Starting phenix.real_space_refine on Sat Mar 16 06:25:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghr_40047/03_2024/8ghr_40047_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghr_40047/03_2024/8ghr_40047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghr_40047/03_2024/8ghr_40047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghr_40047/03_2024/8ghr_40047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghr_40047/03_2024/8ghr_40047_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghr_40047/03_2024/8ghr_40047_updated.pdb" } resolution = 3.2 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= 0.027 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 4 6.06 5 P 2 5.49 5 S 72 5.16 5 C 8870 2.51 5 N 2304 2.21 5 O 2610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 223": "OE1" <-> "OE2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C ASP 28": "OD1" <-> "OD2" Residue "C TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13864 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5887 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 735, 5876 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 680} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 735, 5876 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 680} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 6040 Chain: "B" Number of atoms: 5887 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 735, 5876 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 680} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 735, 5876 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 680} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 6040 Chain: "C" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 932 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 932 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 54 Unusual residues: {' CA': 1, ' ZN': 2, 'NAG': 2} Classifications: {'RNA': 1, 'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 54 Unusual residues: {' CA': 1, ' ZN': 2, 'NAG': 2} Classifications: {'RNA': 1, 'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ACYS A 626 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 626 " occ=0.50 residue: pdb=" N AASN A 700 " occ=0.75 ... (8 atoms not shown) pdb=" CB BASN A 700 " occ=0.25 residue: pdb=" N ACYS B 626 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 626 " occ=0.50 residue: pdb=" N AASN B 700 " occ=0.75 ... (8 atoms not shown) pdb=" CB BASN B 700 " occ=0.25 Time building chain proxies: 12.96, per 1000 atoms: 0.93 Number of scatterers: 13864 At special positions: 0 Unit cell: (120.61, 124.081, 105.859, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 2 19.99 S 72 16.00 P 2 15.00 O 2610 8.00 N 2304 7.00 C 8870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 868 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG ACYS A 626 " - pdb=" SG CYS A 726 " distance=2.03 Simple disulfide: pdb=" SG CYS A 628 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG BCYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 838 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 431 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 868 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG ACYS B 626 " - pdb=" SG CYS B 726 " distance=2.03 Simple disulfide: pdb=" SG CYS B 628 " - pdb=" SG CYS B 711 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG BCYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 838 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1304 " - " ASN A 285 " " NAG A1305 " - " ASN A 477 " " NAG B1304 " - " ASN B 285 " " NAG B1305 " - " ASN B 477 " " NAG E 1 " - " ASN A 341 " " NAG F 1 " - " ASN A 585 " " NAG G 1 " - " ASN B 341 " " NAG H 1 " - " ASN B 585 " Time building additional restraints: 5.07 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 380 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 535 " pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 424 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" NE2 HIS B 380 " pdb="ZN ZN B1301 " - pdb=" NE2 HIS B 535 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" NE2 HIS B 424 " 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 20 sheets defined 24.6% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.816A pdb=" N GLY A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.526A pdb=" N ILE A 263 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 264 " --> pdb=" O HIS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 272 No H-bonds generated for 'chain 'A' and resid 269 through 272' Processing helix chain 'A' and resid 293 through 296 removed outlier: 3.573A pdb=" N PHE A 296 " --> pdb=" O LYS