Starting phenix.real_space_refine on Mon Aug 5 17:53:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghr_40047/08_2024/8ghr_40047.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghr_40047/08_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_40047/08_2024/8ghr_40047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghr_40047/08_2024/8ghr_40047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghr_40047/08_2024/8ghr_40047.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghr_40047/08_2024/8ghr_40047.cif" } 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-5409/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: 14.13, per 1000 atoms: 1.02 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: 5.33 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... Secondary structure from input PDB file: 60 helices and 26 sheets defined 30.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 221 through 228 removed outlier: 4.036A pdb=" N LEU A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.690A pdb=" N ASN A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) 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 268 through 273 Processing helix chain 'A' and resid 292 through 301 removed outlier: 3.969A pdb=" N LYS A 295 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 296 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.677A pdb=" N THR A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.906A pdb=" N GLY A 331 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 375 through 383 Processing helix chain 'A' and resid 386 through 410 removed outlier: 3.857A pdb=" N ILE A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 470 through 478 removed outlier: 4.169A pdb=" N ILE A 474 " --> pdb=" O ASN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 4.104A pdb=" N GLN A 545 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 577 removed outlier: 3.681A pdb=" N LEU A 572 " --> pdb=" O GLU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.838A pdb=" N LEU A 594 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 595 " --> pdb=" O ASN A 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 591 through 595' Processing helix chain 'A' and resid 637 through 642 Processing helix chain 'A' and resid 645 through 657 Processing helix chain 'A' and resid 721 through 724 Processing helix chain 'A' and resid 725 through 730 removed outlier: 3.896A pdb=" N TYR A 729 " --> pdb=" O LYS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 758 Processing helix chain 'A' and resid 768 through 789 removed outlier: 4.171A pdb=" N ILE A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) 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 809 through 816 removed outlier: 3.905A pdb=" N GLN A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 removed outlier: 3.697A pdb=" N CYS A 848 " --> pdb=" O PRO A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 885 removed outlier: 4.473A pdb=" N TRP A 877 " --> pdb=" O HIS A 873 " (cutoff:3.500A) 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 888 through 897 Processing helix chain 'A' and resid 907 through 916 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 221 through 228 removed outlier: 4.037A pdb=" N LEU B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.689A pdb=" N ASN B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) 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 268 through 273 Processing helix chain 'B' and resid 292 through 301 removed outlier: 3.969A pdb=" N LYS B 295 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 296 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Proline residue: B 298 - end of helix Processing helix chain 'B' and resid 305 through 313 removed outlier: 3.675A pdb=" N THR B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 332 removed outlier: 3.906A pdb=" N GLY B 331 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 375 through 383 Processing helix chain 'B' and resid 386 through 410 removed outlier: 3.857A pdb=" N ILE B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 442 Processing helix chain 'B' and resid 470 through 478 removed outlier: 4.170A pdb=" N ILE B 474 " --> pdb=" O ASN B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 545 removed outlier: 4.071A pdb=" N GLN B 545 " --> pdb=" O SER B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 577 removed outlier: 3.682A pdb=" N LEU B 572 " --> pdb=" O GLU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.843A pdb=" N LEU B 594 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 595 " --> pdb=" O ASN B 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 591 through 595' Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 645 through 657 Processing helix chain 'B' and resid 721 