Starting phenix.real_space_refine on Fri Mar 15 06:26:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm9_4592/03_2024/6qm9_4592.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm9_4592/03_2024/6qm9_4592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm9_4592/03_2024/6qm9_4592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm9_4592/03_2024/6qm9_4592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm9_4592/03_2024/6qm9_4592.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm9_4592/03_2024/6qm9_4592.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 Ca 4 9.91 5 S 40 5.16 5 C 7068 2.51 5 N 1818 2.21 5 O 1948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B ASP 367": "OD1" <-> "OD2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 480": "OE1" <-> "OE2" Residue "B GLU 482": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "B ASP 499": "OD1" <-> "OD2" Residue "B GLU 668": "OE1" <-> "OE2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B GLU 677": "OE1" <-> "OE2" Residue "B ARG 699": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10878 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5437 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 29, 'TRANS': 643} Chain breaks: 5 Chain: "B" Number of atoms: 5437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5437 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 29, 'TRANS': 643} Chain breaks: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.97, per 1000 atoms: 0.55 Number of scatterers: 10878 At special positions: 0 Unit cell: (120.428, 110.308, 110.308, 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) Ca 4 19.99 S 40 16.00 O 1948 8.00 N 1818 7.00 C 7068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.31 Conformation dependent library (CDL) restraints added in 1.9 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2552 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 71.2% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 32 through 48 Processing helix chain 'A' and resid 72 through 90 removed outlier: 3.646A pdb=" N GLN A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 111 through 124 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 152 through 166 Processing helix chain 'A' and resid 170 through 198 removed outlier: 3.693A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLU A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N SER A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.599A pdb=" N PHE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 246 removed outlier: 3.777A pdb=" N VAL A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.735A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.751A pdb=" N ALA A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.534A pdb=" N GLU A 313 " --> pdb=" O CYS A 309 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 359 removed outlier: 3.813A pdb=" N ILE A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 341 - end of helix removed outlier: 3.558A pdb=" N SER A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.543A pdb=" N LYS A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 3.728A pdb=" N THR A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.581A pdb=" N ALA A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 453 removed outlier: 3.563A pdb=" N VAL A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLN A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 removed outlier: 3.618A pdb=" N LYS A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 494 removed outlier: 4.243A pdb=" N PHE A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 518 removed outlier: 3.902A pdb=" N GLU A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 546 removed outlier: 3.718A pdb=" N VAL A 530 " --> pdb=" O CYS A 526 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.581A pdb=" N ILE A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 627 removed outlier: 3.697A pdb=" N LEU A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 649 removed outlier: 3.556A pdb=" N GLN