A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'A' and resid 376 through 382 Processing helix chain 'A' and resid 387 through 410 Processing helix chain 'A' and resid 438 through 441 No H-bonds generated for 'chain 'A' and resid 438 through 441' Processing helix chain 'A' and resid 471 through 477 Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 566 through 576 removed outlier: 4.522A pdb=" N TYR A 570 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN A 571 " --> pdb=" O GLU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'A' and resid 646 through 656 Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 726 through 729 No H-bonds generated for 'chain 'A' and resid 726 through 729' Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 769 through 788 removed outlier: 4.783A pdb=" N LEU A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG A 782 " --> pdb=" O ASP A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 815 removed outlier: 3.905A pdb=" N GLN A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 874 through 884 removed outlier: 4.117A pdb=" N VAL A 878 " --> pdb=" O ASP A 874 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 879 " --> pdb=" O SER A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 896 Processing helix chain 'A' and resid 908 through 915 Processing helix chain 'B' and resid 190 through 192 No H-bonds generated for 'chain 'B' and resid 190 through 192' Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.816A pdb=" N GLY B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 256 through 265 removed outlier: 3.518A pdb=" N ILE B 263 " --> pdb=" O ASN B 259 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL B 264 " --> pdb=" O HIS B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 272 No H-bonds generated for 'chain 'B' and resid 269 through 272' Processing helix chain 'B' and resid 293 through 296 removed outlier: 3.574A pdb=" N PHE B 296 " --> pdb=" O LYS B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 346 through 357 Processing helix chain 'B' and resid 376 through 382 Processing helix chain 'B' and resid 387 through 410 Processing helix chain 'B' and resid 438 through 441 No H-bonds generated for 'chain 'B' and resid 438 through 441' Processing helix chain 'B' and resid 471 through 477 Processing helix chain 'B' and resid 542 through 544 No H-bonds generated for 'chain 'B' and resid 542 through 544' Processing helix chain 'B' and resid 566 through 576 removed outlier: 4.522A pdb=" N TYR B 570 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN B 571 " --> pdb=" O GLU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 638 through 642 Processing helix chain 'B' and resid 646 through 656 Processing helix chain 'B' and resid 722 through 724 No H-bonds generated for 'chain 'B' and resid 722 through 724' Processing helix chain 'B' and resid 726 through 729 No H-bonds generated for 'chain 'B' and resid 726 through 729' Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 769 through 788 removed outlier: 4.783A pdb=" N LEU B 781 " --> pdb=" O HIS B 777 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ARG B 782 " --> pdb=" O ASP B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 815 removed outlier: 3.908A pdb=" N GLN B 815 " --> pdb=" O GLU B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 847 No H-bonds generated for 'chain 'B' and resid 845 through 847' Processing helix chain 'B' and resid 874 through 884 removed outlier: 4.096A pdb=" N VAL B 878 " --> pdb=" O ASP B 874 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 896 Processing helix chain 'B' and resid 908 through 915 Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing sheet with id= A, first strand: chain 'A' and resid 367 through 372 removed outlier: 6.411A pdb=" N THR A 212 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N LEU A 370 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 214 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU A 372 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER A 216 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN A 417 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE A 215 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 419 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU A 217 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 421 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 279 through 281 Processing sheet with id= C, first strand: chain 'A' and resid 447 through 450 Processing sheet with id= D, first strand: chain 'A' and resid 487 through 491 Processing sheet with id= E, first strand: chain 'A' and resid 671 through 675 removed outlier: 3.878A pdb=" N TRP