through 724 Processing helix chain 'B' and resid 725 through 730 removed outlier: 3.897A pdb=" N TYR B 729 " --> pdb=" O LYS B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 758 Processing helix chain 'B' and resid 768 through 789 removed outlier: 4.171A pdb=" N ILE B 772 " --> pdb=" O SER B 768 " (cutoff:3.500A) 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 809 through 816 removed outlier: 3.908A pdb=" N GLN B 815 " --> pdb=" O GLU B 811 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 removed outlier: 3.694A pdb=" N CYS B 848 " --> pdb=" O PRO B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 885 removed outlier: 4.470A pdb=" N TRP B 877 " --> pdb=" O HIS B 873 " (cutoff:3.500A) 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 888 through 897 Processing helix chain 'B' and resid 907 through 916 Processing helix chain 'C' and resid 63 through 66 Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.980A pdb=" N THR C 92 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.980A pdb=" N THR D 92 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 243 through 244 removed outlier: 3.573A pdb=" N THR A 369 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA3, first strand: chain 'A' and resid 279 through 281 Processing sheet with id=AA4, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA5, first strand: chain 'A' and resid 447 through 450 removed outlier: 3.806A pdb=" N LEU A 457 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU A 510 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 663 through 664 Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 675 removed outlier: 6.552A pdb=" N MET A 680 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR A 693 " --> pdb=" O MET A 680 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY A 682 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A 689 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 691 " --> pdb=" O PRO A 797 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA A 855 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 702 through 703 removed outlier: 4.589A pdb=" N SER A 702 " --> pdb=" O ASN A 746 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN A 746 " --> pdb=" O SER A 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 736 through 738 Processing sheet with id=AB1, first strand: chain 'A' and resid 818 through 820 Processing sheet with id=AB2, first strand: chain 'B' and resid 243 through 244 removed outlier: 3.572A pdb=" N THR B 369 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 248 through 249 Processing sheet with id=AB4, first strand: chain 'B' and resid 279 through 281 Processing sheet with id=AB5, first strand: chain 'B' and resid 427 through 428 Processing sheet with id=AB6, first strand: chain 'B' and resid 447 through 450 removed outlier: 3.808A pdb=" N LEU B 457 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU B 510 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 663 through 664 Processing sheet with id=AB8, first strand: chain 'B' and resid 671 through 675 removed outlier: 6.552A pdb=" N MET B 680 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 693 " --> pdb=" O MET B 680 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 682 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET B 689 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 691 " --> pdb=" O PRO B 797 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA B 855 " --> pdb=" O ALA B 887 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 702 through 703 removed outlier: 4.589A pdb=" N SER B 702 " --> pdb=" O ASN B 746 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN B 746 " --> pdb=" O SER B 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 736 through 738 Processing sheet with id=AC2, first strand: chain 'B' and resid 818 through 820 Processing sheet with id=AC3, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'C' and resid 11 through 12 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=AC5, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.495A pdb=" N CYS C 97 " --> pdb=" O TRP C 114 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP C 114 " --> pdb=" O CYS C 97 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG C 99 " --> pdb=" O ASP C 112 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'D' and resid 11 through 12 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=AC8, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.493A pdb=" N CYS D 97 " --> pdb=" O TRP D 114 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP D 114 " --> pdb=" O CYS D 97 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG D 99 " --> pdb=" O ASP D 112 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1242 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: 