} Time building chain proxies: 6.98, per 1000 atoms: 0.20 Number of scatterers: 35794 At special positions: 0 Unit cell: (107.52, 131.04, 136.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 121 16.00 O 3374 8.00 N 3103 7.00 C 11305 6.00 H 17891 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: 3.46 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4206 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 26 sheets defined 46.7% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'C' and resid 540 through 556 removed outlier: 4.261A pdb=" N SER C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.748A 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 '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 'C' and resid 635 through 639 Processing sheet with id=AA2, 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=AA3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA4, 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=AA5, first strand: chain 'D' and resid 258 through 259 Processing sheet with id=AA6, 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=AA7, 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=AA8, 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=AA9, first strand: chain 'D' and resid 627 through 629 Processing sheet with id=AB1, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AB2, 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=AB3, first strand: chain 'E' and resid 179 through 183 Processing sheet with id=AB4, 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=AB5, 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=AB6, 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=AB7, first strand: chain 'F' and resid 133 through 134 Processing sheet with id=AB8, 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=AB9, first strand: chain 'F' and resid 319 through 320 Processing sheet with id=AC1, 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=AC2, first strand: chain 'F' and resid 338 through 345 Processing sheet with id=AC3, 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=AC4, first strand: chain 'F' and resid 635 through 639 Processing sheet with id=AC5, 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=AC6, 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=AC7, 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=AC8, 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) 836 hydrogen bonds defined for protein. 2289 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: 9.50 Time building geometry restraints manager: 4.60 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: 17861 1.03 - 1.23: 35 1.23 - 1.42: 7498 1.42 - 1.62: 10537 1.62 - 1.81: 212 Bond restraints: 36143 Sorted by residual: bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" CB PRO C 579 " pdb=" CG PRO C 579 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.65e+00 bond pdb=" CG PRO C 579 " pdb=" CD PRO C 579 " ideal model delta sigma weight residual 1.503 1.450 0.053 3.40e-02 8.65e+02 2.46e+00 bond pdb=" N MET G 1 " pdb=" H MET G 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" N ASN G 13 " pdb=" CA ASN G 13 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.67e-01 ... (remaining 36138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 65075 2.05 - 4.11: 263 4.11 - 6.16: 17 6.16 - 8.21: 4 8.21 - 10.27: 1 Bond angle restraints: 65360 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=" 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 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 angle pdb=" CB PRO F 579 " pdb=" CG PRO F 579 " pdb=" CD PRO F 579 " ideal model delta sigma weight residual 106.10 95.83 10.27 3.20e+00 9.77e-02 1.03e+01 angle pdb=" N PRO C 579 " pdb=" CD PRO C 579 " pdb=" CG PRO C 579 " ideal model delta sigma weight residual 103.20 98.49 4.71 1.50e+00 4.44e-01 9.86e+00 ... (remaining 65355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14722 17.99 - 35.97: 1612 35.97 - 53.96: 471 53.96 - 71.95: 95 71.95 - 89.93: 33 Dihedral angle restraints: 16933 sinusoidal: 9400 harmonic: 7533 Sorted by residual: 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=" CB GLU D 202 " pdb=" CG GLU D 202 " pdb=" CD GLU D 202 " pdb=" OE1 GLU D 202 " ideal model delta sinusoidal sigma weight residual 0.00 89.67 -89.67 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP F 254 " pdb=" CB ASP F 254 " pdb=" CG ASP F 254 " pdb=" OD1 ASP F 254 " ideal model delta sinusoidal sigma weight residual -30.00 -85.74 55.74 