Starting phenix.real_space_refine (version: dev) on Thu Feb 23 11:38:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xew_33161/02_2023/7xew_33161.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xew_33161/02_2023/7xew_33161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xew_33161/02_2023/7xew_33161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xew_33161/02_2023/7xew_33161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xew_33161/02_2023/7xew_33161.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xew_33161/02_2023/7xew_33161.pdb" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.003 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 Process input model Symmetric amino acids flipped Residue "A ASP 71": "OD1" <-> "OD2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 464": "OD1" <-> "OD2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 531": "OD1" <-> "OD2" Residue "A GLU 642": "OE1" <-> "OE2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 464": "OD1" <-> "OD2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 531": "OD1" <-> "OD2" Residue "B GLU 642": "OE1" <-> "OE2" Residue "B GLU 696": "OE1" <-> "OE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 464": "OD1" <-> "OD2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 531": "OD1" <-> "OD2" Residue "C GLU 642": "OE1" <-> "OE2" Residue "C GLU 696": "OE1" <-> "OE2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 464": "OD1" <-> "OD2" Residue "D PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 531": "OD1" <-> "OD2" Residue "D GLU 642": "OE1" <-> "OE2" Residue "D GLU 696": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19988 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4997 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 4997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4997 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "C" Number of atoms: 4997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4997 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "D" Number of atoms: 4997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4997 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Time building chain proxies: 10.32, per 1000 atoms: 0.52 Number of scatterers: 19988 At special positions: 0 Unit cell: (157.17, 157.17, 115.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 3432 8.00 N 3368 7.00 C 13080 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: 7.66 Conformation dependent library (CDL) restraints added in 2.7 seconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 4 sheets defined 62.2% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 83 through 88 removed outlier: 3.721A pdb=" N GLU A 86 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.855A pdb=" N ASN A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.559A pdb=" N VAL A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.561A pdb=" N GLU A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 251 Processing helix chain 'A' and resid 255 through 277 Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.781A pdb=" N ASP A 284 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 373 through 408 Proline residue: A 386 - end of helix Processing helix chain 'A' and resid 424 through 454 Processing helix chain 'A' and resid 455 through 458 removed outlier: 3.994A pdb=" N ILE A 458 " --> pdb=" O ARG A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 467 through 487 removed outlier: 4.026A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.935A pdb=" N LEU A 495 " --> pdb=" O TRP A 491 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' Processing helix chain 'A' and resid 514 through 532 removed outlier: 3.670A pdb=" N LEU A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 553 Processing helix chain 'A' and resid 587 through 601 removed outlier: 3.565A pdb=" N THR A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 629 Processing helix chain 'A' and resid 631 through 668 removed outlier: 5.925A pdb=" N THR A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 714 removed outlier: 3.768A pdb=" N THR A 713 " --> pdb=" O TRP A 710 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 714 " --> pdb=" O GLU A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 83 through 88 removed outlier: 3.721A pdb=" N GLU B 86 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR B 88 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.855A pdb=" N ASN B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 171 through 181 removed outlier: 3.559A pdb=" N VAL B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 217 through 226 removed outlier: 3.561A pdb=" N GLU B 226 " --> pdb=" O THR B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 251 Processing helix chain 'B' and resid 255 through 277 Processing helix chain 'B' and resid 281 through 285 removed outlier: 3.781A pdb=" N ASP B 284 " --> pdb=" O GLN B 281 