5.01 Time building geometry restraints manager: 5.90 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: 9535 3.11 - 3.71: 19723 3.71 - 4.30: 28318 4.30 - 4.90: 49299 Nonbonded interactions: 106948 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 106943 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 7.130 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 50.050 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.110 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.560 ------------------------------------------------------------------------------- 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= 0.185 Angle : 0.583 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 : 1.610 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2484 time to fit residues: 69.3024 Evaluate side-chains 170 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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: 1.9990 chunk 71 optimal weight: 0.0970 chunk 44 optimal weight: 20.0000 chunk 86 optimal weight: 0.0570 chunk 68 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 51 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 overall best weight: 0.4494 ------------------------------------------------------------------------------- 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 260 HIS A 641 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 HIS B 641 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0757 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= 0.157 Angle : 0.574 9.567 19440 Z= 0.286 Chirality : 0.043 0.170 2118 Planarity : 0.005 0.040 2498 Dihedral : 6.411 121.583 2160 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.74 % Allowed : 6.58 % Favored : 92.68 % 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: 0.01 (0.20), residues: 1720 helix: 0.90 (0.29), residues: 358 sheet: 0.01 (0.27), residues: 336 loop : -0.26 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 307 HIS 0.009 0.001 HIS B 272 PHE 0.027 0.001 PHE B 257 TYR 0.014 0.001 TYR A 261 ARG 0.007 0.000 ARG B 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 : 1.497 Fit side-chains REVERT: A 753 TYR cc_start: 0.8455 (t80) cc_final: 0.7887 (t80) REVERT: B 279 MET cc_start: 0.9505 (ptt) cc_final: 0.9263 (ptt) REVERT: B 753 TYR cc_start: 0.8448 (t80) cc_final: 0.8047 (t80) outliers start: 11 outliers final: 7 residues processed: 169 average time/residue: 0.2798 time to fit residues: 68.3647 Evaluate side-chains 171 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 164 time to evaluate : 1.523 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 154 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 124 optimal weight: 0.2980 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 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 GLN A 815 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14262 Z= 0.216 Angle : 0.577 8.859 19440 Z= 0.288 Chirality : 0.043 0.178 2118 Planarity : 0.005 0.039 2498 Dihedral : 6.408 124.043 2160 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.54 % Allowed : 8.52 % Favored : 90.94 % 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: -0.02 (0.20), residues: 1720 helix: 0.85 (0.28), residues: 372 sheet: -0.01 (0.27), residues: 334 loop : -0.27 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 190 HIS 0.008 0.001 HIS A 272 PHE 0.029 0.002 PHE B 257 TYR 0.017 0.001 TYR B 261 ARG 0.004 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 173 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 1.599 Fit side-chains REVERT: B 753 TYR cc_start: 0.8460 (t80) cc_final: 0.8093 (t80) outliers start: 8 outliers final: 6 residues processed: 167 average time/residue: 0.2772 time to fit residues: 66.4747 Evaluate side-chains 171 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 116 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 164 optimal weight: 0.0000 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 overall best weight: 1.5992 ------------------------------------------------------------------------------- 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 260 HIS A 815 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1176 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= 0.334 Angle : 0.644 9.601 19440 Z= 0.320 Chirality : 0.046 0.226 2118 Planarity : 0.005 0.040 2498 Dihedral : 6.645 127.494 2160 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.28 % Allowed : 9.60 % Favored : 89.13 % 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: -0.21 (0.20), residues: 1720 helix: 0.68 (0.28), residues: 370 sheet: -0.18 (0.28), residues: 314 loop : -0.37 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 190 HIS 0.009 0.002 HIS A 380 PHE 0.037 0.002 PHE B 257 TYR 0.019 0.002 TYR A 775 ARG 0.006 0.000 