A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 635 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 649 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 682 removed outlier: 3.825A pdb=" N ILE A 670 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN A 681 " --> pdb=" O GLU A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 696 removed outlier: 3.922A pdb=" N TRP A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 718 removed outlier: 3.729A pdb=" N ALA A 718 " --> pdb=" O GLN A 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 48 Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.646A pdb=" N GLN B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 111 through 124 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 152 through 166 Processing helix chain 'B' and resid 170 through 198 removed outlier: 3.693A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLU B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N SER B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL B 185 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.599A pdb=" N PHE B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 246 removed outlier: 3.777A pdb=" N VAL B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.735A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 302 removed outlier: 3.751A pdb=" N ALA B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 317 removed outlier: 3.534A pdb=" N GLU B 313 " --> pdb=" O CYS B 309 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 359 removed outlier: 3.813A pdb=" N ILE B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.558A pdb=" N SER B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 381 removed outlier: 3.543A pdb=" N LYS B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B 376 " --> pdb=" O GLN B 372 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 392 removed outlier: 3.729A pdb=" N THR B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 412 removed outlier: 3.581A pdb=" N ALA B 409 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 412 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 453 removed outlier: 3.564A pdb=" N VAL B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN B 445 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 471 removed outlier: 3.617A pdb=" N LYS B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 494 removed outlier: 4.243A pdb=" N PHE B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR B 494 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 518 removed outlier: 3.902A pdb=" N GLU B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.718A pdb=" N VAL B 530 " --> pdb=" O CYS B 526 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 584 removed outlier: 3.581A pdb=" N ILE B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 627 removed outlier: 3.697A pdb=" N LEU B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 649 removed outlier: 3.556A pdb=" N GLN B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS B 634 " --> pdb=" O PRO B 630 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU B 635 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 643 " --> pdb=" O ARG B 639 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 646 " --> pdb=" O THR B 642 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 682 removed outlier: 3.825A pdb=" N ILE B 670 " --> pdb=" O HIS B 666 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN B 681 " --> pdb=" O GLU B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 696 removed outlier: 3.921A pdb=" N TRP B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 718 removed outlier: 3.729A pdb=" N ALA B 718 " --> pdb=" O GLN B 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268 removed outlier: 4.038A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 278 " --> pdb=" O HIS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 58 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 268 removed outlier: 4.039A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 278 " --> pdb=" O HIS B 265 