A 692 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N SER A 684 " --> pdb=" O PRO A 690 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 691 " --> pdb=" O PRO A 797 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 736 through 738 Processing sheet with id= G, first strand: chain 'A' and resid 818 through 820 Processing sheet with id= H, first strand: chain 'B' and resid 367 through 372 removed outlier: 6.399A pdb=" N THR B 212 " --> pdb=" O TYR B 368 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LEU B 370 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 214 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU B 372 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER B 216 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN B 417 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE B 215 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE B 419 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU B 217 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 421 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 279 through 281 Processing sheet with id= J, first strand: chain 'B' and resid 447 through 450 Processing sheet with id= K, first strand: chain 'B' and resid 487 through 491 Processing sheet with id= L, first strand: chain 'B' and resid 671 through 675 removed outlier: 3.879A pdb=" N TRP B 692 " --> pdb=" O GLY B 682 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N SER B 684 " --> pdb=" O PRO B 690 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 691 " --> pdb=" O PRO B 797 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 736 through 738 Processing sheet with id= N, first strand: chain 'B' and resid 818 through 820 Processing sheet with id= O, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= P, first strand: chain 'C' and resid 118 through 120 removed outlier: 4.374A pdb=" N TYR C 34 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 50 " --> pdb=" O TRP C 37 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG C 39 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU C 48 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.652A pdb=" N ARG C 99 " --> pdb=" O TYR C 113 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR C 113 " --> pdb=" O ARG C 99 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 3 through 7 Processing sheet with id= S, first strand: chain 'D' and resid 118 through 120 removed outlier: 4.373A pdb=" N TYR D 34 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARG D 39 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.654A pdb=" N ARG D 99 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR D 113 " --> pdb=" O ARG D 99 " (cutoff:3.500A) No H-bonds generated for sheet with id= T 354 hydrogen bonds defined for protein. 948 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: 4.07 Time building geometry restraints manager: 5.51 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: 4407 1.34 - 1.46: 3509 1.46 - 1.58: 6242 1.58 - 1.70: 2 1.70 - 1.82: 102 Bond restraints: 14262 Sorted by residual: bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.80e+00 ... (remaining 14257 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.66: 735 107.66 - 114.79: 8083 114.79 - 121.91: 7486 121.91 - 129.03: 3024 129.03 - 136.15: 112 Bond angle restraints: 19440 Sorted by residual: angle pdb=" C SER A 709 " pdb=" N ASN A 710 " pdb=" CA ASN A 710 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.77e+00 angle pdb=" C SER B 709 " pdb=" N ASN B 710 " pdb=" CA ASN B 710 " ideal model delta sigma weight residual 121.54 127.47 -5.93 1.91e+00 2.74e-01 9.62e+00 angle pdb=" C PRO A 483 " pdb=" N ASN A 484 " pdb=" CA ASN A 484 " ideal model delta sigma weight residual 121.54 127.33 -5.79 1.91e+00 2.74e-01 9.19e+00 angle pdb=" C PRO B 483 " pdb=" N ASN B 484 " pdb=" CA ASN B 484 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.13e+00 angle pdb=" CA LEU A 359 " pdb=" CB LEU A 359 " pdb=" CG LEU A 359 " ideal model delta sigma weight residual 116.30 126.52 -10.22 3.50e+00 8.16e-02 8.52e+00 ... (remaining 19435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.47: 8132 24.47 - 48.94: 452 48.94 - 73.40: 32 73.40 - 97.87: 12 97.87 - 122.34: 2 Dihedral angle restraints: 8630 sinusoidal: 3590 harmonic: 5040 Sorted by residual: dihedral pdb=" CB CYS A 628 " pdb=" SG CYS A 628 " pdb=" SG CYS A 711 " pdb=" CB CYS A 711 " ideal model delta sinusoidal sigma weight residual -86.00 1.66 -87.66 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS B 628 " pdb=" SG CYS B 628 " pdb=" SG CYS B 711 " pdb=" CB CYS B 711 " ideal model delta sinusoidal sigma weight residual -86.00 1.64 -87.64 