ARG A 814 *********************** 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 178 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.583 Fit side-chains REVERT: A 753 TYR cc_start: 0.8502 (t80) cc_final: 0.8044 (t80) REVERT: B 753 TYR cc_start: 0.8502 (t80) cc_final: 0.8107 (t80) outliers start: 19 outliers final: 14 residues processed: 167 average time/residue: 0.2820 time to fit residues: 68.0707 Evaluate side-chains 172 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 75 ILE Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 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: 1.9990 chunk 147 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14262 Z= 0.279 Angle : 0.606 9.804 19440 Z= 0.303 Chirality : 0.044 0.214 2118 Planarity : 0.005 0.039 2498 Dihedral : 6.609 127.418 2160 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.41 % Allowed : 9.87 % Favored : 88.72 % 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: -0.21 (0.20), residues: 1720 helix: 0.70 (0.28), residues: 370 sheet: -0.19 (0.28), residues: 314 loop : -0.38 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 190 HIS 0.008 0.001 HIS A 272 PHE 0.029 0.002 PHE B 257 TYR 0.015 0.001 TYR A 337 ARG 0.006 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 185 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 164 time to evaluate : 1.604 Fit side-chains REVERT: A 678 GLN cc_start: 0.8385 (pm20) cc_final: 0.8055 (pm20) REVERT: B 753 TYR cc_start: 0.8480 (t80) cc_final: 0.8073 (t80) outliers start: 21 outliers final: 19 residues processed: 175 average time/residue: 0.2834 time to fit residues: 70.6237 Evaluate side-chains 181 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 815 GLN 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 810 LEU Chi-restraints excluded: chain B residue 815 GLN 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 C residue 75 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 0.0870 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 GLN B 815 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14262 Z= 0.184 Angle : 0.569 9.857 19440 Z= 0.283 Chirality : 0.042 0.183 2118 Planarity : 0.004 0.039 2498 Dihedral : 6.459 125.823 2160 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.28 % Allowed : 10.74 % Favored : 87.99 % 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: -0.09 (0.20), residues: 1720 helix: 0.96 (0.29), residues: 358 sheet: -0.23 (0.26), residues: 354 loop : -0.30 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 307 HIS 0.007 0.001 HIS A 272 PHE 0.020 0.001 PHE B 257 TYR 0.017 0.001 TYR B 775 ARG 0.008 0.000 ARG A 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 181 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.453 Fit side-chains REVERT: A 678 GLN cc_start: 0.8408 (pm20) cc_final: 0.8059 (pm20) REVERT: B 753 TYR cc_start: 0.8436 (t80) cc_final: 0.8226 (t80) outliers start: 19 outliers final: 17 residues processed: 173 average time/residue: 0.2502 time to fit residues: 62.5883 Evaluate side-chains 176 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 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 810 LEU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 689 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 810 LEU Chi-restraints excluded: chain B residue 815 GLN 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: 10.0000 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 0.3980 chunk 138 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 101 optimal weight: 0.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 GLN B 815 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14262 Z= 0.165 Angle : 0.551 9.248 19440 Z= 0.275 Chirality : 0.042 0.167 2118 Planarity : 0.005 0.041 2498 Dihedral : 6.352 124.628 2160 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.21 % Allowed : 11.07 % Favored : 87.72 % 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: 0.01 (0.20), residues: 1720 helix: 1.09 (0.29), residues: 358 sheet: -0.21 (0.27), residues: 354 loop : -0.24 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 307 HIS 0.007 0.001 HIS B 272 PHE 0.017 0.001 PHE B 257 TYR 0.013 0.001 TYR A 337 ARG 0.006 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 180 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 1.411 Fit side-chains REVERT: A 678 GLN cc_start: 0.8437 (pm20) cc_final: 0.8059 (pm20) REVERT: A 753 TYR cc_start: 0.8440 (t80) cc_final: 0.8065 (t80) REVERT: B 753 TYR cc_start: 0.8414 (t80) cc_final: 0.8176 (t80) outliers start: 18 outliers final: 17 residues processed: 172 average time/residue: 0.2859 time to fit residues: 70.4527 Evaluate side-chains 177 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 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 815 