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1884 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: 2.99 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3438 1.34 - 1.46: 1962 1.46 - 1.57: 5686 1.57 - 1.69: 2 1.69 - 1.81: 66 Bond restraints: 11154 Sorted by residual: bond pdb=" N PRO B 126 " pdb=" CD PRO B 126 " ideal model delta sigma weight residual 1.473 1.613 -0.140 1.40e-02 5.10e+03 1.00e+02 bond pdb=" N PRO A 126 " pdb=" CD PRO A 126 " ideal model delta sigma weight residual 1.473 1.613 -0.140 1.40e-02 5.10e+03 9.93e+01 bond pdb=" C LEU A 331 " pdb=" N PRO A 332 " ideal model delta sigma weight residual 1.336 1.380 -0.045 1.23e-02 6.61e+03 1.33e+01 bond pdb=" C LEU B 331 " pdb=" N PRO B 332 " ideal model delta sigma weight residual 1.336 1.380 -0.045 1.23e-02 6.61e+03 1.33e+01 bond pdb=" C SER A 595 " pdb=" N PRO A 596 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.51e+00 ... (remaining 11149 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.95: 234 105.95 - 113.15: 5970 113.15 - 120.36: 4415 120.36 - 127.56: 4361 127.56 - 134.77: 146 Bond angle restraints: 15126 Sorted by residual: angle pdb=" CA GLU B 60 " pdb=" CB GLU B 60 " pdb=" CG GLU B 60 " ideal model delta sigma weight residual 114.10 123.30 -9.20 2.00e+00 2.50e-01 2.11e+01 angle pdb=" C VAL B 200 " pdb=" N ILE B 201 " pdb=" CA ILE B 201 " ideal model delta sigma weight residual 120.33 124.01 -3.68 8.00e-01 1.56e+00 2.11e+01 angle pdb=" CA GLU A 60 " pdb=" CB GLU A 60 " pdb=" CG GLU A 60 " ideal model delta sigma weight residual 114.10 123.26 -9.16 2.00e+00 2.50e-01 2.10e+01 angle pdb=" C VAL A 200 " pdb=" N ILE A 201 " pdb=" CA ILE A 201 " ideal model delta sigma weight residual 120.33 123.97 -3.64 8.00e-01 1.56e+00 2.07e+01 angle pdb=" C GLU A 452 " pdb=" N VAL A 453 " pdb=" CA VAL A 453 " ideal model delta sigma weight residual 123.08 119.17 3.91 1.01e+00 9.80e-01 1.50e+01 ... (remaining 15121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 5815 17.62 - 35.24: 598 35.24 - 52.86: 119 52.86 - 70.48: 26 70.48 - 88.10: 16 Dihedral angle restraints: 6574 sinusoidal: 2644 harmonic: 3930 Sorted by residual: dihedral pdb=" CA LYS A 140 " pdb=" C LYS A 140 " pdb=" N TRP A 141 " pdb=" CA TRP A 141 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LYS B 140 " pdb=" C LYS B 140 " pdb=" N TRP B 141 " pdb=" CA TRP B 141 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA MET A 516 " pdb=" C MET A 516 " pdb=" N PHE A 517 " pdb=" CA PHE A 517 " ideal model delta harmonic sigma weight residual -180.00 -163.16 -16.84 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 6571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1166 0.042 - 0.085: 354 0.085 - 0.127: 96 0.127 - 0.169: 38 0.169 - 0.212: 6 Chirality restraints: 1660 Sorted by residual: chirality pdb=" CA THR B 340 " pdb=" N THR B 340 " pdb=" C THR B 340 " pdb=" CB THR B 340 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL B 580 " pdb=" CA VAL B 580 " pdb=" CG1 VAL B 580 " pdb=" CG2 VAL B 580 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 1657 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 689 " 0.040 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO A 690 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 690 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 690 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 689 " -0.040 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO B 690 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 690 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 690 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 455 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO A 456 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " -0.032 5.00e-02 4.00e+02 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3179 2.80 - 3.32: 9918 3.32 - 3.85: 18042 3.85 - 4.37: 20520 4.37 - 4.90: 34868 Nonbonded interactions: 86527 Sorted by model distance: nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.275 2.440 nonbonded pdb=" O SER A 667 " pdb=" CG1 ILE A 670 " model vdw 2.277 3.440 nonbonded pdb=" O