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS B 195 " pdb=" SG CYS B 195 " pdb=" SG CYS B 241 " pdb=" CB CYS B 241 " ideal model delta sinusoidal sigma weight residual -86.00 -162.28 76.28 1 1.00e+01 1.00e-02 7.32e+01 ... (remaining 8627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1449 0.038 - 0.076: 485 0.076 - 0.114: 139 0.114 - 0.152: 41 0.152 - 0.189: 4 Chirality restraints: 2118 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 585 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 585 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA PHE A 257 " pdb=" N PHE A 257 " pdb=" C PHE A 257 " pdb=" CB PHE A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 ... (remaining 2115 not shown) Planarity restraints: 2506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 721 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.06e+00 pdb=" N PRO B 722 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 722 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 722 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 721 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO A 722 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 722 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 722 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 257 " 0.015 2.00e-02 2.50e+03 1.34e-02 3.14e+00 pdb=" CG PHE B 257 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 257 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 257 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 257 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 257 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 257 " 0.001 2.00e-02 2.50e+03 ... (remaining 2503 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 73 2.52 - 3.11: 9584 3.11 - 3.71: 19824 3.71 - 4.30: 28550 4.30 - 4.90: 49357 Nonbonded interactions: 107388 Sorted by model distance: nonbonded pdb="ZN ZN B1301 " pdb=" O2P AMP B1303 " model vdw 1.923 2.230 nonbonded pdb="ZN ZN A1301 " pdb=" O2P AMP A1303 " model vdw 1.925 2.230 nonbonded pdb=" OD1 ASP A 218 " pdb="ZN ZN A1302 " model vdw 1.955 2.230 nonbonded pdb=" OD1 ASP B 218 " pdb="ZN ZN B1302 " model vdw 1.955 2.230 nonbonded pdb=" OD1 ASP A 376 " pdb="ZN ZN A1301 " model vdw 2.042 2.230 ... (remaining 107383 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' and (resid 187 through 625 or resid 627 through 699 or resid 701 thro \ ugh 921 or resid 1301 through 1306)) selection = (chain 'B' and (resid 187 through 625 or resid 627 through 699 or resid 701 thro \ ugh 921 or resid 1301 through 1306)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.25 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: 2.440 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: 9.900 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 46.860 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.120 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 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 0.036 14262 Z= 0.179 Angle : 0.582 10.215 19440 Z= 0.289 Chirality : 0.043 0.189 2118 Planarity : 0.005 0.050 2498 Dihedral : 13.784 122.339 5350 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1720 helix: 0.41 (0.28), residues: 350 sheet: 0.15 (0.26), residues: 362 loop : -0.33 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 307 HIS 0.005 0.001 HIS B 272 PHE 0.031 0.001 PHE B 257 TYR 0.017 0.001 TYR A 261 ARG 0.008 0.000 ARG B 814 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.555 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2575 time to fit residues: 72.0526 Evaluate side-chains 170 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 71 optimal weight: 0.0030 chunk 44 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 133 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14262 Z= 0.155 Angle : 0.544 8.954 19440 Z= 0.265 Chirality : 0.042 0.169 2118 Planarity : 0.004 0.040 2498 Dihedral : 6.360 122.715 2160 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.74 % Allowed : 6.11 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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 (0.20), residues: 1720 helix: 0.47 (0.28), residues: 362 sheet: 0.03 (0.28), residues: 342 loop : -0.26 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 307 HIS 0.006 0.001 HIS B 380 PHE 0.029 0.001 PHE B 257 TYR 0.016 0.001 TYR A 261 ARG 0.007 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 1.555 Fit side-chains REVERT: B 279 MET cc_start: 0.9510 (ptt) cc_final: 0.9262 (ptt) REVERT: B 753 TYR cc_start: 0.8399 (t80) cc_final: 0.7832 (t80) outliers start: 11 outliers final: 9 residues processed: 170 average time/residue: 0.2682 time to fit residues: 66.6317 Evaluate side-chains 