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 285 " --> pdb=" O LEU B 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 281 through 285' Processing helix chain 'B' and resid 292 through 301 Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 373 through 408 Proline residue: B 386 - end of helix Processing helix chain 'B' and resid 424 through 454 Processing helix chain 'B' and resid 455 through 458 removed outlier: 3.994A pdb=" N ILE B 458 " --> pdb=" O ARG B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 455 through 458' Processing helix chain 'B' and resid 467 through 487 removed outlier: 4.026A pdb=" N PHE B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 506 removed outlier: 3.934A pdb=" N LEU B 495 " --> pdb=" O TRP B 491 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'B' and resid 514 through 532 removed outlier: 3.670A pdb=" N LEU B 532 " --> pdb=" O ILE B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 553 Processing helix chain 'B' and resid 587 through 601 removed outlier: 3.565A pdb=" N THR B 599 " --> pdb=" O LEU B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 629 Processing helix chain 'B' and resid 631 through 668 removed outlier: 5.924A pdb=" N THR B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASP B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 714 removed outlier: 3.768A pdb=" N THR B 713 " --> pdb=" O TRP B 710 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 714 " --> pdb=" O GLU B 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 82 Processing helix chain 'C' and resid 83 through 88 removed outlier: 3.721A pdb=" N GLU C 86 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR C 88 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.855A pdb=" N ASN C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 140 Processing helix chain 'C' and resid 161 through 169 Processing helix chain 'C' and resid 171 through 181 removed outlier: 3.558A pdb=" N VAL C 175 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 217 through 226 removed outlier: 3.562A pdb=" N GLU C 226 " --> pdb=" O THR C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 255 through 277 Processing helix chain 'C' and resid 281 through 285 removed outlier: 3.781A pdb=" N ASP C 284 " --> pdb=" O GLN C 281 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 285 " --> pdb=" O LEU C 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 281 through 285' Processing helix chain 'C' and resid 292 through 301 Processing helix chain 'C' and resid 302 through 311 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 373 through 408 Proline residue: C 386 - end of helix Processing helix chain 'C' and resid 424 through 454 Processing helix chain 'C' and resid 455 through 458 removed outlier: 3.995A pdb=" N ILE C 458 " --> pdb=" O ARG C 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 455 through 458' Processing helix chain 'C' and resid 467 through 487 removed outlier: 4.026A pdb=" N PHE C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 506 removed outlier: 3.935A pdb=" N LEU C 495 " --> pdb=" O TRP C 491 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 509 No H-bonds generated for 'chain 'C' and resid 507 through 509' Processing helix chain 'C' and resid 514 through 532 removed outlier: 3.669A pdb=" N LEU C 532 " --> pdb=" O ILE C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 553 Processing helix chain 'C' and resid 587 through 601 removed outlier: 3.565A pdb=" N THR C 599 " --> pdb=" O LEU C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 629 Processing helix chain 'C' and resid 631 through 668 removed outlier: 5.926A pdb=" N THR C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 714 removed outlier: 3.768A pdb=" N THR C 713 " --> pdb=" O TRP C 710 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 714 " --> pdb=" O GLU C 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 82 Processing helix chain 'D' and resid 83 through 88 removed outlier: 3.721A pdb=" N GLU D 86 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 Processing helix chain 'D' and resid 114 through 122 removed outlier: 3.855A pdb=" N ASN D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 140 Processing helix chain 'D' and resid 161 through 169 Processing helix chain 'D' and resid 171 through 181 removed outlier: 3.559A pdb=" N VAL D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 Processing helix chain 'D' and resid 217 through 226 removed outlier: 3.561A pdb=" N GLU D 226 " --> pdb=" O THR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 255 through 277 Processing helix chain 'D' and resid 281 through 285 removed outlier: 3.782A pdb=" N ASP D 284 " --> pdb=" O GLN D 281 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 285 " --> pdb=" O LEU D 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 281 through 285' Processing helix chain 'D' and resid 292 through 301 Processing helix