GLN Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 689 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 815 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.0050 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 GLN B 815 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1293 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 : 0.551 9.964 19440 Z= 0.272 Chirality : 0.042 0.163 2118 Planarity : 0.004 0.038 2498 Dihedral : 6.290 124.024 2160 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.28 % Allowed : 11.21 % Favored : 87.52 % 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: 0.05 (0.20), residues: 1720 helix: 1.17 (0.29), residues: 358 sheet: -0.20 (0.26), residues: 354 loop : -0.22 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 307 HIS 0.007 0.001 HIS B 272 PHE 0.016 0.001 PHE A 257 TYR 0.013 0.001 TYR A 337 ARG 0.006 0.000 ARG B 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 183 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.468 Fit side-chains REVERT: A 678 GLN cc_start: 0.8438 (pm20) cc_final: 0.8054 (pm20) REVERT: A 753 TYR cc_start: 0.8428 (t80) cc_final: 0.8049 (t80) outliers start: 19 outliers final: 17 residues processed: 173 average time/residue: 0.2759 time to fit residues: 68.7620 Evaluate side-chains 182 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 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 812 ASN Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 689 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 815 GLN 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: 1.9990 chunk 152 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 GLN B 815 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14262 Z= 0.190 Angle : 0.556 9.857 19440 Z= 0.276 Chirality : 0.042 0.166 2118 Planarity : 0.005 0.046 2498 Dihedral : 6.304 124.306 2160 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.21 % Allowed : 11.48 % Favored : 87.32 % 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: 0.05 (0.20), residues: 1720 helix: 1.17 (0.29), residues: 358 sheet: -0.19 (0.26), residues: 354 loop : -0.23 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 114 HIS 0.007 0.001 HIS B 272 PHE 0.018 0.001 PHE A 257 TYR 0.014 0.001 TYR A 337 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 182 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 1.587 Fit side-chains REVERT: A 678 GLN cc_start: 0.8451 (pm20) cc_final: 0.8059 (pm20) REVERT: A 753 TYR cc_start: 0.8436 (t80) cc_final: 0.8058 (t80) outliers start: 18 outliers final: 17 residues processed: 172 average time/residue: 0.2971 time to fit residues: 72.8449 Evaluate side-chains 179 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 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 815 GLN Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 689 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 815 GLN 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.6013 > 50: distance: 73 - 77: 27.858 distance: 77 - 78: 47.247 distance: 78 - 79: 40.917 distance: 78 - 81: 17.584 distance: 79 - 80: 39.162 distance: 79 - 85: 56.514 distance: 81 - 82: 47.345 distance: 82 - 83: 42.733 distance: 82 - 84: 22.637 distance: 85 - 86: 19.969 distance: 86 - 87: 17.915 distance: 86 - 89: 44.173 distance: 87 - 88: 32.697 distance: 87 - 92: 68.469 distance: 89 - 90: 40.652 distance: 89 - 91: 55.164 distance: 92 - 93: 37.542 distance: 93 - 94: 3.629 distance: 93 - 96: 53.569 distance: 94 - 95: 43.340 distance: 96 - 97: 55.205 distance: 97 - 98: 56.512 distance: 102 - 103: 39.664 distance: 102 - 105: 34.680 distance: 103 - 104: 41.164 distance: 104 - 121: 22.066 distance: 105 - 106: 52.606 distance: 105 - 107: 40.692 distance: 106 - 108: 43.508 distance: 109 - 110: 39.170 distance: 110 - 111: 57.115 distance: 110 - 113: 39.402 distance: 111 - 117: 56.808 distance: 113 - 114: 39.725 distance: 114 - 116: 39.908 distance: 117 - 118: 41.294 distance: 118 - 119: 48.705 distance: 119 - 120: 40.076 distance: 119 - 121: 15.940 distance: 121 - 122: 43.272 distance: 122 - 125: 55.700 distance: 123 - 129: 57.937 distance: 125 - 126: 38.482 distance: 125 - 127: 41.017 distance: 126 - 128: 42.764 distance: 129 - 130: 35.877 distance: 130 - 131: 34.486 distance: 130 - 133: 39.309 distance: 131 - 132: 56.315 distance: 133 - 134: 40.696 distance: 134 - 135: 57.575 distance: 134 - 136: 56.438 distance: 135 - 137: 37.340 distance: 136 - 138: 5.214 distance: 137 - 139: 43.702 distance: 138 - 139: 40.637 distance: 140 - 141: 56.359 distance: 141 - 142: 40.154 distance: 142 - 143: 40.078 distance: 142 - 147: 56.058 distance: 145 - 146: 55.941 distance: 147 - 148: 57.303 distance: 148 - 149: 56.513 distance: 148 - 151: 57.003 distance: 149 - 155: 33.572 distance: 152 - 153: 15.201 distance: 152 - 154: 39.017