SER B 667 " pdb=" CG1 ILE B 670 " model vdw 2.277 3.440 nonbonded pdb=" O GLY B 572 " pdb=" OG SER B 576 " model vdw 2.297 2.440 ... (remaining 86522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.600 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.630 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 11154 Z= 0.321 Angle : 0.888 9.769 15126 Z= 0.529 Chirality : 0.047 0.212 1660 Planarity : 0.006 0.060 1920 Dihedral : 15.520 88.097 4022 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.09 (0.14), residues: 1322 helix: -4.39 (0.07), residues: 906 sheet: -2.25 (0.57), residues: 42 loop : -2.49 (0.27), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 235 HIS 0.004 0.001 HIS A 366 PHE 0.040 0.002 PHE B 396 TYR 0.014 0.001 TYR A 26 ARG 0.006 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.224 Fit side-chains REVERT: A 141 TRP cc_start: 0.7508 (p90) cc_final: 0.7176 (p90) REVERT: A 313 GLU cc_start: 0.8203 (pp20) cc_final: 0.7983 (pp20) REVERT: A 338 ILE cc_start: 0.8607 (mm) cc_final: 0.8343 (mt) REVERT: A 407 TRP cc_start: 0.8506 (m100) cc_final: 0.8159 (m100) REVERT: A 673 GLU cc_start: 0.8299 (tp30) cc_final: 0.8084 (tp30) REVERT: A 691 GLU cc_start: 0.7848 (pp20) cc_final: 0.7467 (pm20) REVERT: B 141 TRP cc_start: 0.7564 (p90) cc_final: 0.7216 (p90) REVERT: B 313 GLU cc_start: 0.8204 (pp20) cc_final: 0.7986 (pp20) REVERT: B 315 PHE cc_start: 0.9007 (t80) cc_final: 0.8785 (t80) REVERT: B 338 ILE cc_start: 0.8598 (mm) cc_final: 0.8357 (mt) REVERT: B 407 TRP cc_start: 0.8526 (m100) cc_final: 0.7967 (m100) REVERT: B 673 GLU cc_start: 0.8270 (tp30) cc_final: 0.8024 (tp30) REVERT: B 691 GLU cc_start: 0.7840 (pp20) cc_final: 0.7515 (pm20) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2510 time to fit residues: 62.0211 Evaluate side-chains 123 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 0.0570 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 overall best weight: 2.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 GLN A 310 ASN A 374 GLN A 378 ASN A 479 HIS ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN B 310 ASN B 374 GLN B 378 ASN B 479 HIS ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11154 Z= 0.344 Angle : 0.657 7.004 15126 Z= 0.351 Chirality : 0.042 0.171 1660 Planarity : 0.005 0.040 1920 Dihedral : 4.909 18.523 1446 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.33 % Allowed : 13.99 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.19), residues: 1322 helix: -1.68 (0.14), residues: 912 sheet: -1.83 (0.66), residues: 48 loop : -1.98 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 141 HIS 0.003 0.001 HIS B 611 PHE 0.019 0.002 PHE B 205 TYR 0.014 0.002 TYR B 360 ARG 0.007 0.001 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.136 Fit side-chains REVERT: A 313 GLU cc_start: 0.8472 (pp20) cc_final: 0.8141 (pp20) REVERT: A 338 ILE cc_start: 0.8721 (mm) cc_final: 0.8477 (mt) REVERT: A 407 TRP cc_start: 0.8586 (m100) cc_final: 0.8196 (m100) REVERT: B 313 GLU cc_start: 0.8443 (pp20) cc_final: 0.8096 (pp20) REVERT: B 315 PHE cc_start: 0.9072 (t80) cc_final: 0.8684 (t80) REVERT: B 338 ILE cc_start: 0.8715 (mm) cc_final: 0.8480 (mt) REVERT: B 406 PHE cc_start: 0.8249 (t80) cc_final: 0.7706 (t80) outliers start: 27 outliers final: 24 residues processed: 139 average time/residue: 0.2023 time to fit residues: 41.9762 Evaluate side-chains 126 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 585 ASN Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS B 317 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11154 Z= 0.232 Angle : 0.554 6.717 15126 Z= 0.288 Chirality : 0.040 0.145 1660 Planarity : 0.004 0.035 1920 Dihedral : 4.487 15.424 1446 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.54 % Allowed : 14.51 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.22), residues: 1322 helix: -0.28 (0.17), residues: 920 sheet: -1.63 (0.70), residues: 48 loop : -2.01 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 235 HIS 0.003 0.001 HIS B 611 PHE 0.032 0.001 PHE B 205 TYR 0.016 0.001 TYR A 26 ARG 0.005 