chain 'D' and resid 302 through 311 Processing helix chain 'D' and resid 350 through 358 Processing helix chain 'D' and resid 373 through 408 Proline residue: D 386 - end of helix Processing helix chain 'D' and resid 424 through 454 Processing helix chain 'D' and resid 455 through 458 removed outlier: 3.995A pdb=" N ILE D 458 " --> pdb=" O ARG D 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 455 through 458' Processing helix chain 'D' and resid 467 through 487 removed outlier: 4.026A pdb=" N PHE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 506 removed outlier: 3.935A pdb=" N LEU D 495 " --> pdb=" O TRP D 491 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 509 No H-bonds generated for 'chain 'D' and resid 507 through 509' Processing helix chain 'D' and resid 514 through 532 removed outlier: 3.669A pdb=" N LEU D 532 " --> pdb=" O ILE D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 553 Processing helix chain 'D' and resid 587 through 601 removed outlier: 3.566A pdb=" N THR D 599 " --> pdb=" O LEU D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 629 Processing helix chain 'D' and resid 631 through 668 removed outlier: 5.925A pdb=" N THR D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 714 removed outlier: 3.767A pdb=" N THR D 713 " --> pdb=" O TRP D 710 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 714 " --> pdb=" O GLU D 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 324 through 330 removed outlier: 7.093A pdb=" N VAL A 335 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N CYS A 329 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG A 697 " --> pdb=" O LEU A 684 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 324 through 330 removed outlier: 7.093A pdb=" N VAL B 335 " --> pdb=" O GLU B 327 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N CYS B 329 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 333 " --> pdb=" O CYS B 329 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG B 697 " --> pdb=" O LEU B 684 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 324 through 330 removed outlier: 7.092A pdb=" N VAL C 335 " --> pdb=" O GLU C 327 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N CYS C 329 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 333 " --> pdb=" O CYS C 329 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 697 " --> pdb=" O LEU C 684 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 324 through 330 removed outlier: 7.092A pdb=" N VAL D 335 " --> pdb=" O GLU D 327 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N CYS D 329 " --> pdb=" O VAL D 333 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 333 " --> pdb=" O CYS D 329 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG D 697 " --> pdb=" O LEU D 684 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3168 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: 5.50 Time building geometry restraints manager: 8.27 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: 5825 1.34 - 1.45: 3418 1.45 - 1.57: 11093 1.57 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 20496 Sorted by residual: bond pdb=" CA ILE C 385 " pdb=" CB ILE C 385 " ideal model delta sigma weight residual 1.537 1.546 -0.009 5.00e-03 4.00e+04 3.52e+00 bond pdb=" CA ILE A 385 " pdb=" CB ILE A 385 " ideal model delta sigma weight residual 1.537 1.546 -0.009 5.00e-03 4.00e+04 3.36e+00 bond pdb=" CA ILE B 385 " pdb=" CB ILE B 385 " ideal model delta sigma weight residual 1.537 1.546 -0.009 5.00e-03 4.00e+04 3.15e+00 bond pdb=" CA ILE D 385 " pdb=" CB ILE D 385 " ideal model delta sigma weight residual 1.537 1.546 -0.009 5.00e-03 4.00e+04 3.11e+00 bond pdb=" CG PRO D 694 " pdb=" CD PRO D 694 " ideal model delta sigma weight residual 1.503 1.444 0.059 3.40e-02 8.65e+02 2.99e+00 ... (remaining 20491 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.51: 496 106.51 - 113.38: 11178 113.38 - 120.26: 7314 120.26 - 127.13: 8568 127.13 - 134.01: 256 Bond angle restraints: 27812 Sorted by residual: angle pdb=" N VAL C 148 " pdb=" CA VAL C 148 " pdb=" C VAL C 148 " ideal model delta sigma weight residual 113.71 107.79 5.92 9.50e-01 1.11e+00 3.88e+01 angle pdb=" N VAL B 148 " pdb=" CA VAL B 148 " pdb=" C VAL B 148 " ideal model delta sigma weight residual 113.71 107.80 5.91 9.50e-01 1.11e+00 3.88e+01 angle pdb=" N VAL A 148 " pdb=" CA VAL A 148 " pdb=" C VAL A 148 " ideal model delta sigma weight residual 113.71 107.83 5.88 9.50e-01 1.11e+00 3.84e+01 angle pdb=" N VAL D 148 " pdb=" CA VAL D 148 " pdb=" C VAL D 148 " ideal model delta sigma weight residual 113.71 107.87 5.84 9.50e-01 1.11e+00 3.78e+01 angle pdb=" N VAL D 368 " pdb=" CA VAL D 368 " pdb=" C VAL D 368 " ideal model delta sigma weight residual 106.21 110.91 -4.70 1.07e+00 8.73e-01 1.93e+01 ... (remaining 27807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 10655 15.29 - 30.59: 1025 30.59 - 45.88: 280 45.88 - 61.18: 44 61.18 - 76.47: 16 