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 16930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2013 0.035 - 0.070: 494 0.070 - 0.105: 138 0.105 - 0.140: 70 0.140 - 0.175: 3 Chirality restraints: 2718 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 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 chirality pdb=" CA ILE F 373 " pdb=" N ILE F 373 " pdb=" C ILE F 373 " pdb=" CB ILE F 373 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 2715 not shown) Planarity restraints: 5316 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 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 delta sigma weight rms_deltas residual plane pdb=" C VAL E 12 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO E 13 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 13 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 13 " -0.028 5.00e-02 4.00e+02 ... (remaining 5313 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.97: 256 1.97 - 2.63: 46808 2.63 - 3.29: 107258 3.29 - 3.94: 133356 3.94 - 4.60: 211265 Nonbonded interactions: 498943 Sorted by model distance: nonbonded pdb="HG21 VAL D 450 " pdb="HD22 LEU D 641 " model vdw 1.318 2.440 nonbonded pdb=" O ASN E 425 " pdb="HD21 ASN E 425 " model vdw 1.529 2.450 nonbonded pdb=" H ASP F 83 " pdb=" O ARG F 88 " model vdw 1.539 2.450 nonbonded pdb="HG21 VAL D 450 " pdb="HD23 LEU D 641 " model vdw 1.563 2.440 nonbonded pdb=" H THR D 418 " pdb=" O HIS D 452 " model vdw 1.573 2.450 ... (remaining 498938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.220 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 35.730 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 18252 Z= 0.097 Angle : 0.482 10.266 24637 Z= 0.249 Chirality : 0.037 0.175 2718 Planarity : 0.003 0.083 3187 Dihedral : 17.523 89.933 6954 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.46 % Favored : 95.40 % Rotamer: Outliers : 0.25 % Allowed : 23.98 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.19), residues: 2219 helix: 1.70 (0.18), residues: 940 sheet: -0.52 (0.32), residues: 286 loop : -0.98 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 179 TYR 0.008 0.001 TYR F 531 PHE 0.009 0.001 PHE F 323 TRP 0.013 0.001 TRP F 78 HIS 0.002 0.000 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00231 (18252) covalent geometry : angle 0.48214 (24637) hydrogen bonds : bond 0.15660 ( 828) hydrogen bonds : angle 6.04822 ( 2289) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 284 time to evaluate : 1.026 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: D 368 TRP cc_start: 0.7640 (m100) cc_final: 0.7251 (m100) REVERT: E 40 MET cc_start: 0.7298 (mmp) cc_final: 0.6999 (mmp) REVERT: G 137 LYS cc_start: 0.7725 (mttt) cc_final: 0.7245 (tmmt) outliers start: 5 outliers final: 4 residues processed: 286 average time/residue: 0.3613 time to fit residues: 153.0939 Evaluate side-chains 272 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 268 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 345 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 HIS ** D 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN E 600 ASN F 100 ASN F 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.188050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.146373 restraints weight = 84711.057| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.77 r_work: 0.3802 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18252 Z= 0.126 Angle : 0.507 6.275 24637 Z= 0.268 Chirality : 0.039 0.147 2718 Planarity : 0.004 0.055 3187 Dihedral : 4.036 46.142 2437 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 1.86 % Allowed : 23.02 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.19), residues: 2219 helix: 1.59 (0.17), residues: 949 sheet: -0.50 (0.33), residues: 272 loop : -1.14 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 476 TYR 0.008 0.001 TYR E 129 PHE 0.010 0.001 PHE F 323 TRP 0.010 0.001 TRP E 438 HIS 0.004 0.001 HIS D 452 Details of bonding type rmsd covalent geometry : bond 0.00284 (18252) covalent geometry : angle 0.50653 (24637) hydrogen bonds : bond 0.04151 ( 828) hydrogen bonds : angle 5.03642 ( 2289) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 1.019 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: D 59 GLU cc_start: 0.6658 (pt0) cc_final: 0.6090 (pm20) REVERT: D 368 TRP cc_start: 0.7751 (m100) cc_final: 0.7371 (m100) REVERT: E 491 GLU cc_start: 0.8748 (pp20) cc_final: 0.8462 (pp20) REVERT: G 137 LYS cc_start: 0.7770 (mttt) cc_final: 0.7206 (tmmt) outliers start: 37 