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 125 time to evaluate : 1.307 Fit side-chains REVERT: A 313 GLU cc_start: 0.8463 (pp20) cc_final: 0.8229 (pp20) REVERT: A 338 ILE cc_start: 0.8776 (mm) cc_final: 0.8495 (mt) REVERT: A 406 PHE cc_start: 0.7718 (t80) cc_final: 0.7383 (t80) REVERT: B 313 GLU cc_start: 0.8387 (pp20) cc_final: 0.8151 (pp20) REVERT: B 315 PHE cc_start: 0.9077 (t80) cc_final: 0.8558 (t80) REVERT: B 338 ILE cc_start: 0.8772 (mm) cc_final: 0.8514 (mt) REVERT: B 406 PHE cc_start: 0.8098 (t80) cc_final: 0.7616 (t80) outliers start: 41 outliers final: 29 residues processed: 145 average time/residue: 0.1968 time to fit residues: 43.3004 Evaluate side-chains 142 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11154 Z= 0.194 Angle : 0.542 7.621 15126 Z= 0.273 Chirality : 0.040 0.172 1660 Planarity : 0.003 0.034 1920 Dihedral : 4.261 14.210 1446 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.80 % Allowed : 15.54 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.23), residues: 1322 helix: 0.33 (0.17), residues: 920 sheet: -1.32 (0.74), residues: 48 loop : -1.83 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 407 HIS 0.002 0.001 HIS B 611 PHE 0.028 0.001 PHE B 205 TYR 0.015 0.001 TYR B 26 ARG 0.006 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 124 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8308 (pp20) cc_final: 0.8067 (pp20) REVERT: A 338 ILE cc_start: 0.8740 (mm) cc_final: 0.8469 (mt) REVERT: A 460 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8376 (mm-40) REVERT: B 313 GLU cc_start: 0.8372 (pp20) cc_final: 0.8165 (pp20) REVERT: B 315 PHE cc_start: 0.9039 (t80) cc_final: 0.8609 (t80) REVERT: B 338 ILE cc_start: 0.8736 (mm) cc_final: 0.8469 (mt) REVERT: B 406 PHE cc_start: 0.8017 (t80) cc_final: 0.7553 (t80) outliers start: 44 outliers final: 29 residues processed: 149 average time/residue: 0.1953 time to fit residues: 43.7433 Evaluate side-chains 151 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11154 Z= 0.225 Angle : 0.543 6.837 15126 Z= 0.274 Chirality : 0.040 0.144 1660 Planarity : 0.003 0.031 1920 Dihedral : 4.171 13.816 1446 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.45 % Allowed : 16.93 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.23), residues: 1322 helix: 0.59 (0.17), residues: 924 sheet: -1.17 (0.75), residues: 48 loop : -1.71 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 235 HIS 0.003 0.001 HIS B 611 PHE 0.035 0.001 PHE A 205 TYR 0.015 0.001 TYR A 26 ARG 0.007 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 124 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 141 TRP cc_start: 0.8151 (OUTLIER) cc_final: 0.7198 (p90) REVERT: A 313 GLU cc_start: 0.8334 (pp20) cc_final: 0.8064 (pp20) REVERT: A 338 ILE cc_start: 0.8686 (mm) cc_final: 0.8431 (mt) REVERT: A 406 PHE cc_start: 0.8102 (t80) cc_final: 0.7612 (t80) REVERT: A 460 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8360 (mm-40) REVERT: B 141 TRP cc_start: 0.8164 (OUTLIER) cc_final: 0.7215 (p90) REVERT: B 313 GLU cc_start: 0.8452 (pp20) cc_final: 0.8252 (pp20) REVERT: B 315 PHE cc_start: 0.9027 (t80) cc_final: 0.8626 (t80) REVERT: B 338 ILE cc_start: 0.8692 (mm) cc_final: 0.8440 (mt) outliers start: 40 outliers final: 31 residues processed: 146 average time/residue: 0.1972 time to fit residues: 43.3858 Evaluate side-chains 150 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 0.0670 chunk 124 optimal weight: 5.9990 overall best weight: 2.