Dihedral angle restraints: 12020 sinusoidal: 4852 harmonic: 7168 Sorted by residual: dihedral pdb=" CA PRO B 146 " pdb=" C PRO B 146 " pdb=" N LEU B 147 " pdb=" CA LEU B 147 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PRO A 146 " pdb=" C PRO A 146 " pdb=" N LEU A 147 " pdb=" CA LEU A 147 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PRO D 146 " pdb=" C PRO D 146 " pdb=" N LEU D 147 " pdb=" CA LEU D 147 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 12017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2233 0.040 - 0.080: 687 0.080 - 0.119: 199 0.119 - 0.159: 17 0.159 - 0.199: 4 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CA VAL C 369 " pdb=" N VAL C 369 " pdb=" C VAL C 369 " pdb=" CB VAL C 369 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA VAL A 369 " pdb=" N VAL A 369 " pdb=" C VAL A 369 " pdb=" CB VAL A 369 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA VAL B 369 " pdb=" N VAL B 369 " pdb=" C VAL B 369 " pdb=" CB VAL B 369 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.23e-01 ... (remaining 3137 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 693 " 0.045 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO D 694 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 694 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 694 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 693 " 0.045 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO C 694 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 694 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 694 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 693 " 0.045 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO A 694 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 694 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 694 " 0.037 5.00e-02 4.00e+02 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2256 2.75 - 3.29: 20079 3.29 - 3.82: 33531 3.82 - 4.36: 37806 4.36 - 4.90: 65770 Nonbonded interactions: 159442 Sorted by model distance: nonbonded pdb=" OE1 GLU B 711 " pdb=" NZ LYS C 216 " model vdw 2.210 2.520 nonbonded pdb=" NZ LYS A 216 " pdb=" OE1 GLU D 711 " model vdw 2.217 2.520 nonbonded pdb=" OE1 GLU C 711 " pdb=" NZ LYS D 216 " model vdw 2.233 2.520 nonbonded pdb=" OE1 GLU A 711 " pdb=" NZ LYS B 216 " model vdw 2.247 2.520 nonbonded pdb=" NH1 ARG B 275 " pdb=" OH TYR B 318 " model vdw 2.249 2.520 ... (remaining 159437 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' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 13080 2.51 5 N 3368 2.21 5 O 3432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 4.990 Check model and map are aligned: 0.290 Process input model: 47.030 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.170 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.003 0.060 20496 Z= 0.221 Angle : 0.704 9.954 27812 Z= 0.426 Chirality : 0.042 0.199 3140 Planarity : 0.005 0.067 3432 Dihedral : 13.276 76.474 7396 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.47 % Favored : 94.04 % Rotamer Outliers : 1.10 % 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: 0.26 (0.18), residues: 2432 helix: 1.84 (0.14), residues: 1432 sheet: -2.98 (0.42), residues: 84 loop : -2.36 (0.20), residues: 916 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 331 time to evaluate : 2.436 Fit side-chains outliers start: 24 outliers final: 8 residues processed: 339 average time/residue: 1.1296 time to fit residues: 440.3928 Evaluate side-chains 210 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 202 time to evaluate : 2.324 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 1.7528 time to fit residues: 10.7562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 678 HIS ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 20496 Z= 0.218 Angle : 0.594 8.401 27812 Z= 0.305 Chirality : 0.039 0.159 3140 Planarity : 0.004 0.050 3432 Dihedral : 3.864 18.455 2696 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.65 % Favored : 95.19 % Rotamer Outliers : 2.80 % 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 (0.18), residues: 2432 helix: 2.22 (0.14), residues: 1448 sheet: -2.44 (0.43), residues: 84 loop : -2.34 (0.20), residues: 900 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 239 time to evaluate : 2.241 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 33 residues processed: 282 average time/residue: 1.0877 time to fit residues: 354.6877 Evaluate side-chains 241 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 208 time to evaluate : 2.486 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 22 residues processed: 11 average time/residue: 0.4643 time to fit residues: 10.2096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 0.0770 chunk 184 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 221 optimal weight: 8.9990 chunk 239 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 20496 Z= 0.217 Angle : 0.561 8.325 27812 Z= 0.290 