outliers final: 20 residues processed: 311 average time/residue: 0.3675 time to fit residues: 170.9325 Evaluate side-chains 292 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 272 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 495 ARG Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 408 ASP Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 728 GLN Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 26 ASN Chi-restraints excluded: chain G residue 39 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 167 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 HIS E 425 ASN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 545 GLN E 582 GLN E 600 ASN ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.184984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.143068 restraints weight = 85211.503| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.76 r_work: 0.3744 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18252 Z= 0.187 Angle : 0.549 5.539 24637 Z= 0.294 Chirality : 0.040 0.148 2718 Planarity : 0.004 0.056 3187 Dihedral : 4.112 21.585 2430 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.13 % Favored : 93.74 % Rotamer: Outliers : 3.02 % Allowed : 23.17 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.18), residues: 2219 helix: 1.09 (0.17), residues: 941 sheet: -0.69 (0.32), residues: 281 loop : -1.42 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 630 TYR 0.014 0.002 TYR E 30 PHE 0.013 0.002 PHE G 136 TRP 0.013 0.001 TRP E 309 HIS 0.004 0.001 HIS D 452 Details of bonding type rmsd covalent geometry : bond 0.00433 (18252) covalent geometry : angle 0.54851 (24637) hydrogen bonds : bond 0.04437 ( 828) hydrogen bonds : angle 5.10981 ( 2289) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 276 time to evaluate : 1.014 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: D 59 GLU cc_start: 0.6715 (pt0) cc_final: 0.6177 (pm20) REVERT: D 155 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5600 (ppp) REVERT: E 491 GLU cc_start: 0.8828 (pp20) cc_final: 0.8614 (pp20) REVERT: F 53 MET cc_start: 0.7929 (ptp) cc_final: 0.7719 (ptm) REVERT: G 137 LYS cc_start: 0.7720 (mttt) cc_final: 0.7219 (tmmt) outliers start: 60 outliers final: 46 residues processed: 315 average time/residue: 0.3401 time to fit residues: 159.3269 Evaluate side-chains 309 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 392 GLN Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 699 TRP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 417 THR Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 311 CYS Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 408 ASP Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 728 GLN Chi-restraints excluded: chain G residue 3 MET Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 26 ASN Chi-restraints excluded: chain G residue 39 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN F 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.187172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.145459 restraints weight = 84614.449| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.76 r_work: 0.3781 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18252 Z= 0.105 Angle : 0.489 4.735 24637 Z= 0.257 Chirality : 0.038 0.149 2718 Planarity : 0.004 0.054 3187 Dihedral : 3.851 21.319 2430 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.96 % Favored : 94.91 % Rotamer: Outliers : 1.91 % Allowed : 24.23 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.18), residues: 2219 helix: 1.46 (0.17), residues: 942 sheet: -0.59 (0.32), residues: 271 loop : -1.31 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 664 TYR 0.016 0.001 TYR E 217 PHE 0.010 0.001 PHE F 323 TRP 0.009 0.001 TRP E 438 HIS 0.002 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00244 (18252) covalent geometry : angle 0.48949 (24637) hydrogen bonds : bond 0.03569 ( 828) hydrogen bonds : angle 4.73371 ( 2289) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 0.812 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: D 59 GLU cc_start: 0.6684 (pt0) cc_final: 0.6137 (mp0) REVERT: D 155 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.5610 (ppp) REVERT: D 368 TRP cc_start: 0.7694 (m100) cc_final: 0.7286 (m100) REVERT: E 40 MET cc_start: 0.7539 (mmp) cc_final: 0.7105 (mmp) REVERT: E 392 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6735 (tt) REVERT: E 491 GLU cc_start: 0.8782 (pp20) cc_final: 0.8515 (pp20) REVERT: G 137 LYS cc_start: 0.7688 (mttt) cc_final: 0.7180 (tmmt) outliers start: 38 outliers final: 28 residues processed: 305 average time/residue: 0.2931 time to fit residues: 132.1470 Evaluate side-chains 292 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 262 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain D residue 55 ASP 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 421 SER Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 408 ASP Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 728 GLN Chi-restraints excluded: chain G residue 3 MET Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 39 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 218 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 141 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 212 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 chunk 186 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 202 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.187941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146085 restraints weight = 84465.323| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.79 r_work: 0.3790 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18252 Z= 0.099 Angle : 0.477 5.710 24637 Z= 0.250 Chirality : 0.038 0.143 2718 Planarity : 0.003 0.055 3187 Dihedral : 3.744 21.056 2430 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.69 % Favored : 95.18 % Rotamer: Outliers : 1.71 % Allowed : 24.53 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.18), residues: 2219 helix: 1.61 (0.17), residues: 944 sheet: -0.45 (0.32), residues: 279 loop : -1.22 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 664 TYR 0.011 0.001 TYR C 592 PHE 0.012 0.001 PHE F 323 TRP 0.008 0.001 TRP E 438 HIS 0.002 0.000 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00225 (18252) covalent geometry : angle 0.47745 (24637) hydrogen bonds : bond 0.03336 ( 828) hydrogen bonds : angle 4.58903 ( 2289) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 0.863 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: C 589 ARG cc_start: 0.6806 (ptp-170) cc_final: 0.6580 (ptp-170) REVERT: D 59 GLU cc_start: 0.6692 (pt0) cc_final: 0.6180 (pm20) REVERT: D 155 MET cc_start: 0.6255 (OUTLIER) cc_final: 0.5625 (ppp) REVERT: D 182 MET cc_start: 0.2391 (mpp) cc_final: 0.2139 (mpp) REVERT: D 368 TRP cc_start: 0.7712 (m100) cc_final: 0.7308 (m100) REVERT: E 109 GLU cc_start: 0.7559 (pt0) cc_final: 0.7345 (pt0) REVERT: E 491 GLU cc_start: 0.8774 (pp20) cc_final: 0.8539 (pp20) REVERT: G 65 LYS cc_start: 0.7146 (tptt) cc_final: 0.6773 (tptt) REVERT: G 94 ASN cc_start: 0.5600 (OUTLIER) cc_final: 0.5249 (t0) REVERT: G 137 LYS cc_start: 0.7696 (mttt) cc_final: 0.7177 (tmmt) outliers start: 34 outliers final: 27 residues processed: 299 average time/residue: 0.3149 time to fit residues: 140.3845 Evaluate side-chains 290 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 421 SER Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 408 ASP Chi-restraints excluded: chain F residue 467 MET Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 728 GLN Chi-restraints excluded: chain G residue 3 MET Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 196 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 485 ASN E 582 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.186802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.145052 restraints weight = 84681.337| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.76 r_work: 0.3770 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18252 Z= 0.126 Angle : 0.494 5.042 24637 Z= 0.260 Chirality : 0.038 0.145 2718 Planarity : 0.004 0.056 3187 Dihedral : 3.821 20.932 2430 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.32 % Favored : 94.55 % Rotamer: Outliers : 2.52 % Allowed : 24.13 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.18), residues: 2219 helix: 1.48 (0.17), residues: 945 sheet: -0.54 (0.32), residues: 280 loop : -1.30 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 264 TYR 0.012 0.001 TYR E 559 PHE 0.011 0.001 PHE F 323 TRP 0.010 0.001 TRP E 438 HIS 0.002 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00294 (18252) covalent geometry : angle 0.49447 (24637) hydrogen bonds : bond 0.03514 ( 828) hydrogen bonds : angle 4.65318 ( 2289) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 1.041 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: C 575 MET cc_start: 0.7387 (tmm) cc_final: 0.7144 (tmm) REVERT: D 155 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.5631 (ppp) REVERT: D 182 MET