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11154 Z= 0.280 Angle : 0.572 6.915 15126 Z= 0.289 Chirality : 0.041 0.152 1660 Planarity : 0.003 0.030 1920 Dihedral : 4.199 13.356 1446 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.80 % Allowed : 17.79 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.23), residues: 1322 helix: 0.69 (0.17), residues: 924 sheet: -1.11 (0.76), residues: 48 loop : -1.72 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 141 HIS 0.003 0.001 HIS B 611 PHE 0.036 0.001 PHE B 205 TYR 0.015 0.001 TYR B 26 ARG 0.006 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 116 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 141 TRP cc_start: 0.8430 (OUTLIER) cc_final: 0.6987 (p90) REVERT: A 313 GLU cc_start: 0.8325 (pp20) cc_final: 0.8063 (pp20) REVERT: A 338 ILE cc_start: 0.8630 (mm) cc_final: 0.8373 (mt) REVERT: A 460 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8320 (mm-40) REVERT: B 141 TRP cc_start: 0.8455 (OUTLIER) cc_final: 0.6912 (p90) REVERT: B 315 PHE cc_start: 0.8990 (t80) cc_final: 0.8530 (t80) REVERT: B 338 ILE cc_start: 0.8641 (mm) cc_final: 0.8385 (mt) REVERT: B 406 PHE cc_start: 0.7955 (t80) cc_final: 0.7636 (t80) outliers start: 44 outliers final: 34 residues processed: 137 average time/residue: 0.2000 time to fit residues: 41.1015 Evaluate side-chains 150 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.0050 chunk 59 optimal weight: 0.0030 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11154 Z= 0.141 Angle : 0.523 7.857 15126 Z= 0.257 Chirality : 0.038 0.141 1660 Planarity : 0.003 0.032 1920 Dihedral : 4.048 13.787 1446 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.68 % Allowed : 19.95 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.23), residues: 1322 helix: 0.90 (0.17), residues: 922 sheet: -0.97 (0.77), residues: 48 loop : -1.62 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 235 HIS 0.002 0.000 HIS B 611 PHE 0.036 0.001 PHE B 205 TYR 0.013 0.001 TYR B 26 ARG 0.007 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8276 (tp) REVERT: A 141 TRP cc_start: 0.8279 (OUTLIER) cc_final: 0.7384 (p90) REVERT: A 313 GLU cc_start: 0.8270 (pp20) cc_final: 0.8029 (pp20) REVERT: A 338 ILE cc_start: 0.8619 (mm) cc_final: 0.8372 (mt) REVERT: A 460 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8301 (mm-40) REVERT: A 521 TRP cc_start: 0.8966 (OUTLIER) cc_final: 0.8732 (t60) REVERT: B 43 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8259 (tp) REVERT: B 141 TRP cc_start: 0.8299 (OUTLIER) cc_final: 0.7303 (p90) REVERT: B 315 PHE cc_start: 0.9000 (t80) cc_final: 0.8701 (t80) REVERT: B 338 ILE cc_start: 0.8637 (mm) cc_final: 0.8390 (mt) REVERT: B 406 PHE cc_start: 0.7796 (t80) cc_final: 0.7524 (t80) REVERT: B 521 TRP cc_start: 0.8961 (OUTLIER) cc_final: 0.8730 (t60) outliers start: 31 outliers final: 22 residues processed: 142 average time/residue: 0.1970 time to fit residues: 42.1669 Evaluate side-chains 152 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.0000 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 117 optimal weight: 0.3980 chunk 123 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN A 531 ASN B 510 GLN B 531 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11154 Z= 0.142 Angle : 0.519 8.083 15126 Z= 0.256 Chirality : 0.038 0.141 1660 Planarity : 0.003 0.030 1920 Dihedral : 3.900 13.929 1446 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.02 % Allowed : 20.29 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1322 helix: 1.07 (0.17), residues: 926 sheet: -0.96 (0.79), residues: 48 loop : -1.53 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 235 HIS 0.002 0.000 HIS B 153 PHE 0.038 0.001 PHE B 205 TYR 0.012 0.001 TYR B 26 ARG 0.007 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: A 141 TRP cc_start: 0.8173 (OUTLIER) cc_final: 0.7543 (p90) REVERT: A 313 GLU cc_start: 0.8303 (pp20) cc_final: 0.8076 (pp20) REVERT: A 338 ILE cc_start: 0.8650 (mm) cc_final: 0.8412 (mt) REVERT: A 460 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8292 (mm-40) REVERT: A 521 TRP cc_start: 0.9005 (OUTLIER) cc_final: 0.8744 (t60) REVERT: B 141 TRP cc_start: 0.8153 (OUTLIER) cc_final: 0.7450 (p90) REVERT: B 315 PHE cc_start: 0.8974 (t80) cc_final: 0.8634 (t80) REVERT: B 338 ILE cc_start: 0.8661 (mm) cc_final: 0.8421 (mt) REVERT: B 406 PHE cc_start: 0.7808 (t80) cc_final: 0.7572 (t80) REVERT: B 521 TRP cc_start: 0.9006 (OUTLIER) cc_final: 0.8743 (t60) outliers start: 35 outliers final: 27 residues processed: 152 average time/residue: 0.1919 time to fit residues: 44.0848 Evaluate side-chains 153 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 79 optimal