Starting phenix.real_space_refine on Wed Nov 15 06:31:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm9_4592/11_2023/6qm9_4592.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm9_4592/11_2023/6qm9_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_4592/11_2023/6qm9_4592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm9_4592/11_2023/6qm9_4592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm9_4592/11_2023/6qm9_4592.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm9_4592/11_2023/6qm9_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 5.76, per 1000 atoms: 0.53 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: 3.92 Conformation dependent library (CDL) restraints added in 1.8 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: 1.02 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: 3.20 Time building geometry restraints manager: 4.30 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: 0.560 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: 3.560 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.310 Find NCS groups from input model: 0.570 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.320 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.227 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2582 time to fit residues: 63.7944 Evaluate side-chains 118 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.356 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6025 ------------------------------------------------------------------------------- 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: 0.5980 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: 2.8786 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11154 Z= 0.355 Angle : 0.669 7.477 15126 Z= 0.357 Chirality : 0.042 0.174 1660 Planarity : 0.005 0.039 1920 Dihedral : 4.910 17.900 1446 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.42 % Allowed : 14.16 % Favored : 83.42 % 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: -2.93 (0.19), residues: 1322 helix: -1.72 (0.14), residues: 916 sheet: -1.77 (0.66), residues: 48 loop : -2.02 (0.29), residues: 358 *********************** 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 151 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 1.130 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 23 residues processed: 138 average time/residue: 0.2060 time to fit residues: 42.5651 Evaluate side-chains 129 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 1.228 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.0975 time to fit residues: 5.9192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 479 HIS ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2466 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= 0.218 Angle : 0.555 7.195 15126 Z= 0.287 Chirality : 0.040 0.144 1660 Planarity : 0.004 0.035 1920 Dihedral : 4.507 14.840 1446 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.16 % Allowed : 15.72 % Favored : 82.12 % 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: -1.35 (0.22), residues: 1322 helix: -0.33 (0.17), residues: 920 sheet: -1.57 (0.71), residues: 48 loop : -2.03 (0.29), residues: 354 *********************** 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 145 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.147 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 137 average time/residue: 0.1961 time to fit residues: 41.0534 Evaluate side-chains 125 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1035 time to fit residues: 3.9250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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: 0.8320 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11154 Z= 0.302 Angle : 0.595 8.397 15126 Z= 0.305 Chirality : 0.042 0.149 1660 Planarity : 0.004 0.034 1920 Dihedral : 4.427 14.258 1446 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.85 % Allowed : 16.23 % Favored : 80.92 % 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: -0.71 (0.23), residues: 1322 helix: 0.18 (0.17), residues: 918 sheet: -1.49 (0.73), residues: 48 loop : -1.83 (0.30), residues: 356 *********************** 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 155 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 1.280 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 134 average time/residue: 0.2067 time to fit residues: 41.8396 Evaluate side-chains 130 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.263 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1016 time to fit residues: 4.7718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 116 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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: 0.8301 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11154 Z= 0.232 Angle : 0.558 6.962 15126 Z= 0.283 Chirality : 0.040 0.182 1660 Planarity : 0.004 0.033 1920 Dihedral : 4.318 13.208 1446 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.12 % Allowed : 18.39 % Favored : 80.48 % 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: -0.37 (0.23), residues: 1322 helix: 0.46 (0.17), residues: 924 sheet: -1.36 (0.74), residues: 48 loop : -1.82 (0.31), residues: 350 *********************** 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 142 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.350 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 132 average time/residue: 0.2093 time to fit residues: 41.4685 Evaluate side-chains 128 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1143 time to fit residues: 2.6047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 129 optimal weight: 0.0270 chunk 107 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.6642 ------------------------------------------------------------------------------- 