Chirality : 0.039 0.262 3140 Planarity : 0.004 0.050 3432 Dihedral : 3.850 17.499 2696 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.81 % Favored : 95.02 % Rotamer Outliers : 3.54 % 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: 0.75 (0.18), residues: 2432 helix: 2.25 (0.14), residues: 1452 sheet: -1.57 (0.45), residues: 84 loop : -2.46 (0.19), residues: 896 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 220 time to evaluate : 2.496 Fit side-chains revert: symmetry clash outliers start: 77 outliers final: 42 residues processed: 272 average time/residue: 1.0432 time to fit residues: 330.8260 Evaluate side-chains 241 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 199 time to evaluate : 2.432 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 32 residues processed: 10 average time/residue: 0.3952 time to fit residues: 8.8397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 20496 Z= 0.184 Angle : 0.579 14.423 27812 Z= 0.289 Chirality : 0.038 0.256 3140 Planarity : 0.004 0.048 3432 Dihedral : 3.833 17.314 2696 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.36 % Favored : 95.48 % Rotamer Outliers : 4.04 % 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: 0.85 (0.18), residues: 2432 helix: 2.30 (0.14), residues: 1452 sheet: -1.45 (0.40), residues: 112 loop : -2.37 (0.20), residues: 868 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 214 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 47 residues processed: 278 average time/residue: 0.9757 time to fit residues: 318.5463 Evaluate side-chains 244 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 197 time to evaluate : 2.535 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 33 residues processed: 14 average time/residue: 0.4317 time to fit residues: 11.2809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 120 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 20496 Z= 0.296 Angle : 0.618 13.298 27812 Z= 0.311 Chirality : 0.042 0.372 3140 Planarity : 0.004 0.046 3432 Dihedral : 4.007 20.467 2696 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.94 % Rotamer Outliers : 5.42 % 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: 0.76 (0.18), residues: 2432 helix: 2.15 (0.14), residues: 1456 sheet: -0.69 (0.50), residues: 88 loop : -2.35 (0.19), residues: 888 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 205 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 61 residues processed: 289 average time/residue: 0.9868 time to fit residues: 335.0947 Evaluate side-chains 250 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 189 time to evaluate : 2.319 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 49 residues processed: 13 average time/residue: 0.5156 time to fit residues: 11.9292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 138 optimal weight: 0.0370 chunk 58 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 195 optimal weight: 8.9990 chunk 109 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 678 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 20496 Z= 0.157 Angle : 0.575 14.133 27812 Z= 0.285 Chirality : 0.039 0.297 3140 Planarity : 0.004 0.045 3432 Dihedral : 3.926 20.757 2696 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.95 % Favored : 95.89 % Rotamer Outliers : 4.46 % 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: 0.96 (0.18), residues: 2432 helix: 2.27 (0.14), residues: 1460 sheet: -0.55 (0.50), residues: 88 loop : -2.23 (0.19), residues: 884 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 220 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 68 residues processed: 297 average time/residue: 0.9721 time to fit residues: 339.7095 Evaluate side-chains 269 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 201 time to evaluate : 2.190 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 54 residues processed: 17 average time/residue: 0.3249 time to fit residues: 11.1712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 GLN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 678 HIS ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN D 678 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 20496 Z= 0.339 Angle : 0.663 13.627 27812 Z= 0.330 Chirality : 0.043 0.309 3140 Planarity : 0.005 0.054 3432 Dihedral : 4.104 23.026 2696 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.57 % Rotamer Outliers : 5.24 % 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: 0.77 (0.18), residues: 2432 helix: 2.10 (0.14), residues: 1452 sheet: -0.18 (0.52), residues: 88 loop : -2.30 (0.19), residues: 892 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 211 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 69 residues processed: 295 average time/residue: 0.9262 time to fit residues: 325.2832 Evaluate side-chains 265 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 196 time to evaluate : 2.139 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 