weight: 0.3980 chunk 127 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11154 Z= 0.225 Angle : 0.559 10.087 15126 Z= 0.276 Chirality : 0.040 0.146 1660 Planarity : 0.003 0.029 1920 Dihedral : 3.915 13.448 1446 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.20 % Allowed : 20.55 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1322 helix: 1.12 (0.17), residues: 926 sheet: -0.83 (0.80), residues: 48 loop : -1.52 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 141 HIS 0.003 0.001 HIS B 611 PHE 0.037 0.001 PHE B 205 TYR 0.012 0.001 TYR A 26 ARG 0.007 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 141 TRP cc_start: 0.8300 (OUTLIER) cc_final: 0.7339 (p90) REVERT: A 313 GLU cc_start: 0.8324 (pp20) cc_final: 0.8112 (pp20) REVERT: A 338 ILE cc_start: 0.8637 (mm) cc_final: 0.8404 (mt) REVERT: A 460 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8290 (mm-40) REVERT: A 638 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8039 (mt-10) REVERT: B 141 TRP cc_start: 0.8329 (OUTLIER) cc_final: 0.7289 (p90) REVERT: B 315 PHE cc_start: 0.8986 (t80) cc_final: 0.8668 (t80) REVERT: B 338 ILE cc_start: 0.8662 (mm) cc_final: 0.8428 (mt) REVERT: B 406 PHE cc_start: 0.7803 (t80) cc_final: 0.7585 (t80) REVERT: B 638 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8016 (mt-10) outliers start: 37 outliers final: 29 residues processed: 141 average time/residue: 0.1905 time to fit residues: 40.8275 Evaluate side-chains 149 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11154 Z= 0.262 Angle : 0.583 9.146 15126 Z= 0.291 Chirality : 0.041 0.158 1660 Planarity : 0.003 0.029 1920 Dihedral : 4.041 13.529 1446 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.02 % Allowed : 20.55 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.23), residues: 1322 helix: 1.11 (0.17), residues: 926 sheet: -0.71 (0.82), residues: 48 loop : -1.46 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 141 HIS 0.003 0.001 HIS A 611 PHE 0.037 0.001 PHE A 205 TYR 0.013 0.001 TYR B 26 ARG 0.007 0.000 ARG B 710 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 114 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 141 TRP cc_start: 0.8438 (OUTLIER) cc_final: 0.7203 (p90) REVERT: A 313 GLU cc_start: 0.8323 (pp20) cc_final: 0.8107 (pp20) REVERT: A 338 ILE cc_start: 0.8661 (mm) cc_final: 0.8424 (mt) REVERT: A 460 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8282 (mm-40) REVERT: A 521 TRP cc_start: 0.9051 (OUTLIER) cc_final: 0.8749 (t60) REVERT: A 638 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8054 (mt-10) REVERT: B 141 TRP cc_start: 0.8456 (OUTLIER) cc_final: 0.7194 (p90) REVERT: B 315 PHE cc_start: 0.9023 (t80) cc_final: 0.8655 (t80) REVERT: B 338 ILE cc_start: 0.8656 (mm) cc_final: 0.8424 (mt) REVERT: B 406 PHE cc_start: 0.7855 (t80) cc_final: 0.7627 (t80) REVERT: B 638 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8046 (mt-10) outliers start: 35 outliers final: 30 residues processed: 136 average time/residue: 0.1860 time to fit residues: 38.6236 Evaluate side-chains 146 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.120266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.088412 restraints weight = 20434.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.091125 restraints weight = 10412.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.092773 restraints weight = 7224.341| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11154 Z= 0.186 Angle : 0.556 9.580 15126 Z= 0.275 Chirality : 0.039 0.148 1660 Planarity : 0.003 0.029 1920 Dihedral : 3.984 13.477 1446 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.85 % Allowed : 20.64 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1322 helix: 1.19 (0.17), residues: 926 sheet: -0.71 (0.81), residues: 48 loop : -1.37 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 141 HIS 0.002 0.001 HIS B 611 PHE 0.039 0.001 PHE A 205 TYR 0.013 0.001 TYR A 26 ARG 0.008 0.000 ARG B 710 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1944.93 seconds wall clock time: 36 minutes 1.95 seconds (2161.95 seconds total)