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 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: 0.8301 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11154 Z= 0.233 Angle : 0.556 7.363 15126 Z= 0.281 Chirality : 0.040 0.143 1660 Planarity : 0.003 0.029 1920 Dihedral : 4.224 13.204 1446 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.55 % Allowed : 19.43 % Favored : 79.02 % 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: -0.13 (0.23), residues: 1322 helix: 0.62 (0.17), residues: 924 sheet: -1.21 (0.75), residues: 48 loop : -1.69 (0.31), residues: 350 *********************** 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 142 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 130 average time/residue: 0.2116 time to fit residues: 41.0343 Evaluate side-chains 133 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1432 time to fit residues: 4.4289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11154 Z= 0.181 Angle : 0.537 7.990 15126 Z= 0.269 Chirality : 0.039 0.145 1660 Planarity : 0.003 0.031 1920 Dihedral : 4.162 13.623 1446 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.69 % Allowed : 20.21 % Favored : 79.10 % 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: 0.78 (0.17), residues: 924 sheet: -1.26 (0.75), residues: 48 loop : -1.63 (0.31), residues: 350 *********************** 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 128 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 1.344 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 124 average time/residue: 0.2109 time to fit residues: 39.2923 Evaluate side-chains 120 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1110 time to fit residues: 2.8198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 82 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 GLN ** 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: 0.8306 moved from start: 0.3089 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= 0.267 Angle : 0.575 7.623 15126 Z= 0.289 Chirality : 0.041 0.154 1660 Planarity : 0.003 0.029 1920 Dihedral : 4.180 14.542 1446 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.73 % Allowed : 20.47 % Favored : 77.81 % 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: 0.12 (0.23), residues: 1322 helix: 0.83 (0.17), residues: 924 sheet: -1.18 (0.76), residues: 48 loop : -1.63 (0.31), residues: 350 *********************** 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 141 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.329 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 125 average time/residue: 0.2053 time to fit residues: 39.2864 Evaluate side-chains 130 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.257 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1032 time to fit residues: 4.3011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 72 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 GLN ** 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: 0.8285 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11154 Z= 0.208 Angle : 0.581 11.736 15126 Z= 0.283 Chirality : 0.040 0.146 1660 Planarity : 0.003 0.031 1920 Dihedral : 4.147 13.700 1446 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.60 % Allowed : 20.81 % Favored : 78.58 % 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: 0.24 (0.23), residues: 1322 helix: 0.90 (0.17), residues: 924 sheet: -1.14 (0.76), residues: 48 loop : -1.53 (0.31), residues: 350 *********************** 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 127 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.267 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 124 average time/residue: 0.2052 time to fit residues: 38.7318 Evaluate side-chains 113 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0998 time to fit residues: 1.8953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8263 moved from start: 0.3265 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= 0.171 Angle : 0.579 10.800 15126 Z= 0.282 Chirality : 0.039 0.144 1660 Planarity : 0.003 0.031 1920 Dihedral : 4.091 13.707 1446 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.26 % Allowed : 22.11 % Favored : 77.63 % 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: 0.34 (0.23), residues: 1322 helix: 0.97 (0.17), residues: 926 sheet: -1.14 (0.77), residues: 48 loop : -1.48 (0.31), residues: 348 ********************** 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 121 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.615 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 119 average time/residue: 0.2078 time to fit residues: 37.2070 Evaluate side-chains 117 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0996 time to fit residues: 2.4817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 106 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN B 143 HIS ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.121613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090382 restraints weight = 20505.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.093024 restraints weight = 10624.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.094665 restraints weight = 7439.037| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11154 Z= 0.151 Angle : 0.567 10.803 15126 Z= 0.274 Chirality : 0.039 0.146 1660 Planarity : 0.003 0.032 1920 Dihedral : 3.995 13.621 1446 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.52 % Allowed : 21.59 % Favored : 77.89 % 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: 1.09 (0.17), residues: 926 sheet: -1.15 (0.79), residues: 48 loop : -1.31 (0.32), residues: 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1938.49 seconds wall clock time: 36 minutes 22.60 seconds (2182.60 seconds total)