168 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 159 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 869 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 128 optimal weight: 0.0980 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN A 815 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN B 815 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14262 Z= 0.322 Angle : 0.619 7.619 19440 Z= 0.306 Chirality : 0.045 0.231 2118 Planarity : 0.005 0.041 2498 Dihedral : 6.612 128.373 2160 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.01 % Allowed : 8.26 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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 (0.20), residues: 1720 helix: 0.18 (0.27), residues: 362 sheet: -0.13 (0.29), residues: 314 loop : -0.38 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 114 HIS 0.008 0.002 HIS A 380 PHE 0.042 0.002 PHE B 257 TYR 0.021 0.002 TYR A 261 ARG 0.005 0.000 ARG B 814 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.525 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 160 average time/residue: 0.2765 time to fit residues: 64.5030 Evaluate side-chains 160 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 820 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 HIS ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 14262 Z= 0.530 Angle : 0.749 9.559 19440 Z= 0.373 Chirality : 0.050 0.286 2118 Planarity : 0.005 0.042 2498 Dihedral : 7.167 133.812 2160 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.61 % Allowed : 9.46 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.88 (0.19), residues: 1720 helix: -0.41 (0.26), residues: 360 sheet: -0.34 (0.29), residues: 318 loop : -0.67 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 190 HIS 0.010 0.002 HIS A 380 PHE 0.051 0.003 PHE A 257 TYR 0.020 0.002 TYR A 337 ARG 0.004 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 1.537 Fit side-chains REVERT: B 753 TYR cc_start: 0.8423 (t80) cc_final: 0.7902 (t80) outliers start: 24 outliers final: 17 residues processed: 173 average time/residue: 0.2761 time to fit residues: 68.9769 Evaluate side-chains 172 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** 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: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14262 Z= 0.262 Angle : 0.602 11.767 19440 Z= 0.297 Chirality : 0.044 0.222 2118 Planarity : 0.005 0.042 2498 Dihedral : 6.843 131.400 2160 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.28 % Allowed : 10.60 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.66 (0.20), residues: 1720 helix: -0.18 (0.27), residues: 360 sheet: -0.28 (0.29), residues: 318 loop : -0.52 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 307 HIS 0.006 0.001 HIS B 272 PHE 0.025 0.002 PHE A 257 TYR 0.012 0.001 TYR B 337 ARG 0.009 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 1.639 Fit side-chains REVERT: B 753 TYR cc_start: 0.8455 (t80) cc_final: 0.8162 (t80) outliers start: 19 outliers final: 13 residues processed: 163 average time/residue: 0.2412 time to fit residues: 58.4844 Evaluate side-chains 162 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain D residue 2 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 54 optimal weight: 6.9990 chunk 86 optimal weight: 0.0270 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14262 Z= 0.223 Angle : 0.569 10.215 19440 Z= 0.282 Chirality : 0.043 0.200 2118 Planarity : 0.005 0.041 2498 Dihedral : 6.679 130.026 2160 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.28 % Allowed : 10.81 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1720 helix: -0.02 (0.28), residues: 360 sheet: -0.16 (0.27), residues: 338 loop : -0.46 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 307 HIS 0.006 0.001 HIS B 272 PHE 0.022 0.002 PHE B 257 TYR 0.015 0.001 TYR A 337 ARG 0.009 0.000 ARG B 814 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 1.399 Fit side-chains REVERT: A 678 GLN cc_start: 0.8491 (pm20) cc_final: 0.8264 (pm20) REVERT: B 753 TYR cc_start: 0.8390 (t80) cc_final: 0.8134 (t80) outliers start: 19 outliers final: 14 residues processed: 167 average time/residue: 0.2673 time to fit residues: 65.3441 Evaluate side-chains 165 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain D residue 2 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 99 optimal weight: 0.0060 chunk 75 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14262 Z= 0.150 Angle : 0.527 9.437 19440 Z= 0.259 Chirality : 0.041 0.165 2118 Planarity : 0.004 0.040 2498 Dihedral : 6.302 125.928 2160 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.81 % Allowed : 12.01 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.29 (0.20), residues: 1720 helix: 0.19 (0.28), residues: 360 sheet: -0.00 (0.28), residues: 334 loop : -0.32 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 307 HIS 0.006 0.001 HIS B 830 PHE 0.014 0.001 PHE A 257 TYR 0.013 0.001 TYR A 337 ARG 0.009 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 1.683 Fit side-chains REVERT: A 678 GLN cc_start: 0.8524 (pm20) cc_final: 0.8287 (pm20) outliers start: 12 outliers final: 10 residues processed: 166 average time/residue: 0.2877 time to fit residues: 68.6973 Evaluate side-chains 167 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 157 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain D residue 2 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14262 Z= 0.221 Angle : 0.559 9.285 19440 Z= 0.276 Chirality : 0.042 0.187 2118 Planarity : 0.005 0.040 2498 Dihedral : 6.395 126.952 2160 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.94 % Allowed : 12.42 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1720 helix: 0.12 (0.28), residues: 360 sheet: -0.04 (0.28), residues: 334 loop : -0.36 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 307 HIS 0.006 0.001 HIS B 272 PHE 0.019 0.002 PHE B 257 TYR 0.028 0.001 TYR B 753 ARG 0.009 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 1.501 Fit side-chains REVERT: A 678 GLN cc_start: 0.8528 (pm20) cc_final: 0.8269 (pm20) outliers start: 14 outliers final: 14 residues processed: 165 average time/residue: 0.2820 time to fit residues: 67.1402 Evaluate side-chains 169 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain D residue 2 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 1.9990 chunk 143 optimal weight: 0.0040 chunk 152 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14262 Z= 0.207 Angle : 0.557 8.886 19440 Z= 0.274 Chirality : 0.042 0.187 2118 Planarity : 0.005 0.040 2498 Dihedral : 6.372 126.549 2160 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.94 % Allowed : 12.55 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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 (0.20), residues: 1720 helix: 0.12 (0.28), residues: 360 sheet: -0.03 (0.28), residues: 334 loop : -0.35 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 307 HIS 0.006 0.001 HIS A 272 PHE 0.018 0.001 PHE B 257 TYR 0.030 0.001 TYR B 753 ARG 0.009 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.504 Fit side-chains REVERT: A 678 GLN cc_start: 0.8543 (pm20) cc_final: 0.8282 (pm20) outliers start: 14 outliers final: 14 residues processed: 171 average time/residue: 0.2697 time to fit residues: 66.6176 Evaluate side-chains 171 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain D residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 169 optimal weight: 0.0060 chunk 155 optimal weight: 0.8980 chunk 134 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14262 Z= 0.142 Angle : 0.516 8.397 19440 Z= 0.255 Chirality : 0.041 0.159 2118 Planarity : 0.004 0.040 2498 Dihedral : 6.175 123.747 2160 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.81 % Allowed : 12.62 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1720 helix: 0.25 (0.28), residues: 362 sheet: 0.05 (0.28), residues: 334 loop : -0.25 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 307 HIS 0.005 0.001 HIS A 830 PHE 0.014 0.001 PHE A 257 TYR 0.013 0.001 TYR B 337 ARG 0.009 0.000 ARG A 814 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 1.735 Fit side-chains REVERT: A 678 GLN cc_start: 0.8532 (pm20) cc_final: 0.8273 (pm20) outliers start: 12 outliers final: 12 residues processed: 174 average time/residue: 0.2742 time to fit residues: 69.1508 Evaluate side-chains 174 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain D residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 chunk 17 optimal weight: 0.0270 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.102839 restraints weight = 16814.516| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.22 r_work: 0.2833 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14262 Z= 0.163 Angle : 0.533 8.372 19440 Z= 0.261 Chirality : 0.041 0.162 2118 Planarity : 0.004 0.040 2498 Dihedral : 6.178 123.846 2160 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.21 % Allowed : 12.48 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.18 (0.20), residues: 1720 helix: 0.25 (0.28), residues: 362 sheet: 0.07 (0.28), residues: 334 loop : -0.24 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 307 HIS 0.006 0.001 HIS A 830 PHE 0.014 0.001 PHE A 257 TYR 0.014 0.001 TYR B 337 ARG 0.009 0.000 ARG A 814 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3185.47 seconds wall clock time: 59 minutes 38.73 seconds (3578.73 seconds total)