cc_start: 0.2499 (mpp) cc_final: 0.2260 (mpp) REVERT: D 368 TRP cc_start: 0.7741 (m100) cc_final: 0.7332 (m100) REVERT: E 40 MET cc_start: 0.7546 (mmp) cc_final: 0.7122 (mmp) REVERT: E 491 GLU cc_start: 0.8807 (pp20) cc_final: 0.8537 (pp20) REVERT: F 242 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.5894 (tm-30) REVERT: F 365 MET cc_start: -0.0802 (mmp) cc_final: -0.1073 (mmp) REVERT: G 65 LYS cc_start: 0.7174 (tptt) cc_final: 0.6800 (tptt) REVERT: G 137 LYS cc_start: 0.7708 (mttt) cc_final: 0.7186 (tmmt) outliers start: 50 outliers final: 39 residues processed: 300 average time/residue: 0.3363 time to fit residues: 152.7261 Evaluate side-chains 295 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 254 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain D residue 55 ASP 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 327 GLU Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 688 GLU Chi-restraints excluded: chain D residue 699 TRP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 242 GLN Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 728 GLN Chi-restraints excluded: chain G residue 3 MET Chi-restraints excluded: chain G residue 26 ASN Chi-restraints excluded: chain G residue 39 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 183 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 ASN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.186481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.144645 restraints weight = 85245.186| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.78 r_work: 0.3769 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18252 Z= 0.128 Angle : 0.498 5.153 24637 Z= 0.262 Chirality : 0.039 0.149 2718 Planarity : 0.004 0.056 3187 Dihedral : 3.869 21.266 2430 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.32 % Favored : 94.55 % Rotamer: Outliers : 2.67 % Allowed : 24.13 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.18), residues: 2219 helix: 1.40 (0.17), residues: 947 sheet: -0.59 (0.32), residues: 280 loop : -1.38 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 630 TYR 0.024 0.001 TYR E 217 PHE 0.013 0.001 PHE E 551 TRP 0.010 0.001 TRP C 557 HIS 0.002 0.001 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00299 (18252) covalent geometry : angle 0.49809 (24637) hydrogen bonds : bond 0.03544 ( 828) hydrogen bonds : angle 4.64809 ( 2289) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 260 time to evaluate : 1.083 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: D 155 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.5627 (ppp) REVERT: D 182 MET cc_start: 0.2627 (mpp) cc_final: 0.2399 (mpp) REVERT: D 368 TRP cc_start: 0.7703 (m100) cc_final: 0.7270 (m100) REVERT: F 242 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.6057 (tm-30) REVERT: F 243 MET cc_start: 0.5905 (mpt) cc_final: 0.5402 (mpt) REVERT: F 365 MET cc_start: -0.0622 (mmp) cc_final: -0.0905 (mmp) REVERT: G 65 LYS cc_start: 0.7221 (tptt) cc_final: 0.6861 (tptt) REVERT: G 137 LYS cc_start: 0.7709 (mttt) cc_final: 0.7187 (tmmt) outliers start: 53 outliers final: 44 residues processed: 300 average time/residue: 0.3543 time to fit residues: 159.7838 Evaluate side-chains 303 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 257 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain D residue 55 ASP 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 327 GLU Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 688 GLU Chi-restraints excluded: chain D residue 699 TRP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 242 GLN Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 728 GLN Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain G residue 3 MET Chi-restraints excluded: chain G residue 26 ASN Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 81 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 204 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 86 optimal weight: 0.0470 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 310 ASN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN ** 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 = 0.4351 r_free = 0.4351 target = 0.185647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.143375 restraints weight = 84948.504| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.88 r_work: 0.3751 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18252 Z= 0.144 Angle : 0.510 5.062 24637 Z= 0.270 Chirality : 0.039 0.147 2718 Planarity : 0.004 0.056 3187 Dihedral : 3.963 20.931 2430 