56 residues processed: 14 average time/residue: 0.6666 time to fit residues: 14.8446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 21 optimal weight: 0.0030 chunk 184 optimal weight: 40.0000 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 HIS ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 678 HIS ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 678 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 20496 Z= 0.164 Angle : 0.626 14.189 27812 Z= 0.308 Chirality : 0.041 0.325 3140 Planarity : 0.004 0.046 3432 Dihedral : 3.963 22.463 2696 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.91 % Favored : 95.93 % Rotamer Outliers : 3.72 % 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: 1.00 (0.18), residues: 2432 helix: 2.24 (0.14), residues: 1456 sheet: -0.13 (0.50), residues: 88 loop : -2.10 (0.20), residues: 888 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 211 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 58 residues processed: 281 average time/residue: 0.9064 time to fit residues: 303.7941 Evaluate side-chains 256 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 198 time to evaluate : 2.444 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 53 residues processed: 5 average time/residue: 0.6064 time to fit residues: 7.0730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.8980 chunk 225 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 218 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 HIS ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN B 678 HIS ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 678 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 20496 Z= 0.164 Angle : 0.617 14.784 27812 Z= 0.300 Chirality : 0.041 0.403 3140 Planarity : 0.004 0.046 3432 Dihedral : 3.881 21.960 2696 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.24 % Favored : 95.60 % Rotamer Outliers : 3.86 % 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: 1.04 (0.18), residues: 2432 helix: 2.25 (0.14), residues: 1456 sheet: -0.05 (0.50), residues: 88 loop : -2.05 (0.20), residues: 888 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 208 time to evaluate : 2.389 Fit side-chains revert: symmetry clash outliers start: 84 outliers final: 55 residues processed: 276 average time/residue: 0.9421 time to fit residues: 310.3040 Evaluate side-chains 253 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 198 time to evaluate : 2.250 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 51 residues processed: 4 average time/residue: 0.5983 time to fit residues: 6.3885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.0770 chunk 231 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 223 optimal weight: 7.9990 chunk 193 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 HIS ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 678 HIS ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 678 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 20496 Z= 0.305 Angle : 0.680 14.264 27812 Z= 0.334 Chirality : 0.043 0.315 3140 Planarity : 0.005 0.050 3432 Dihedral : 4.096 24.862 2696 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer Outliers : 3.49 % 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: 0.89 (0.18), residues: 2432 helix: 2.11 (0.14), residues: 1456 sheet: 0.30 (0.53), residues: 88 loop : -2.13 (0.19), residues: 888 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 198 time to evaluate : 2.355 Fit side-chains revert: symmetry clash outliers start: 76 outliers final: 55 residues processed: 261 average time/residue: 0.9604 time to fit residues: 296.5754 Evaluate side-chains 242 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 187 time to evaluate : 2.563 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 47 residues processed: 8 average time/residue: 0.8488 time to fit residues: 11.3407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 HIS ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 678 HIS ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 678 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.118405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.081315 restraints weight = 35542.046| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.61 r_work: 0.3003 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 20496 Z= 0.166 Angle : 0.621 14.755 27812 Z= 0.304 Chirality : 0.040 0.316 3140 Planarity : 0.004 0.047 3432 Dihedral : 3.980 24.655 2696 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.07 % Favored : 95.76 % Rotamer Outliers : 2.76 % 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: 1.06 (0.18), residues: 2432 helix: 2.21 (0.14), residues: 1460 sheet: 0.31 (0.52), residues: 88 loop : -2.00 (0.20), residues: 884 =============================================================================== Job complete usr+sys time: 6233.33 seconds wall clock time: 111 minutes 38.08 seconds (6698.08 seconds total)