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.59 % Favored : 94.28 % Rotamer: Outliers : 3.02 % Allowed : 24.08 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.18), residues: 2219 helix: 1.32 (0.17), residues: 948 sheet: -0.65 (0.32), residues: 280 loop : -1.47 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 572 TYR 0.021 0.001 TYR E 217 PHE 0.015 0.001 PHE E 551 TRP 0.012 0.001 TRP D 338 HIS 0.003 0.001 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00336 (18252) covalent geometry : angle 0.51046 (24637) hydrogen bonds : bond 0.03662 ( 828) hydrogen bonds : angle 4.69594 ( 2289) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 265 time to evaluate : 0.979 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: D 155 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.5604 (ppp) REVERT: D 368 TRP cc_start: 0.7722 (m100) cc_final: 0.7272 (m100) REVERT: E 491 GLU cc_start: 0.8856 (pp20) cc_final: 0.8655 (pp20) REVERT: F 58 THR cc_start: 0.5432 (OUTLIER) cc_final: 0.5212 (t) REVERT: F 242 GLN cc_start: 0.6891 (OUTLIER) cc_final: 0.6408 (tm-30) REVERT: F 243 MET cc_start: 0.5967 (mpt) cc_final: 0.5547 (mpt) REVERT: G 65 LYS cc_start: 0.7223 (tptt) cc_final: 0.6868 (tptt) REVERT: G 137 LYS cc_start: 0.7739 (mttt) cc_final: 0.7193 (tmmt) outliers start: 60 outliers final: 48 residues processed: 310 average time/residue: 0.3679 time to fit residues: 169.8292 Evaluate side-chains 309 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 688 GLU Chi-restraints excluded: chain D residue 699 TRP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 242 GLN Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 635 SER Chi-restraints excluded: chain F residue 728 GLN Chi-restraints excluded: chain G residue 3 MET Chi-restraints excluded: chain G residue 26 ASN Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 204 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 310 ASN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN ** 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 = 0.4328 r_free = 0.4328 target = 0.183848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.141832 restraints weight = 85232.021| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.76 r_work: 0.3738 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18252 Z= 0.188 Angle : 0.555 5.857 24637 Z= 0.297 Chirality : 0.040 0.154 2718 Planarity : 0.004 0.057 3187 Dihedral : 4.194 22.083 2430 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.31 % Favored : 93.56 % Rotamer: Outliers : 3.07 % Allowed : 24.33 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.18), residues: 2219 helix: 0.98 (0.17), residues: 946 sheet: -0.82 (0.32), residues: 282 loop : -1.62 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 572 TYR 0.017 0.002 TYR E 217 PHE 0.038 0.002 PHE F 323 TRP 0.015 0.002 TRP F 78 HIS 0.004 0.001 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00436 (18252) covalent geometry : angle 0.55490 (24637) hydrogen bonds : bond 0.04029 ( 828) hydrogen bonds : angle 4.93772 ( 2289) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 263 time to evaluate : 1.100 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: D 59 GLU cc_start: 0.6385 (pt0) cc_final: 0.5907 (mp0) REVERT: D 155 MET cc_start: 0.6194 (OUTLIER) cc_final: 0.5558 (ppp) REVERT: D 368 TRP cc_start: 0.7538 (m100) cc_final: 0.6997 (m100) REVERT: E 227 MET cc_start: 0.5983 (mpp) cc_final: 0.5650 (mpp) REVERT: E 491 GLU cc_start: 0.8877 (pp20) cc_final: 0.8658 (pp20) REVERT: F 58 THR cc_start: 0.5414 (OUTLIER) cc_final: 0.5189 (t) REVERT: F 242 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6486 (tm-30) REVERT: F 243 MET cc_start: 0.6052 (mpt) cc_final: 0.5514 (mpt) REVERT: F 283 MET cc_start: 0.6844 (mtp) cc_final: 0.6494 (mtp) REVERT: F 365 MET cc_start: -0.0715 (mmp) cc_final: -0.0965 (mmp) REVERT: F 710 ILE cc_start: 0.8421 (mm) cc_final: 0.8155 (mt) REVERT: G 20 LYS cc_start: 0.5938 (mttt) cc_final: 0.5654 (mptt) REVERT: G 65 LYS cc_start: 0.7292 (tptt) cc_final: 0.6950 (tptt) REVERT: G 137 LYS cc_start: 0.7734 (mttt) cc_final: 0.7181 (tmmt) outliers start: 61 outliers final: 53 residues processed: 307 average time/residue: 0.3529 time to fit residues: 162.7438 Evaluate side-chains 315 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 259 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 688 GLU Chi-restraints excluded: chain D residue 699 TRP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 242 GLN Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 553 ILE 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 728 GLN Chi-restraints excluded: chain G residue 3 MET Chi-restraints excluded: chain G residue 26 ASN Chi-restraints excluded: chain G residue 39 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 180 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 206 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 310 ASN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.183968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.141945 restraints weight = 85427.782| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.76 r_work: 0.3743 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 18252 Z= 0.186 Angle : 0.723 59.199 24637 Z= 0.421 Chirality : 0.040 0.149 2718 Planarity : 0.004 0.057 3187 Dihedral : 4.195 21.887 2430 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.35 % Favored : 93.51 % Rotamer: Outliers : 3.07 % Allowed : 24.38 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.18), residues: 2219 helix: 0.98 (0.17), residues: 946 sheet: -0.83 (0.31), residues: 282 loop : -1.62 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 572 TYR 0.015 0.001 TYR E 217 PHE 0.036 0.001 PHE F 323 TRP 0.013 0.001 TRP E 438 HIS 0.004 0.001 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00419 (18252) covalent geometry : angle 0.72292 (24637) hydrogen bonds : bond 0.03964 ( 828) hydrogen bonds : angle 4.92590 ( 2289) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 260 time to evaluate : 1.093 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: D 59 GLU cc_start: 0.6409 (pt0) cc_final: 0.5921 (mp0) REVERT: D 155 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5542 (ppp) REVERT: D 368 TRP cc_start: 0.7522 (m100) cc_final: 0.6980 (m100) REVERT: E 227 MET cc_start: 0.5988 (mpp) cc_final: 0.5648 (mpp) REVERT: E 491 GLU cc_start: 0.8872 (pp20) cc_final: 0.8634 (pp20) REVERT: F 58 THR cc_start: 0.5433 (OUTLIER) cc_final: 0.5207 (t) REVERT: F 242 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6470 (tm-30) REVERT: F 243 MET cc_start: 0.6060 (mpt) cc_final: 0.5501 (mpt) REVERT: F 283 MET cc_start: 0.6814 (mtp) cc_final: 0.6446 (mtp) REVERT: F 365 MET cc_start: -0.0621 (mmp) cc_final: -0.0906 (mmp) REVERT: F 710 ILE cc_start: 0.8413 (mm) cc_final: 0.8146 (mt) REVERT: G 20 LYS cc_start: 0.5956 (mttt) cc_final: 0.5672 (mptt) REVERT: G 65 LYS cc_start: 0.7309 (tptt) cc_final: 0.6969 (tptt) REVERT: G 137 LYS cc_start: 0.7718 (mttt) cc_final: 0.7149 (tmmt) outliers start: 61 outliers final: 54 residues processed: 304 average time/residue: 0.3472 time to fit residues: 159.6330 Evaluate side-chains 319 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 262 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 682 ASP Chi-restraints excluded: chain D residue 688 GLU Chi-restraints excluded: chain D residue 699 TRP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 242 GLN Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 553 ILE 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 728 GLN Chi-restraints excluded: chain G residue 3 MET Chi-restraints excluded: chain G residue 26 ASN Chi-restraints excluded: chain G residue 39 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 200 optimal weight: 0.0980 chunk 129 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 219 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.183882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.141943 restraints weight = 84902.749| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.75 r_work: 0.3742 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 18252 Z= 0.186 Angle : 0.723 59.199 24637 Z= 0.421 Chirality : 0.040 0.149 2718 Planarity : 0.004 0.057 3187 Dihedral : 4.195 21.887 2430 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.35 % Favored : 93.51 % Rotamer: Outliers : 2.87 % Allowed : 24.53 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.18), residues: 2219 helix: 0.98 (0.17), residues: 946 sheet: -0.83 (0.31), residues: 282 loop : -1.62 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 572 TYR 0.015 0.001 TYR E 217 PHE 0.036 0.001 PHE F 323 TRP 0.013 0.001 TRP E 438 HIS 0.004 0.001 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00419 (18252) covalent geometry : angle 0.72293 (24637) hydrogen bonds : bond 0.03964 ( 828) hydrogen bonds : angle 4.92590 ( 2289) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11477.38 seconds wall clock time: 195 minutes 26.08 seconds (11726.08 seconds total)